diff --git a/.env.local.example b/.env.local.example new file mode 100644 index 000000000..f3a204fe1 --- /dev/null +++ b/.env.local.example @@ -0,0 +1,29 @@ +# ============================================================================= +# Beagle Local Dev - Minimum Required Environment Variables +# ============================================================================= +# Copy this file to .env.local: +# cp .env.local.example .env.local +# +# Then run: +# docker compose -f compose.local.yaml up --build +# ============================================================================= + +# --- REQUIRED (no defaults in settings.py - app will crash without these) --- +BEAGLE_DB_NAME=beagle +BEAGLE_DB_USERNAME=beagle +BEAGLE_DB_PASSWORD=beagle123 + +# --- Django --- +ENVIRONMENT=dev +BEAGLE_ALLOWED_HOSTS=localhost,0.0.0.0,127.0.0.1 + +# --- Ridgeback (pipeline runner) --- +# If running Ridgeback locally, set this to its URL. +# Use host.docker.internal to reach services on the Docker host. +# BEAGLE_RIDGEBACK_URL=http://host.docker.internal:5003 + +# --- Notifier (disabled for local dev) --- +BEAGLE_NOTIFIER_ACTIVE=False + +# --- LDAP (disabled for local dev) --- +# BEAGLE_AUTH_LDAP_SERVER_URI= diff --git a/beagle_etl/tests/jobs/test_lims_etl_jobs.py b/beagle_etl/tests/jobs/test_lims_etl_jobs.py index 714b1b53f..a1b10a38a 100644 --- a/beagle_etl/tests/jobs/test_lims_etl_jobs.py +++ b/beagle_etl/tests/jobs/test_lims_etl_jobs.py @@ -39,7 +39,7 @@ class TestFetchSamples(TestCase): # self.assertTrue(len(files_metadata) == 0) # self.assertTrue(len(jobs) == 0) # - # request_id = "10075_D" + # request_id = "99990_D" # # child_jobs = fetch_samples(request_id=request_id) # # # check that jobs were created successfully diff --git a/beagle_etl/tests/jobs/test_metadb.py b/beagle_etl/tests/jobs/test_metadb.py index 7959cec0f..1c25070b1 100644 --- a/beagle_etl/tests/jobs/test_metadb.py +++ b/beagle_etl/tests/jobs/test_metadb.py @@ -48,15 +48,15 @@ def setUp(self): self.job_group = JobGroup.objects.create() self.job_group_notifier = JobGroupNotifier.objects.create(job_group=self.job_group, notifier_type=self.notifier) self.file_keys = ["R"] - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "etl/10075_D_2.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "etl/99990_D_2.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "etl/10075_D_2.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "etl/99990_D_2.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) - new_request_json_path = os.path.join(settings.TEST_FIXTURE_DIR, "etl/10075_D_2.update.json") + new_request_json_path = os.path.join(settings.TEST_FIXTURE_DIR, "etl/99990_D_2.update.json") call_command("loaddata", test_files_fixture, verbosity=0) - update_sample_json_path = os.path.join(settings.TEST_FIXTURE_DIR, "etl/10075_D_2.update_sample.json") + update_sample_json_path = os.path.join(settings.TEST_FIXTURE_DIR, "etl/99990_D_2.update_sample.json") call_command("loaddata", test_files_fixture, verbosity=0) - update_request_json_path = os.path.join(settings.TEST_FIXTURE_DIR, "etl/10075_D_request_update.json") + update_request_json_path = os.path.join(settings.TEST_FIXTURE_DIR, "etl/99990_D_request_update.json") with open(update_sample_json_path) as new_sample_json_file: self.new_sample_data = json.load(new_sample_json_file) self.new_sample_data_str = json.dumps(self.new_sample_data) @@ -68,29 +68,29 @@ def setUp(self): self.update_request_data = json.load(update_request_json_file) self.update_request_str = json.dumps(self.update_request_data) - test_new_request_08944_B = os.path.join(settings.TEST_FIXTURE_DIR, "08944_B_new_request.json") - with open(test_new_request_08944_B) as new_request_08944_B: - self.new_request = json.load(new_request_08944_B) + test_new_request_99991_B = os.path.join(settings.TEST_FIXTURE_DIR, "99991_B_new_request.json") + with open(test_new_request_99991_B) as new_request_99991_B: + self.new_request = json.load(new_request_99991_B) self.new_request_str = json.dumps(self.new_request) - test_new_request_14269_C = os.path.join(settings.TEST_FIXTURE_DIR, "14269_C_new_request.json") - with open(test_new_request_14269_C) as new_request_14269_C: - self.new_request_14269_C = json.load(new_request_14269_C) - self.new_request_14269_C_str = json.dumps(self.new_request_14269_C) + test_new_request_99908_C = os.path.join(settings.TEST_FIXTURE_DIR, "99908_C_new_request.json") + with open(test_new_request_99908_C) as new_request_99908_C: + self.new_request_99908_C = json.load(new_request_99908_C) + self.new_request_99908_C_str = json.dumps(self.new_request_99908_C) - test_14269_C_1_update_sample = os.path.join(settings.TEST_FIXTURE_DIR, "14269_C_1_update_sample.json") - with open(test_14269_C_1_update_sample) as update_sample_14269_C_1: - self.update_sample_14269_C_1 = json.load(update_sample_14269_C_1) - self.update_sample_14269_C_1_str = json.dumps(self.update_sample_14269_C_1) + test_99908_C_1_update_sample = os.path.join(settings.TEST_FIXTURE_DIR, "99908_C_1_update_sample.json") + with open(test_99908_C_1_update_sample) as update_sample_99908_C_1: + self.update_sample_99908_C_1 = json.load(update_sample_99908_C_1) + self.update_sample_99908_C_1_str = json.dumps(self.update_sample_99908_C_1) - test_14269_C_1_update_sample_new_files = os.path.join( - settings.TEST_FIXTURE_DIR, "14269_C_1_update_sample_new_files.json" + test_99908_C_1_update_sample_new_files = os.path.join( + settings.TEST_FIXTURE_DIR, "99908_C_1_update_sample_new_files.json" ) - with open(test_14269_C_1_update_sample_new_files) as update_sample_14269_C_1_new_files: - self.update_sample_14269_C_1_new_files = json.load(update_sample_14269_C_1_new_files) - self.update_sample_14269_C_1_new_files_str = json.dumps(self.update_sample_14269_C_1_new_files) + with open(test_99908_C_1_update_sample_new_files) as update_sample_99908_C_1_new_files: + self.update_sample_99908_C_1_new_files = json.load(update_sample_99908_C_1_new_files) + self.update_sample_99908_C_1_new_files_str = json.dumps(self.update_sample_99908_C_1_new_files) - self.etl_user = User.objects.create_superuser("ETL", "voyager-etl@mskcc.org", "password") + self.etl_user = User.objects.create_superuser("ETL", "etl@example.org", "password") self.file_group_id = "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" settings.ETL_USER = self.etl_user.username settings.NOTIFIER_ACTIVE = False @@ -121,18 +121,18 @@ def test_new_request( send_notification.return_value = True access.return_value = os.R_OK msg = SMILEMessage.objects.create( - topic="new-request", request_id="08944_B", gene_panel="", message=self.new_request_str + topic="new-request", request_id="99991_B", gene_panel="", message=self.new_request_str ) msg.in_progress() new_request(str(msg.id)) msg.refresh_from_db() - request = Request.objects.filter(request_id="08944_B") - sample_1 = Sample.objects.filter(sample_id="08944_B_1") - sample_2 = Sample.objects.filter(sample_id="08944_B_2") - sample_3 = Sample.objects.filter(sample_id="08944_B_3") - sample_4 = Sample.objects.filter(sample_id="08944_B_4") - patient_1 = Patient.objects.filter(patient_id="C-MP76JR") - patient_2 = Patient.objects.filter(patient_id="C-4LM16H") + request = Request.objects.filter(request_id="99991_B") + sample_1 = Sample.objects.filter(sample_id="99991_B_1") + sample_2 = Sample.objects.filter(sample_id="99991_B_2") + sample_3 = Sample.objects.filter(sample_id="99991_B_3") + sample_4 = Sample.objects.filter(sample_id="99991_B_4") + patient_1 = Patient.objects.filter(patient_id="C-PPPP10") + patient_2 = Patient.objects.filter(patient_id="C-PPPPP1") self.assertEqual(request.count(), 1) self.assertEqual(sample_1.count(), 1) self.assertEqual(sample_2.count(), 1) @@ -140,16 +140,16 @@ def test_new_request( self.assertEqual(sample_4.count(), 1) self.assertTrue(patient_1.count(), 1) self.assertTrue(patient_2.count(), 1) - study = StudyObject.get_by_request("08944_B") + study = StudyObject.get_by_request("99991_B") self.assertIsNotNone(study) self.assertListEqual(list(study[0].requests), list(request.all())) files = FileRepository.filter( - metadata={settings.REQUEST_ID_METADATA_KEY: "08944_B"}, file_group=self.file_group_id + metadata={settings.REQUEST_ID_METADATA_KEY: "99991_B"}, file_group=self.file_group_id ) self.assertEqual(msg.status, SmileMessageStatus.COMPLETED) self.assertEqual(files.count(), 8) request = request.first() - samples = Sample.objects.filter(sample_id__startswith="08944_B").order_by("created_date").all() + samples = Sample.objects.filter(sample_id__startswith="99991_B").order_by("created_date").all() for sample in samples: self.assertEqual(sample.request_id, request.request_id) self.assertListEqual(study[0].samples, list(samples)) @@ -198,7 +198,7 @@ def test_update_request_metadata( msg = SMILEMessage.objects.create(topic="update_request", message=self.update_request_str) msg.in_progress() update_request_job(str(msg.id)) - files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "10075_D"}) + files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "99990_D"}) for file in files: self.assertEqual( file.metadata[settings.REQUEST_ID_METADATA_KEY], @@ -249,7 +249,7 @@ def test_update_request_ticket( msg = SMILEMessage.objects.create(topic="update_request", message=self.update_request_str) msg.in_progress() update_request_job(str(msg.id)) - files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "10075_D_2"}) + files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "99990_D_2"}) sample_names = [] for file in files: sample_name = file.metadata[settings.SAMPLE_ID_METADATA_KEY] @@ -277,7 +277,7 @@ def test_update_request_sample( jobGroupNotifierObjectGet.return_value = None send_notification.return_value = None sample_metadata = {} - sample_files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "10075_D_2"}) + sample_files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "99990_D_2"}) for single_file in sample_files: sample_name = single_file.metadata[settings.SAMPLE_ID_METADATA_KEY] if sample_name not in sample_metadata: @@ -285,7 +285,7 @@ def test_update_request_sample( msg = SMILEMessage.objects.create(topic="update_request", message=self.update_request_str) msg.in_progress() update_request_job(str(msg.id)) - files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "10075_D_2"}) + files = FileRepository.filter(metadata={settings.REQUEST_ID_METADATA_KEY: "99990_D_2"}) for file in files: metadata_keys = file.metadata.keys() sample_name = file.metadata[settings.SAMPLE_ID_METADATA_KEY] @@ -349,7 +349,7 @@ def test_update_sample_preserve( msg = SMILEMessage.objects.create(topic="update_sample", message=self.new_sample_data_str) msg.in_progress() update_sample_job(str(msg.id)) - sample_files = FileRepository.filter(metadata={settings.SAMPLE_ID_METADATA_KEY: "10075_D_2"}) + sample_files = FileRepository.filter(metadata={settings.SAMPLE_ID_METADATA_KEY: "99990_D_2"}) for f in sample_files: self.assertEqual(f.metadata["sampleName"], "TestSample001") @@ -387,25 +387,25 @@ def test_update_sample( access.return_value = os.R_OK settings.NOTIFIER_ACTIVE = False - new_request_msg = SMILEMessage.objects.create(request_id="14269_C", message=self.new_request_14269_C_str) + new_request_msg = SMILEMessage.objects.create(request_id="99908_C", message=self.new_request_99908_C_str) new_request_msg.in_progress() update_sample_msg = SMILEMessage.objects.create( - request_id="14269_C_1", message=self.update_sample_14269_C_1_str + request_id="99908_C_1", message=self.update_sample_99908_C_1_str ) new_request(new_request_msg.id) tumor_or_normal = FileRepository.filter( - metadata={settings.SAMPLE_ID_METADATA_KEY: "14269_C_1"}, + metadata={settings.SAMPLE_ID_METADATA_KEY: "99908_C_1"}, values_metadata=settings.TUMOR_OR_NORMAL_METADATA_KEY, ).first() self.assertEqual(tumor_or_normal, "Normal") update_sample_job(update_sample_msg.id) tumor_or_normal = FileRepository.filter( - metadata={settings.SAMPLE_ID_METADATA_KEY: "14269_C_1"}, + metadata={settings.SAMPLE_ID_METADATA_KEY: "99908_C_1"}, values_metadata=settings.TUMOR_OR_NORMAL_METADATA_KEY, ).first() self.assertEqual(tumor_or_normal, "Tumor") - files = FileRepository.filter(metadata={settings.SAMPLE_ID_METADATA_KEY: "14269_C_1"}) + files = FileRepository.filter(metadata={settings.SAMPLE_ID_METADATA_KEY: "99908_C_1"}) self.assertEqual(len(files), 2) for file in files: @@ -449,26 +449,26 @@ def test_update_sample_new_fastqs( settings.NOTIFIER_ACTIVE = False path_exists.return_value = True - new_request_msg = SMILEMessage.objects.create(request_id="14269_C", message=self.new_request_14269_C_str) + new_request_msg = SMILEMessage.objects.create(request_id="99908_C", message=self.new_request_99908_C_str) new_request_msg.in_progress() update_sample_msg = SMILEMessage.objects.create( - request_id="14269_C_1", message=self.update_sample_14269_C_1_new_files_str + request_id="99908_C_1", message=self.update_sample_99908_C_1_new_files_str ) update_sample_msg.in_progress() new_request(new_request_msg.id) tumor_or_normal = FileRepository.filter( - metadata={settings.SAMPLE_ID_METADATA_KEY: "14269_C_1"}, + metadata={settings.SAMPLE_ID_METADATA_KEY: "99908_C_1"}, values_metadata=settings.TUMOR_OR_NORMAL_METADATA_KEY, ).first() self.assertEqual(tumor_or_normal, "Normal") update_sample_job(update_sample_msg.id) tumor_or_normal = FileRepository.filter( - metadata={settings.SAMPLE_ID_METADATA_KEY: "14269_C_1"}, + metadata={settings.SAMPLE_ID_METADATA_KEY: "99908_C_1"}, values_metadata=settings.TUMOR_OR_NORMAL_METADATA_KEY, ).first() self.assertEqual(tumor_or_normal, "Tumor") - files = FileRepository.filter(metadata={settings.SAMPLE_ID_METADATA_KEY: "14269_C_1"}) + files = FileRepository.filter(metadata={settings.SAMPLE_ID_METADATA_KEY: "99908_C_1"}) self.assertEqual(len(files), 2) for file in files: @@ -509,16 +509,16 @@ def test_update_sample_update( path_exists.return_value = True calculate_checksum.return_value = None - new_request_msg = SMILEMessage.objects.create(request_id="14269_C", message=self.new_request_14269_C_str) + new_request_msg = SMILEMessage.objects.create(request_id="99908_C", message=self.new_request_99908_C_str) new_request(new_request_msg.id) - test_14269_C_1_update_sample = os.path.join(settings.TEST_FIXTURE_DIR, "14269_C_1_update_sample.json") - with open(test_14269_C_1_update_sample) as update_sample_14269_C_1: - self.update_sample_14269_C_1 = json.load(update_sample_14269_C_1) - self.update_sample_14269_C_1_str = json.dumps(self.update_sample_14269_C_1) + test_99908_C_1_update_sample = os.path.join(settings.TEST_FIXTURE_DIR, "99908_C_1_update_sample.json") + with open(test_99908_C_1_update_sample) as update_sample_99908_C_1: + self.update_sample_99908_C_1 = json.load(update_sample_99908_C_1) + self.update_sample_99908_C_1_str = json.dumps(self.update_sample_99908_C_1) msg = SMILEMessage.objects.create( topic="MDB_STREAM.server.cpt-gateway.cmo-sample-update", - request_id="14269_C", - message=self.update_sample_14269_C_1_str, + request_id="99908_C", + message=self.update_sample_99908_C_1_str, status=SmileMessageStatus.PENDING, ) update_sample_job(str(msg.id)) diff --git a/beagle_etl/tests/test_smile_message.py b/beagle_etl/tests/test_smile_message.py index 105a0b03e..772a6a700 100644 --- a/beagle_etl/tests/test_smile_message.py +++ b/beagle_etl/tests/test_smile_message.py @@ -15,7 +15,7 @@ def setUp(self): "genePanel": "TestPanel500", "projectManagerName": "Smith, John", "piEmail": "pi@example.org", - "labHeadName": "Jane Doe", + "labHeadName": "Test Scientist", "labHeadEmail": "labhead@example.org", "investigatorName": "Bob Researcher", "investigatorEmail": "researcher@example.org", @@ -183,7 +183,7 @@ def test_deserialize_request_metadata(self): self.assertEqual(request.genePanel, "TestPanel500") self.assertEqual(request.projectManagerName, "Smith, John") self.assertEqual(request.piEmail, "pi@example.org") - self.assertEqual(request.labHeadName, "Jane Doe") + self.assertEqual(request.labHeadName, "Test Scientist") self.assertEqual(request.labHeadEmail, "labhead@example.org") self.assertEqual(request.investigatorName, "Bob Researcher") self.assertEqual(request.investigatorEmail, "researcher@example.org") diff --git a/compose.local.yaml b/compose.local.yaml new file mode 100644 index 000000000..99749b664 --- /dev/null +++ b/compose.local.yaml @@ -0,0 +1,139 @@ +name: "Beagle Local Dev" + +services: + beagle_postgres: + image: postgres:17-trixie + restart: on-failure + volumes: + - postgres_data:/var/lib/postgresql/data/ + environment: + POSTGRES_USER: beagle + POSTGRES_PASSWORD: beagle123 + POSTGRES_DB: beagle + ports: + - "5432:5432" + command: + - -c + - max_connections=100 + - -c + - shared_buffers=256MB + - -c + - effective_cache_size=512MB + - -c + - work_mem=4MB + - -c + - shared_preload_libraries=pg_stat_statements + healthcheck: + test: ["CMD-SHELL", "pg_isready -U beagle -d beagle"] + interval: 10s + timeout: 5s + retries: 5 + + beagle_memcached: + image: memcached:1.6-alpine + restart: on-failure + expose: + - "11211" + healthcheck: + test: ["CMD-SHELL", "echo stats | nc localhost 11211"] + interval: 10s + timeout: 5s + retries: 3 + + beagle_rabbitmq: + image: rabbitmq:4.0.6-management-alpine + restart: on-failure + hostname: beagle_rabbitmq + volumes: + - rabbitmq_data:/var/lib/rabbitmq/ + - ./conf/rabbitmq.conf:/etc/rabbitmq/conf.d/20-beagle.conf:ro + ports: + - "15672:15672" + - "5672:5672" + environment: + RABBITMQ_NODENAME: rabbitmq_beagle + RABBITMQ_DEFAULT_USER: guest + RABBITMQ_DEFAULT_PASS: guest + healthcheck: + test: ["CMD", "rabbitmq-diagnostics", "check_running"] + interval: 10s + timeout: 5s + retries: 5 + + beagle: + build: . + restart: on-failure + env_file: .env.local + environment: + BEAGLE_DB_URL: beagle_postgres + BEAGLE_DB_PORT: "5432" + BEAGLE_MEMCACHED_HOST: beagle_memcached + BEAGLE_MEMCACHED_PORT: "11211" + BEAGLE_RABBITMQ_URL: beagle_rabbitmq + BEAGLE_RABBITMQ_PORT: "5672" + BEAGLE_URL: http://localhost:8000 + BEAGLE_LOG_PATH: /tmp/django_server.log + volumes: + - .:/app/beagle + ports: + - "8000:8000" + entrypoint: ["/bin/bash", "-c"] + command: + - | + python3 /app/beagle/manage.py migrate --noinput + echo "User.objects.filter(username='admin').exists() or User.objects.create_superuser('admin','admin@localhost.com','admin')" | python3 /app/beagle/manage.py shell_plus + python3 /app/beagle/manage.py collectstatic --noinput --clear 2>/dev/null || true + gunicorn beagle.wsgi --log-file /tmp/django_server.log --bind 0.0.0.0:8000 --threads 4 --reload --pythonpath /app/beagle + healthcheck: + test: ["CMD-SHELL", "curl -sSf http://localhost:8000/ || exit 1"] + interval: 15s + timeout: 5s + retries: 5 + depends_on: + beagle_postgres: + condition: service_healthy + beagle_memcached: + condition: service_healthy + beagle_rabbitmq: + condition: service_healthy + + beagle_celery: + build: . + restart: on-failure + env_file: .env.local + environment: + BEAGLE_DB_URL: beagle_postgres + BEAGLE_DB_PORT: "5432" + BEAGLE_MEMCACHED_HOST: beagle_memcached + BEAGLE_MEMCACHED_PORT: "11211" + BEAGLE_RABBITMQ_URL: beagle_rabbitmq + BEAGLE_RABBITMQ_PORT: "5672" + BEAGLE_URL: http://beagle:8000 + BEAGLE_LOG_PATH: /tmp/celery.log + volumes: + - .:/app/beagle + entrypoint: ["/bin/bash", "-c"] + command: + - | + celery --workdir /app/beagle \ + -A beagle_etl worker \ + -B \ + -l info \ + -Q beagle_default_queue,beagle_runner_queue,beagle_check_files_queue,beagle_job_scheduler_queue,beagle_file_manager_queue \ + --concurrency=4 + healthcheck: + test: "celery --workdir /app/beagle -A beagle_etl status || exit 1" + interval: 30s + timeout: 10s + retries: 3 + depends_on: + beagle_postgres: + condition: service_healthy + beagle_memcached: + condition: service_healthy + beagle_rabbitmq: + condition: service_healthy + +volumes: + postgres_data: + rabbitmq_data: diff --git a/file_system/fixtures/13893_B.filemetadata.json b/file_system/fixtures/13893_B.filemetadata.json index 2a6e20071..a6304363b 100644 --- a/file_system/fixtures/13893_B.filemetadata.json +++ b/file_system/fixtures/13893_B.filemetadata.json @@ -11,7 +11,7 @@ "metadata": { "R": "R2", "sex": "M", - "ciTag": "s_C_F6H84U_N001_d01", + "ciTag": "s_C_PPPP23_N001_d01", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -53,7 +53,7 @@ "cmoPatientId": "ALLANT2", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_1_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -81,15 +81,15 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-F6H84U", + "value": "C-PPPP23", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "ef4ff892-f7b2-4e80-9d0e-cab12a1c6d9b", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -99,8 +99,8 @@ "naToExtract": "", "normalizedPatientId": "P-0025928" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -125,7 +125,7 @@ "metadata": { "R": "R1", "sex": "M", - "ciTag": "s_C_F6H84U_N001_d01", + "ciTag": "s_C_PPPP23_N001_d01", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -167,7 +167,7 @@ "cmoPatientId": "ALLANT2", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_1_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -195,15 +195,15 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-F6H84U", + "value": "C-PPPP23", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "ef4ff892-f7b2-4e80-9d0e-cab12a1c6d9b", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -213,8 +213,8 @@ "naToExtract": "", "normalizedPatientId": "P-0025928" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -239,7 +239,7 @@ "metadata": { "R": "R2", "sex": "M", - "ciTag": "s_C_F6H84U_N001_d01", + "ciTag": "s_C_PPPP23_N001_d01", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -281,7 +281,7 @@ "cmoPatientId": "ALLANT2", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_1_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -309,15 +309,15 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-F6H84U", + "value": "C-PPPP23", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "ef4ff892-f7b2-4e80-9d0e-cab12a1c6d9b", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -327,8 +327,8 @@ "naToExtract": "", "normalizedPatientId": "P-0025928" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -353,7 +353,7 @@ "metadata": { "R": "R2", "sex": "M", - "ciTag": "s_C_13TFTU_N003_d02", + "ciTag": "s_C_PPPP22_N003_d02", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -395,7 +395,7 @@ "cmoPatientId": "ALLANT3", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_2_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -427,15 +427,15 @@ "namespace": "dmpId" }, { - "value": "C-13TFTU", + "value": "C-PPPP22", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "946b154e-e899-4485-ad07-456de38afcbc", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -445,8 +445,8 @@ "naToExtract": "", "normalizedPatientId": "P-0010017" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -513,7 +513,7 @@ "cmoPatientId": "ALLANT", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_3_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -545,11 +545,11 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "193a0d5e-ca18-4e36-939a-45e837b17158", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -559,8 +559,8 @@ "naToExtract": "", "normalizedPatientId": "P-0017716" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -585,7 +585,7 @@ "metadata": { "R": "R2", "sex": "M", - "ciTag": "s_C_13TFTU_N003_d02", + "ciTag": "s_C_PPPP22_N003_d02", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -627,7 +627,7 @@ "cmoPatientId": "ALLANT3", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_2_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -659,15 +659,15 @@ "namespace": "dmpId" }, { - "value": "C-13TFTU", + "value": "C-PPPP22", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "946b154e-e899-4485-ad07-456de38afcbc", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -677,8 +677,8 @@ "naToExtract": "", "normalizedPatientId": "P-0010017" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -703,7 +703,7 @@ "metadata": { "R": "R1", "sex": "M", - "ciTag": "s_C_13TFTU_N003_d02", + "ciTag": "s_C_PPPP22_N003_d02", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -745,7 +745,7 @@ "cmoPatientId": "ALLANT3", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_2_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -777,15 +777,15 @@ "namespace": "dmpId" }, { - "value": "C-13TFTU", + "value": "C-PPPP22", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "946b154e-e899-4485-ad07-456de38afcbc", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -795,8 +795,8 @@ "naToExtract": "", "normalizedPatientId": "P-0010017" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -821,7 +821,7 @@ "metadata": { "R": "R1", "sex": "M", - "ciTag": "s_C_13TFTU_N003_d02", + "ciTag": "s_C_PPPP22_N003_d02", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -863,7 +863,7 @@ "cmoPatientId": "ALLANT3", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_2_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -895,15 +895,15 @@ "namespace": "dmpId" }, { - "value": "C-13TFTU", + "value": "C-PPPP22", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "946b154e-e899-4485-ad07-456de38afcbc", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -913,8 +913,8 @@ "naToExtract": "", "normalizedPatientId": "P-0010017" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -939,7 +939,7 @@ "metadata": { "R": "R1", "sex": "M", - "ciTag": "s_C_F6H84U_N001_d01", + "ciTag": "s_C_PPPP23_N001_d01", "runId": "DIANA_0568", "tubeId": "", "baitSet": "MSK-ACCESS-v1_0-probesAllwFP", @@ -981,7 +981,7 @@ "cmoPatientId": "ALLANT2", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_1_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -1009,15 +1009,15 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-F6H84U", + "value": "C-PPPP23", "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "ef4ff892-f7b2-4e80-9d0e-cab12a1c6d9b", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -1027,8 +1027,8 @@ "naToExtract": "", "normalizedPatientId": "P-0025928" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1095,7 +1095,7 @@ "cmoPatientId": "ALLANT", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_3_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -1127,11 +1127,11 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "193a0d5e-ca18-4e36-939a-45e837b17158", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -1141,8 +1141,8 @@ "naToExtract": "", "normalizedPatientId": "P-0017716" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1209,7 +1209,7 @@ "cmoPatientId": "ALLANT", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_3_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -1241,11 +1241,11 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "193a0d5e-ca18-4e36-939a-45e837b17158", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -1255,8 +1255,8 @@ "naToExtract": "", "normalizedPatientId": "P-0017716" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1323,7 +1323,7 @@ "cmoPatientId": "ALLANT", "igoProjectId": "13893", "igoRequestId": "13893_B", - "labHeadEmail": "name@mskcc.org", + "labHeadEmail": "name@example.org", "libraryIgoId": "13893_B_3_1_1_1", "oncotreeCode": null, "preservation": "EDTA-Streck", @@ -1355,11 +1355,11 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "193a0d5e-ca18-4e36-939a-45e837b17158", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org", + "dataAccessEmails": "pm1@example.org,accessteam@example.org", "dataAnalystEmail": "", "investigatorName": "name", "sequencingCenter": "MSKCC", @@ -1369,8 +1369,8 @@ "naToExtract": "", "normalizedPatientId": "P-0017716" }, - "investigatorEmail": "name@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,zzPDL_SKI_CMO_ACCESS@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "name@example.org", + "otherContactEmails": "pm1@example.org,accessteam@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", diff --git a/fixtures/tests/08944_B_new_request.json b/fixtures/tests/08944_B_new_request.json deleted file mode 100644 index 8d09fd819..000000000 --- a/fixtures/tests/08944_B_new_request.json +++ /dev/null @@ -1,368 +0,0 @@ -{ - "smileRequestId": "7203e4e8-ab74-4928-b31f-5089908ab051", - "igoProjectId": "08944", - "igoRequestId": "08944_B", - "genePanel": "IMPACT468", - "projectManagerName": "Ling, Lilan", - "piEmail": "rudinc@mskcc.org", - "labHeadName": "Charles Rudin", - "labHeadEmail": "rudinc@mskcc.org", - "investigatorName": "Viola Allaj", - "investigatorEmail": "allajv@mskcc.org", - "dataAnalystName": "John Poirier", - "dataAnalystEmail": "poirierj@mskcc.org", - "otherContactEmails": "poirierj@mskcc.org", - "dataAccessEmails": "", - "qcAccessEmails": ",zzPDL_SKI_PDXTeam@mskcc.org", - "strand": null, - "libraryType": null, - "isCmoRequest": true, - "bicAnalysis": true, - "requestJson": "{\"requestId\":\"08944_B\",\"projectId\":\"08944\",\"dataAccessEmails\":\"\",\"dataAnalystEmail\":\"poirierj@mskcc.org\",\"dataAnalystName\":\"John Poirier\",\"investigatorEmail\":\"allajv@mskcc.org\",\"investigatorName\":\"Viola Allaj\",\"labHeadEmail\":\"rudinc@mskcc.org\",\"labHeadName\":\"Charles Rudin\",\"libraryType\":null,\"otherContactEmails\":\"poirierj@mskcc.org\",\"piEmail\":\"rudinc@mskcc.org\",\"projectManagerName\":\"Ling, 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"modified_date": "2021-08-13T14:59:25.566Z", - "file_name": "Myeloid200-7_IGO_05500_HJ_7_S16_L001_R2_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-7_IGO_05500_HJ_7/Myeloid200-7_IGO_05500_HJ_7_S16_L001_R2_001.fastq.gz", + "file_name": "Myeloid200-7_IGO_99900_H_7_S16_L001_R2_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-7_IGO_99900_H_7/Myeloid200-7_IGO_99900_H_7_S16_L001_R2_001.fastq.gz", "file_type": 1, "size": 9344592073, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", @@ -8219,8 +8219,8 @@ "fields": { "created_date": "2021-08-13T14:59:25.466Z", "modified_date": "2021-08-13T14:59:25.468Z", - "file_name": "Myeloid200-8_IGO_05500_HJ_8_S17_L001_R1_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-8_IGO_05500_HJ_8/Myeloid200-8_IGO_05500_HJ_8_S17_L001_R1_001.fastq.gz", + "file_name": "Myeloid200-8_IGO_99900_H_8_S17_L001_R1_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-8_IGO_99900_H_8/Myeloid200-8_IGO_99900_H_8_S17_L001_R1_001.fastq.gz", "file_type": 1, "size": 8305637392, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", @@ -8237,8 +8237,8 @@ "fields": { "created_date": "2021-08-13T14:59:25.498Z", "modified_date": "2021-08-13T14:59:25.500Z", - "file_name": "Myeloid200-8_IGO_05500_HJ_8_S17_L001_R2_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-8_IGO_05500_HJ_8/Myeloid200-8_IGO_05500_HJ_8_S17_L001_R2_001.fastq.gz", + "file_name": "Myeloid200-8_IGO_99900_H_8_S17_L001_R2_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-8_IGO_99900_H_8/Myeloid200-8_IGO_99900_H_8_S17_L001_R2_001.fastq.gz", "file_type": 1, "size": 8676114173, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", diff --git a/fixtures/tests/05500_HJ.filemetadata.json b/fixtures/tests/99900_H.filemetadata.json similarity index 84% rename from fixtures/tests/05500_HJ.filemetadata.json rename to fixtures/tests/99900_H.filemetadata.json index 05a161d56..cce91924c 100644 --- a/fixtures/tests/05500_HJ.filemetadata.json +++ b/fixtures/tests/99900_H.filemetadata.json @@ -12,7 +12,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_4_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -21,23 +21,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -49,20 +49,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-4", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-4", "captureConcentrationNm": null, @@ -84,7 +84,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_1_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -93,23 +93,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -121,20 +121,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-1", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-1", "captureConcentrationNm": null, @@ -156,7 +156,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_1_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -165,23 +165,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -193,20 +193,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-1", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-1", "captureConcentrationNm": null, @@ -228,7 +228,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_2_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -237,23 +237,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -265,20 +265,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-2", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-2", "captureConcentrationNm": null, @@ -300,7 +300,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_2_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -309,23 +309,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -337,20 +337,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-2", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-2", "captureConcentrationNm": null, @@ -372,7 +372,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_6_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -381,23 +381,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -409,20 +409,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-6", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-6", "captureConcentrationNm": null, @@ -444,7 +444,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_6_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -453,23 +453,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -481,20 +481,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-6", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-6", "captureConcentrationNm": null, @@ -516,7 +516,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_BC200_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -525,23 +525,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "BC200-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -553,20 +553,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "BC200", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "BC200", "captureConcentrationNm": null, @@ -588,7 +588,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_BC200_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -597,23 +597,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "BC200-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -625,20 +625,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "BC200", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "BC200", "captureConcentrationNm": null, @@ -660,7 +660,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_6_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -669,23 +669,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -697,20 +697,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-6", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-6", "captureConcentrationNm": null, @@ -732,7 +732,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_6_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -741,23 +741,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -769,20 +769,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-6", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-6", "captureConcentrationNm": null, @@ -804,7 +804,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_8_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -813,23 +813,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -841,20 +841,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-8", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-8", "captureConcentrationNm": null, @@ -876,7 +876,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_8_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -885,23 +885,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -913,20 +913,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-8", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-8", "captureConcentrationNm": null, @@ -948,7 +948,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_BC100_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -957,23 +957,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "BC100-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -985,20 +985,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "BC100", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "BC100", "captureConcentrationNm": null, @@ -1020,7 +1020,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_BC100_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1029,23 +1029,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "BC100-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1057,20 +1057,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "BC100", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "BC100", "captureConcentrationNm": null, @@ -1092,7 +1092,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_5_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1101,23 +1101,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1129,20 +1129,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-5", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-5", "captureConcentrationNm": null, @@ -1164,7 +1164,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_5_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1173,23 +1173,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1201,20 +1201,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-5", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-5", "captureConcentrationNm": null, @@ -1235,11 +1235,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1268,11 +1268,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1301,11 +1301,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1334,11 +1334,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1367,11 +1367,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1400,11 +1400,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1433,11 +1433,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1466,11 +1466,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1499,11 +1499,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1532,11 +1532,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1565,11 +1565,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -1598,11 +1598,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1631,11 +1631,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1664,11 +1664,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1697,11 +1697,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1730,11 +1730,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1763,11 +1763,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1796,11 +1796,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1829,11 +1829,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1862,11 +1862,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1895,11 +1895,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1928,11 +1928,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -1961,11 +1961,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -1994,11 +1994,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2027,11 +2027,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2060,11 +2060,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2093,11 +2093,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "cmoPatientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "cmoPatientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2126,11 +2126,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2159,11 +2159,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2192,11 +2192,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2225,11 +2225,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2258,11 +2258,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2291,11 +2291,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -2324,11 +2324,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2357,11 +2357,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2390,11 +2390,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2423,11 +2423,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2456,11 +2456,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2489,11 +2489,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2522,11 +2522,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2555,11 +2555,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2588,11 +2588,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2621,11 +2621,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2654,11 +2654,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -2687,11 +2687,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2720,11 +2720,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2753,11 +2753,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2786,11 +2786,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2819,11 +2819,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2852,11 +2852,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2885,11 +2885,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2918,11 +2918,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2951,11 +2951,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -2984,11 +2984,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -3017,11 +3017,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -3050,11 +3050,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -3083,11 +3083,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -3116,11 +3116,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3149,11 +3149,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3182,11 +3182,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3215,11 +3215,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3248,11 +3248,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3281,11 +3281,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3314,11 +3314,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3347,11 +3347,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3380,11 +3380,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3413,11 +3413,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3446,11 +3446,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3479,11 +3479,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3512,11 +3512,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3545,11 +3545,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3578,11 +3578,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3611,11 +3611,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3644,11 +3644,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3677,11 +3677,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3710,11 +3710,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3743,11 +3743,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3776,11 +3776,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3809,11 +3809,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3842,11 +3842,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3875,11 +3875,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, @@ -3908,11 +3908,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -3941,11 +3941,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -3974,11 +3974,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4007,11 +4007,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4040,11 +4040,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4073,11 +4073,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4106,11 +4106,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4139,11 +4139,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4172,11 +4172,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4205,11 +4205,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4238,11 +4238,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4271,11 +4271,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4304,11 +4304,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4337,11 +4337,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4370,11 +4370,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4403,11 +4403,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4436,11 +4436,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4469,11 +4469,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4502,11 +4502,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4535,11 +4535,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4568,11 +4568,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4601,11 +4601,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4634,11 +4634,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4667,11 +4667,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_15", - "primaryId": "05500_HJ_15", + "sampleId": "99900_H_15", + "primaryId": "99900_H_15", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, @@ -4700,11 +4700,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4733,11 +4733,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4766,11 +4766,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4799,11 +4799,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4832,11 +4832,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4865,11 +4865,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4898,11 +4898,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4931,11 +4931,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4964,11 +4964,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -4997,11 +4997,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5030,11 +5030,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5063,11 +5063,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5096,11 +5096,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5129,11 +5129,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5162,11 +5162,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5195,11 +5195,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5228,11 +5228,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5261,11 +5261,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5294,11 +5294,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5327,11 +5327,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5360,11 +5360,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5393,11 +5393,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5426,11 +5426,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5459,11 +5459,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_14", - "primaryId": "05500_HJ_14", + "sampleId": "99900_H_14", + "primaryId": "99900_H_14", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, @@ -5492,11 +5492,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5525,11 +5525,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5558,11 +5558,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5591,11 +5591,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5624,11 +5624,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5657,11 +5657,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5690,11 +5690,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5723,11 +5723,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5756,11 +5756,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5789,11 +5789,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5822,11 +5822,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5855,11 +5855,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5888,11 +5888,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5921,11 +5921,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5954,11 +5954,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -5987,11 +5987,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6020,11 +6020,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6053,11 +6053,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6086,11 +6086,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6119,11 +6119,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6152,11 +6152,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6185,11 +6185,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6218,11 +6218,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6251,11 +6251,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, @@ -6284,11 +6284,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6317,11 +6317,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6350,11 +6350,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6383,11 +6383,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6416,11 +6416,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6449,11 +6449,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6482,11 +6482,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6515,11 +6515,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6548,11 +6548,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6581,11 +6581,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6614,11 +6614,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6647,11 +6647,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6680,11 +6680,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6713,11 +6713,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6746,11 +6746,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6779,11 +6779,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6812,11 +6812,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6845,11 +6845,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6878,11 +6878,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6911,11 +6911,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6944,11 +6944,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -6977,11 +6977,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -7010,11 +7010,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -7043,11 +7043,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, @@ -7076,11 +7076,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7109,11 +7109,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7142,11 +7142,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7175,11 +7175,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7208,11 +7208,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7241,11 +7241,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7274,11 +7274,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7307,11 +7307,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7340,11 +7340,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7373,11 +7373,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7406,11 +7406,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7439,11 +7439,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7472,11 +7472,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7505,11 +7505,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7538,11 +7538,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7571,11 +7571,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7604,11 +7604,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7637,11 +7637,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7670,11 +7670,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7703,11 +7703,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7736,11 +7736,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7769,11 +7769,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7802,11 +7802,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7835,11 +7835,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_1", - "primaryId": "05500_HJ_1", + "sampleId": "99900_H_1", + "primaryId": "99900_H_1", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, @@ -7868,11 +7868,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -7901,11 +7901,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -7934,11 +7934,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -7967,11 +7967,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8000,11 +8000,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8033,11 +8033,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8066,11 +8066,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8099,11 +8099,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8132,11 +8132,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8165,11 +8165,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8198,11 +8198,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8231,11 +8231,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8264,11 +8264,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8297,11 +8297,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8330,11 +8330,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8363,11 +8363,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8396,11 +8396,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8429,11 +8429,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8462,11 +8462,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8495,11 +8495,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8528,11 +8528,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8561,11 +8561,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8594,11 +8594,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8627,11 +8627,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_2", - "primaryId": "05500_HJ_2", + "sampleId": "99900_H_2", + "primaryId": "99900_H_2", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, @@ -8660,11 +8660,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8693,11 +8693,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8726,11 +8726,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8759,11 +8759,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8792,11 +8792,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8825,11 +8825,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8858,11 +8858,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8891,11 +8891,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8924,11 +8924,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8957,11 +8957,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -8990,11 +8990,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9023,11 +9023,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9056,11 +9056,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9089,11 +9089,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9122,11 +9122,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9155,11 +9155,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9188,11 +9188,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9221,11 +9221,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9254,11 +9254,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9287,11 +9287,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9320,11 +9320,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9353,11 +9353,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9386,11 +9386,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9419,11 +9419,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_6", - "primaryId": "05500_HJ_6", + "sampleId": "99900_H_6", + "primaryId": "99900_H_6", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, @@ -9452,11 +9452,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9485,11 +9485,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9518,11 +9518,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9551,11 +9551,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9584,11 +9584,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9617,11 +9617,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9650,11 +9650,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9683,11 +9683,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9716,11 +9716,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9749,11 +9749,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9782,11 +9782,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9815,11 +9815,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9848,11 +9848,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9881,11 +9881,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9914,11 +9914,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9947,11 +9947,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -9980,11 +9980,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10013,11 +10013,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10046,11 +10046,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10079,11 +10079,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10112,11 +10112,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10145,11 +10145,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10178,11 +10178,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10211,11 +10211,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, @@ -10244,11 +10244,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10277,11 +10277,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10310,11 +10310,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10343,11 +10343,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10376,11 +10376,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10409,11 +10409,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10442,11 +10442,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10475,11 +10475,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10508,11 +10508,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10541,11 +10541,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10574,11 +10574,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10607,11 +10607,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10640,11 +10640,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10673,11 +10673,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10706,11 +10706,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10739,11 +10739,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10772,11 +10772,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10805,11 +10805,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10838,11 +10838,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10871,11 +10871,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10904,11 +10904,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10937,11 +10937,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -10970,11 +10970,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -11003,11 +11003,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, @@ -11036,11 +11036,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11069,11 +11069,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11102,11 +11102,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11135,11 +11135,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11168,11 +11168,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11201,11 +11201,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11234,11 +11234,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11267,11 +11267,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11300,11 +11300,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11333,11 +11333,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11366,11 +11366,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11399,11 +11399,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11432,11 +11432,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11465,11 +11465,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11498,11 +11498,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11531,11 +11531,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11564,11 +11564,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11597,11 +11597,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11630,11 +11630,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11663,11 +11663,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11696,11 +11696,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11729,11 +11729,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11762,11 +11762,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11795,11 +11795,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, @@ -11828,11 +11828,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -11861,11 +11861,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -11894,11 +11894,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -11927,11 +11927,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -11960,11 +11960,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -11993,11 +11993,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12026,11 +12026,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12059,11 +12059,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12092,11 +12092,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12125,11 +12125,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12158,11 +12158,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12191,11 +12191,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12224,11 +12224,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12257,11 +12257,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12290,11 +12290,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12323,11 +12323,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12356,11 +12356,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12389,11 +12389,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12422,11 +12422,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12455,11 +12455,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12488,11 +12488,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12521,11 +12521,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12554,11 +12554,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12587,11 +12587,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_9", - "primaryId": "05500_HJ_9", + "sampleId": "99900_H_9", + "primaryId": "99900_H_9", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC200-05500HJ", "captureName": null, @@ -12620,11 +12620,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12653,11 +12653,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12686,11 +12686,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12719,11 +12719,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12752,11 +12752,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12785,11 +12785,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12818,11 +12818,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12851,11 +12851,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12884,11 +12884,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12917,11 +12917,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12950,11 +12950,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -12983,11 +12983,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13016,11 +13016,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13049,11 +13049,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13082,11 +13082,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13115,11 +13115,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13148,11 +13148,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13181,11 +13181,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13214,11 +13214,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13247,11 +13247,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13280,11 +13280,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13313,11 +13313,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13346,11 +13346,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13379,11 +13379,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, @@ -13413,7 +13413,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_8_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13422,23 +13422,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13450,20 +13450,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-8", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-8", "captureConcentrationNm": null, @@ -13485,7 +13485,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_8_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13494,23 +13494,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_8", - "primaryId": "05500_HJ_8", + "sampleId": "99900_H_8", + "primaryId": "99900_H_8", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13522,20 +13522,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-8", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-8", "captureConcentrationNm": null, @@ -13557,7 +13557,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_3_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13566,23 +13566,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13594,20 +13594,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-3", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-3", "captureConcentrationNm": null, @@ -13629,7 +13629,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_3_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13638,23 +13638,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_3", - "primaryId": "05500_HJ_3", + "sampleId": "99900_H_3", + "primaryId": "99900_H_3", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13666,20 +13666,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-3", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-3", "captureConcentrationNm": null, @@ -13701,7 +13701,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_7_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13710,23 +13710,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13738,20 +13738,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-7", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-7", "captureConcentrationNm": null, @@ -13773,7 +13773,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_7_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13782,23 +13782,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_7", - "primaryId": "05500_HJ_7", + "sampleId": "99900_H_7", + "primaryId": "99900_H_7", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13810,20 +13810,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-7", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-7", "captureConcentrationNm": null, @@ -13845,7 +13845,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_5_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13854,23 +13854,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13882,20 +13882,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-5", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-5", "captureConcentrationNm": null, @@ -13917,7 +13917,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_5_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13926,23 +13926,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_5", - "primaryId": "05500_HJ_5", + "sampleId": "99900_H_5", + "primaryId": "99900_H_5", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -13954,20 +13954,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-5", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-5", "captureConcentrationNm": null, @@ -13989,7 +13989,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_4_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -13998,23 +13998,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14026,20 +14026,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-4", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-4", "captureConcentrationNm": null, @@ -14061,7 +14061,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_4_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14070,23 +14070,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_13", - "primaryId": "05500_HJ_13", + "sampleId": "99900_H_13", + "primaryId": "99900_H_13", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14098,20 +14098,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-4", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-4", "captureConcentrationNm": null, @@ -14133,7 +14133,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_7_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14142,23 +14142,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14170,20 +14170,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-7", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-7", "captureConcentrationNm": null, @@ -14205,7 +14205,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_7_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14214,23 +14214,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14242,20 +14242,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-7", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-7", "captureConcentrationNm": null, @@ -14277,7 +14277,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_2_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14286,23 +14286,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14314,20 +14314,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-2", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-2", "captureConcentrationNm": null, @@ -14349,7 +14349,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_2_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14358,23 +14358,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_11", - "primaryId": "05500_HJ_11", + "sampleId": "99900_H_11", + "primaryId": "99900_H_11", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14386,20 +14386,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-2", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-2", "captureConcentrationNm": null, @@ -14421,7 +14421,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_1_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14430,23 +14430,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14458,20 +14458,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-1", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-1", "captureConcentrationNm": null, @@ -14493,7 +14493,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_1_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14502,23 +14502,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14530,20 +14530,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-1", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-1", "captureConcentrationNm": null, @@ -14565,7 +14565,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_3_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14574,23 +14574,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14602,20 +14602,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-3", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-3", "captureConcentrationNm": null, @@ -14637,7 +14637,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid100_3_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -14646,23 +14646,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -14674,20 +14674,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-3", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-3", "captureConcentrationNm": null, @@ -14708,11 +14708,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14741,11 +14741,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14774,11 +14774,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14807,11 +14807,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14840,11 +14840,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14873,11 +14873,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14906,11 +14906,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14939,11 +14939,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -14972,11 +14972,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -15005,11 +15005,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -15038,11 +15038,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -15071,11 +15071,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -15104,11 +15104,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_10", - "primaryId": "05500_HJ_10", + "sampleId": "99900_H_10", + "primaryId": "99900_H_10", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, @@ -15137,11 +15137,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15170,11 +15170,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15203,11 +15203,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15236,11 +15236,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15269,11 +15269,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15302,11 +15302,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15335,11 +15335,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15368,11 +15368,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15401,11 +15401,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15434,11 +15434,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15467,11 +15467,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15500,11 +15500,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15533,11 +15533,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_12", - "primaryId": "05500_HJ_12", + "sampleId": "99900_H_12", + "primaryId": "99900_H_12", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, @@ -15566,11 +15566,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15599,11 +15599,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15632,11 +15632,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15665,11 +15665,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15698,11 +15698,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15731,11 +15731,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15764,11 +15764,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15797,11 +15797,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15830,11 +15830,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15863,11 +15863,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15896,11 +15896,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15929,11 +15929,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15962,11 +15962,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_18", - "primaryId": "05500_HJ_18", + "sampleId": "99900_H_18", + "primaryId": "99900_H_18", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "BC100-05500HJ", "captureName": null, @@ -15995,11 +15995,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16028,11 +16028,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16061,11 +16061,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16094,11 +16094,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16127,11 +16127,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16160,11 +16160,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16193,11 +16193,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16226,11 +16226,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16259,11 +16259,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16292,11 +16292,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16325,11 +16325,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16358,11 +16358,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16391,11 +16391,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_16", - "primaryId": "05500_HJ_16", + "sampleId": "99900_H_16", + "primaryId": "99900_H_16", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, @@ -16424,11 +16424,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16457,11 +16457,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16490,11 +16490,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16523,11 +16523,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16556,11 +16556,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16589,11 +16589,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16622,11 +16622,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16655,11 +16655,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16688,11 +16688,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16721,11 +16721,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16754,11 +16754,11 @@ "metadata": { "sex": "NA", "baitSet": "MSK-CH", - "sampleId": "05500_HJ_17", - "primaryId": "05500_HJ_17", + "sampleId": "99900_H_17", + "primaryId": "99900_H_17", "barcodeId": null, - "patientId": "C-UJ1WNV", - "requestId": "05500_HJ", + "patientId": "C-PPPP17", + "requestId": "99900_H", "dnaInputNg": 0, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, @@ -16788,7 +16788,7 @@ "R": "R2", "sex": "NA", "ciTag": "s_Myeloid200_4_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -16797,23 +16797,23 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_4", - "primaryId": "05500_HJ_4", + "sampleId": "99900_H_4", + "primaryId": "99900_H_4", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": null, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -16825,20 +16825,20 @@ "captureInputNg": null, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-4", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-4", "captureConcentrationNm": null, diff --git a/fixtures/tests/05500_HJ.input.json b/fixtures/tests/99900_H.input.json similarity index 85% rename from fixtures/tests/05500_HJ.input.json rename to fixtures/tests/99900_H.input.json index 0fb28c7bf..f6a5d6eb8 100644 --- a/fixtures/tests/05500_HJ.input.json +++ b/fixtures/tests/99900_H.input.json @@ -43,11 +43,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-4_IGO_05500_HJ_4/Myeloid200-4_IGO_05500_HJ_4_S13_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-4_IGO_99900_H_4/Myeloid200-4_IGO_99900_H_4_S13_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-4_IGO_05500_HJ_4/Myeloid200-4_IGO_05500_HJ_4_S13_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-4_IGO_99900_H_4/Myeloid200-4_IGO_99900_H_4_S13_L001_R2_001.fastq.gz" } ] ], @@ -70,7 +70,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_4_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -79,22 +79,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_4", + "sampleId": "99900_H_4", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-4-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -106,20 +106,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-4", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-4", "captureConcentrationNm": 0, @@ -170,11 +170,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-1_IGO_05500_HJ_1/Myeloid200-1_IGO_05500_HJ_1_S10_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-1_IGO_99900_H_1/Myeloid200-1_IGO_99900_H_1_S10_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-1_IGO_05500_HJ_1/Myeloid200-1_IGO_05500_HJ_1_S10_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-1_IGO_99900_H_1/Myeloid200-1_IGO_99900_H_1_S10_L001_R2_001.fastq.gz" } ] ], @@ -197,7 +197,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_1_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -206,22 +206,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_1", + "sampleId": "99900_H_1", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-1-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -233,20 +233,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-1", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-1", "captureConcentrationNm": 0, @@ -297,11 +297,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-2_IGO_05500_HJ_2/Myeloid200-2_IGO_05500_HJ_2_S11_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-2_IGO_99900_H_2/Myeloid200-2_IGO_99900_H_2_S11_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-2_IGO_05500_HJ_2/Myeloid200-2_IGO_05500_HJ_2_S11_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-2_IGO_99900_H_2/Myeloid200-2_IGO_99900_H_2_S11_L001_R2_001.fastq.gz" } ] ], @@ -324,7 +324,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_2_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -333,22 +333,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_2", + "sampleId": "99900_H_2", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-2-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -360,20 +360,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-2", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-2", "captureConcentrationNm": 0, @@ -424,11 +424,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-6_IGO_05500_HJ_6/Myeloid200-6_IGO_05500_HJ_6_S15_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-6_IGO_99900_H_6/Myeloid200-6_IGO_99900_H_6_S15_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-6_IGO_05500_HJ_6/Myeloid200-6_IGO_05500_HJ_6_S15_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-6_IGO_99900_H_6/Myeloid200-6_IGO_99900_H_6_S15_L001_R2_001.fastq.gz" } ] ], @@ -451,7 +451,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_6_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -460,22 +460,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_6", + "sampleId": "99900_H_6", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-6-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -487,20 +487,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-6", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-6", "captureConcentrationNm": 0, @@ -551,11 +551,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_BC200_IGO_05500_HJ_9/BC200_IGO_05500_HJ_9_S18_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_BC200_IGO_99900_H_9/BC200_IGO_99900_H_9_S18_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_BC200_IGO_05500_HJ_9/BC200_IGO_05500_HJ_9_S18_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_BC200_IGO_99900_H_9/BC200_IGO_99900_H_9_S18_L001_R2_001.fastq.gz" } ] ], @@ -578,7 +578,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_BC200_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -587,22 +587,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_9", + "sampleId": "99900_H_9", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "BC200-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -614,20 +614,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "BC200", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "BC200", "captureConcentrationNm": 0, @@ -678,11 +678,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-6_IGO_05500_HJ_15/Myeloid100-6_IGO_05500_HJ_15_S6_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-6_IGO_99900_H_15/Myeloid100-6_IGO_99900_H_15_S6_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-6_IGO_05500_HJ_15/Myeloid100-6_IGO_05500_HJ_15_S6_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-6_IGO_99900_H_15/Myeloid100-6_IGO_99900_H_15_S6_L001_R2_001.fastq.gz" } ] ], @@ -705,7 +705,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_6_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -714,22 +714,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_15", + "sampleId": "99900_H_15", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-6-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -741,20 +741,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-6", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-6", "captureConcentrationNm": 0, @@ -805,11 +805,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-8_IGO_05500_HJ_17/Myeloid100-8_IGO_05500_HJ_17_S8_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-8_IGO_99900_H_17/Myeloid100-8_IGO_99900_H_17_S8_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-8_IGO_05500_HJ_17/Myeloid100-8_IGO_05500_HJ_17_S8_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-8_IGO_99900_H_17/Myeloid100-8_IGO_99900_H_17_S8_L001_R2_001.fastq.gz" } ] ], @@ -832,7 +832,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_8_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -841,22 +841,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_17", + "sampleId": "99900_H_17", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-8-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -868,20 +868,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-8", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-8", "captureConcentrationNm": 0, @@ -932,11 +932,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_BC100_IGO_05500_HJ_18/BC100_IGO_05500_HJ_18_S9_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_BC100_IGO_99900_H_18/BC100_IGO_99900_H_18_S9_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_BC100_IGO_05500_HJ_18/BC100_IGO_05500_HJ_18_S9_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_BC100_IGO_99900_H_18/BC100_IGO_99900_H_18_S9_L001_R2_001.fastq.gz" } ] ], @@ -959,7 +959,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_BC100_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -968,22 +968,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_18", + "sampleId": "99900_H_18", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "BC100-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -995,20 +995,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "BC100", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "BC100", "captureConcentrationNm": 0, @@ -1059,11 +1059,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-5_IGO_05500_HJ_14/Myeloid100-5_IGO_05500_HJ_14_S5_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-5_IGO_99900_H_14/Myeloid100-5_IGO_99900_H_14_S5_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-5_IGO_05500_HJ_14/Myeloid100-5_IGO_05500_HJ_14_S5_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-5_IGO_99900_H_14/Myeloid100-5_IGO_99900_H_14_S5_L001_R2_001.fastq.gz" } ] ], @@ -1086,7 +1086,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_5_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1095,22 +1095,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_14", + "sampleId": "99900_H_14", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-5-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1122,20 +1122,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-5", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-5", "captureConcentrationNm": 0, @@ -1186,11 +1186,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-8_IGO_05500_HJ_8/Myeloid200-8_IGO_05500_HJ_8_S17_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-8_IGO_99900_H_8/Myeloid200-8_IGO_99900_H_8_S17_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-8_IGO_05500_HJ_8/Myeloid200-8_IGO_05500_HJ_8_S17_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-8_IGO_99900_H_8/Myeloid200-8_IGO_99900_H_8_S17_L001_R2_001.fastq.gz" } ] ], @@ -1213,7 +1213,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_8_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1222,22 +1222,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_8", + "sampleId": "99900_H_8", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-8-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1249,20 +1249,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-8", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-8", "captureConcentrationNm": 0, @@ -1313,11 +1313,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-3_IGO_05500_HJ_3/Myeloid200-3_IGO_05500_HJ_3_S12_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-3_IGO_99900_H_3/Myeloid200-3_IGO_99900_H_3_S12_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-3_IGO_05500_HJ_3/Myeloid200-3_IGO_05500_HJ_3_S12_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-3_IGO_99900_H_3/Myeloid200-3_IGO_99900_H_3_S12_L001_R2_001.fastq.gz" } ] ], @@ -1340,7 +1340,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_3_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1349,22 +1349,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_3", + "sampleId": "99900_H_3", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-3-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1376,20 +1376,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-3", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-3", "captureConcentrationNm": 0, @@ -1440,11 +1440,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-7_IGO_05500_HJ_7/Myeloid200-7_IGO_05500_HJ_7_S16_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-7_IGO_99900_H_7/Myeloid200-7_IGO_99900_H_7_S16_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-7_IGO_05500_HJ_7/Myeloid200-7_IGO_05500_HJ_7_S16_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-7_IGO_99900_H_7/Myeloid200-7_IGO_99900_H_7_S16_L001_R2_001.fastq.gz" } ] ], @@ -1467,7 +1467,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_7_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1476,22 +1476,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_7", + "sampleId": "99900_H_7", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-7-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1503,20 +1503,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-7", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-7", "captureConcentrationNm": 0, @@ -1567,11 +1567,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-5_IGO_05500_HJ_5/Myeloid200-5_IGO_05500_HJ_5_S14_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-5_IGO_99900_H_5/Myeloid200-5_IGO_99900_H_5_S14_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid200-5_IGO_05500_HJ_5/Myeloid200-5_IGO_05500_HJ_5_S14_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid200-5_IGO_99900_H_5/Myeloid200-5_IGO_99900_H_5_S14_L001_R2_001.fastq.gz" } ] ], @@ -1594,7 +1594,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid200_5_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1603,22 +1603,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_5", + "sampleId": "99900_H_5", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid200-5-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1630,20 +1630,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid200-5", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid200-5", "captureConcentrationNm": 0, @@ -1694,11 +1694,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-4_IGO_05500_HJ_13/Myeloid100-4_IGO_05500_HJ_13_S4_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-4_IGO_99900_H_13/Myeloid100-4_IGO_99900_H_13_S4_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-4_IGO_05500_HJ_13/Myeloid100-4_IGO_05500_HJ_13_S4_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-4_IGO_99900_H_13/Myeloid100-4_IGO_99900_H_13_S4_L001_R2_001.fastq.gz" } ] ], @@ -1721,7 +1721,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_4_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1730,22 +1730,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_13", + "sampleId": "99900_H_13", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-UJ1WNV", + "cmoPatientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-4-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1757,20 +1757,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-4", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-4", "captureConcentrationNm": 0, @@ -1821,11 +1821,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-7_IGO_05500_HJ_16/Myeloid100-7_IGO_05500_HJ_16_S7_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-7_IGO_99900_H_16/Myeloid100-7_IGO_99900_H_16_S7_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-7_IGO_05500_HJ_16/Myeloid100-7_IGO_05500_HJ_16_S7_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-7_IGO_99900_H_16/Myeloid100-7_IGO_99900_H_16_S7_L001_R2_001.fastq.gz" } ] ], @@ -1848,7 +1848,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_7_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1857,22 +1857,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_16", + "sampleId": "99900_H_16", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-7-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -1884,20 +1884,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-7", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-7", "captureConcentrationNm": 0, @@ -1948,11 +1948,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-2_IGO_05500_HJ_11/Myeloid100-2_IGO_05500_HJ_11_S2_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-2_IGO_99900_H_11/Myeloid100-2_IGO_99900_H_11_S2_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-2_IGO_05500_HJ_11/Myeloid100-2_IGO_05500_HJ_11_S2_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-2_IGO_99900_H_11/Myeloid100-2_IGO_99900_H_11_S2_L001_R2_001.fastq.gz" } ] ], @@ -1975,7 +1975,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_2_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -1984,22 +1984,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_11", + "sampleId": "99900_H_11", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-2-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -2011,20 +2011,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-2", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-2", "captureConcentrationNm": 0, @@ -2075,11 +2075,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-1_IGO_05500_HJ_10/Myeloid100-1_IGO_05500_HJ_10_S1_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-1_IGO_99900_H_10/Myeloid100-1_IGO_99900_H_10_S1_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-1_IGO_05500_HJ_10/Myeloid100-1_IGO_05500_HJ_10_S1_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-1_IGO_99900_H_10/Myeloid100-1_IGO_99900_H_10_S1_L001_R2_001.fastq.gz" } ] ], @@ -2102,7 +2102,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_1_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -2111,22 +2111,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_10", + "sampleId": "99900_H_10", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-1-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -2138,20 +2138,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-1", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-1", "captureConcentrationNm": 0, @@ -2202,11 +2202,11 @@ [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-3_IGO_05500_HJ_12/Myeloid100-3_IGO_05500_HJ_12_S3_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-3_IGO_99900_H_12/Myeloid100-3_IGO_99900_H_12_S3_L001_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0401_AHKJYJDSX2/Project_05500_HJ/Sample_Myeloid100-3_IGO_05500_HJ_12/Myeloid100-3_IGO_05500_HJ_12_S3_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0001_AFCELLAAAA8/Project_99900_H/Sample_Myeloid100-3_IGO_99900_H_12/Myeloid100-3_IGO_99900_H_12_S3_L001_R2_001.fastq.gz" } ] ], @@ -2229,7 +2229,7 @@ "R": "R1", "sex": "NA", "ciTag": "s_Myeloid100_3_05500HJ", - "runId": "DIANA_0401", + "runId": "SEQRUN_0001", "recipe": "CMO-CH", "tubeId": "", "baitSet": "MSK-CH", @@ -2238,22 +2238,22 @@ "runMode": null, "species": "Human", "platform": "Illumina", - "sampleId": "05500_HJ_12", + "sampleId": "99900_H_12", "barcodeId": null, "libraryIgoId": null, - "patientId": "C-UJ1WNV", + "patientId": "C-PPPP17", "qcReports": [], - "requestId": "05500_HJ", + "requestId": "99900_H", "dnaInputNg": 0, - "flowCellId": "HKJYJDSX2", + "flowCellId": "FCELLAAAA8", "readLength": null, "sampleName": "Myeloid100-3-05500HJ", "captureName": null, "igoComplete": true, - "labHeadName": "Michael Berger", + "labHeadName": "Lab Head A", "sampleClass": "Unknown Tumor", "barcodeIndex": null, - "labHeadEmail": "bergerm1@mskcc.org", + "labHeadEmail": "analyst2@example.org", "oncoTreeCode": "MYELOID", "preservation": "Frozen", "sampleOrigin": "Other", @@ -2265,20 +2265,20 @@ "captureInputNg": 0, "cfDNA2dBarcode": null, "collectionYear": "", - "qcAccessEmails": "tamg@mskcc.org,loomisb@mskcc.org", + "qcAccessEmails": "analyst13@example.org,analyst6@example.org", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "tamg@mskcc.org", + "dataAccessEmails": "analyst13@example.org", "dataAnalystEmail": "", "externalSampleId": "Myeloid100-3", - "investigatorName": "Grittney Tam", + "investigatorName": "Investigator A", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "naToExtract": "", "normalizedPatientId": "CELLLINE_GM24385" }, - "investigatorEmail": "tamg@mskcc.org", - "otherContactEmails": "bergerm1@mskcc.org,tamg@mskcc.org,loomisb@mskcc.org", + "investigatorEmail": "analyst13@example.org", + "otherContactEmails": "analyst2@example.org,analyst13@example.org,analyst6@example.org", "projectManagerName": "", "investigatorSampleId": "Myeloid100-3", "captureConcentrationNm": 0, diff --git a/fixtures/tests/14269_C_1_update_sample.json b/fixtures/tests/99908_C_1_update_sample.json similarity index 72% rename from fixtures/tests/14269_C_1_update_sample.json rename to fixtures/tests/99908_C_1_update_sample.json index b93ce1a73..3dc0274bc 100644 --- a/fixtures/tests/14269_C_1_update_sample.json +++ b/fixtures/tests/99908_C_1_update_sample.json @@ -19,22 +19,22 @@ "smileSampleList": null, "patientAliases": [ { - "value": "C-D45N9T", + "value": "C-PPPPP6", "namespace": "cmoId" } ], "cmoPatientId": { - "value": "C-D45N9T", + "value": "C-PPPPP6", "namespace": "cmoId" } }, "latestSampleMetadata": { - "primaryId": "14269_C_1", - "cmoPatientId": "C-D45N9T", + "primaryId": "99908_C_1", + "cmoPatientId": "C-PPPPP6", "investigatorSampleId": "CU0c", - "cmoSampleName": "C-D45N9T-X001-d01", + "cmoSampleName": "C-PPPPP6-X001-d01", "sampleName": "CU0c", - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "importDate": "2023-04-26", "collectionYear": "", "tubeId": "", @@ -61,26 +61,26 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "14269_C_1_1_1_1", + "libraryIgoId": "99908_C_1_1_1_1", "libraryVolume": 25.0, "libraryConcentrationNgul": 38.3, "dnaInputNg": null, "captureConcentrationNm": "5.221932115", "captureInputNg": "200.0000000045", - "captureName": "Pool-14269_C-E3_1", + "captureName": "Pool-99908_C-E3_1", "runs": [ { "runMode": "NovaSeq S2", - "runId": "RUTH_0214", - "flowCellId": "HJ5VNDMXY", + "runId": "SEQRUN_0009", + "flowCellId": "FCELLAAAA7", "readLength": "101/8/8/101", "runDate": "2023-04-13", "flowCellLanes": [ 2 ], "fastqs": [ - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R1_001.fastq.gz", - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R2_001.fastq.gz" + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R1_001.fastq.gz", + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R2_001.fastq.gz" ] } ] @@ -93,7 +93,7 @@ "recipe": "IMPACT505" }, "additionalProperties": { - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "isCmoSample": "true" }, "status": { @@ -103,12 +103,12 @@ }, "sampleMetadataList": [ { - "primaryId": "14269_C_1", - "cmoPatientId": "C-D45N9T", + "primaryId": "99908_C_1", + "cmoPatientId": "C-PPPPP6", "investigatorSampleId": "CU0c", - "cmoSampleName": "C-D45N9T-X001-d01", + "cmoSampleName": "C-PPPPP6-X001-d01", "sampleName": "CU0c", - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "importDate": "2023-04-19", "collectionYear": "", "tubeId": "", @@ -135,26 +135,26 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "14269_C_1_1_1_1", + "libraryIgoId": "99908_C_1_1_1_1", "libraryVolume": 25.0, "libraryConcentrationNgul": 38.3, "dnaInputNg": null, "captureConcentrationNm": "5.221932115", "captureInputNg": "200.0000000045", - "captureName": "Pool-14269_C-E3_1", + "captureName": "Pool-99908_C-E3_1", "runs": [ { "runMode": "NovaSeq S2", - "runId": "RUTH_0214", - "flowCellId": "HJ5VNDMXY", + "runId": "SEQRUN_0009", + "flowCellId": "FCELLAAAA7", "readLength": "101/8/8/101", "runDate": "2023-04-13", "flowCellLanes": [ 2 ], "fastqs": [ - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R1_001.fastq.gz", - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R2_001.fastq.gz" + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R1_001.fastq.gz", + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R2_001.fastq.gz" ] } ] @@ -167,7 +167,7 @@ "recipe": "IMPACT505" }, "additionalProperties": { - "igoRequestId": "14269_C" + "igoRequestId": "99908_C" }, "status": { "validationStatus": true, @@ -175,12 +175,12 @@ } }, { - "primaryId": "14269_C_1", - "cmoPatientId": "C-D45N9T", + "primaryId": "99908_C_1", + "cmoPatientId": "C-PPPPP6", "investigatorSampleId": "CU0c", - "cmoSampleName": "C-D45N9T-X001-d01", + "cmoSampleName": "C-PPPPP6-X001-d01", "sampleName": "CU0c", - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "importDate": "2023-04-26", "collectionYear": "", "tubeId": "", @@ -207,26 +207,26 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "14269_C_1_1_1_1", + "libraryIgoId": "99908_C_1_1_1_1", "libraryVolume": 25.0, "libraryConcentrationNgul": 38.3, "dnaInputNg": null, "captureConcentrationNm": "5.221932115", "captureInputNg": "200.0000000045", - "captureName": "Pool-14269_C-E3_1", + "captureName": "Pool-99908_C-E3_1", "runs": [ { "runMode": "NovaSeq S2", - "runId": "RUTH_0214", - "flowCellId": "HJ5VNDMXY", + "runId": "SEQRUN_0009", + "flowCellId": "FCELLAAAA7", "readLength": "101/8/8/101", "runDate": "2023-04-13", "flowCellLanes": [ 2 ], "fastqs": [ - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R1_001.fastq.gz", - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R2_001.fastq.gz" + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R1_001.fastq.gz", + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R2_001.fastq.gz" ] } ] @@ -239,7 +239,7 @@ "recipe": "IMPACT505" }, "additionalProperties": { - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "isCmoSample": "true" }, "status": { diff --git a/fixtures/tests/14269_C_1_update_sample_new_files.json b/fixtures/tests/99908_C_1_update_sample_new_files.json similarity index 72% rename from fixtures/tests/14269_C_1_update_sample_new_files.json rename to fixtures/tests/99908_C_1_update_sample_new_files.json index daec0447b..fe71619ef 100644 --- a/fixtures/tests/14269_C_1_update_sample_new_files.json +++ b/fixtures/tests/99908_C_1_update_sample_new_files.json @@ -18,22 +18,22 @@ "smileSampleList": null, "patientAliases": [ { - "value": "C-D45N9T", + "value": "C-PPPPP6", "namespace": "cmoId" } ], "cmoPatientId": { - "value": "C-D45N9T", + "value": "C-PPPPP6", "namespace": "cmoId" } }, "latestSampleMetadata": { - "primaryId": "14269_C_1", - "cmoPatientId": "C-D45N9T", + "primaryId": "99908_C_1", + "cmoPatientId": "C-PPPPP6", "investigatorSampleId": "CU0c", - "cmoSampleName": "C-D45N9T-X001-d01", + "cmoSampleName": "C-PPPPP6-X001-d01", "sampleName": "CU0c", - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "importDate": "2023-04-26", "collectionYear": "", "tubeId": "", @@ -60,26 +60,26 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "14269_C_1_1_1_1", + "libraryIgoId": "99908_C_1_1_1_1", "libraryVolume": 25.0, "libraryConcentrationNgul": 38.3, "dnaInputNg": null, "captureConcentrationNm": "5.221932115", "captureInputNg": "200.0000000045", - "captureName": "Pool-14269_C-E3_1", + "captureName": "Pool-99908_C-E3_1", "runs": [ { "runMode": "NovaSeq S2", - "runId": "RUTH_0214", - "flowCellId": "HJ5VNDMXY", + "runId": "SEQRUN_0009", + "flowCellId": "FCELLAAAA7", "readLength": "101/8/8/101", "runDate": "2023-04-13", "flowCellLanes": [ 2 ], "fastqs": [ - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R1_001_new.fastq.gz", - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R2_001_new.fastq.gz" + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R1_001_new.fastq.gz", + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R2_001_new.fastq.gz" ] } ] @@ -92,7 +92,7 @@ "recipe": "IMPACT505" }, "additionalProperties": { - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "isCmoSample": "true" }, "status": { @@ -102,12 +102,12 @@ }, "sampleMetadataList": [ { - "primaryId": "14269_C_1", - "cmoPatientId": "C-D45N9T", + "primaryId": "99908_C_1", + "cmoPatientId": "C-PPPPP6", "investigatorSampleId": "CU0c", - "cmoSampleName": "C-D45N9T-X001-d01", + "cmoSampleName": "C-PPPPP6-X001-d01", "sampleName": "CU0c", - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "importDate": "2023-04-19", "collectionYear": "", "tubeId": "", @@ -134,26 +134,26 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "14269_C_1_1_1_1", + "libraryIgoId": "99908_C_1_1_1_1", "libraryVolume": 25.0, "libraryConcentrationNgul": 38.3, "dnaInputNg": null, "captureConcentrationNm": "5.221932115", "captureInputNg": "200.0000000045", - "captureName": "Pool-14269_C-E3_1", + "captureName": "Pool-99908_C-E3_1", "runs": [ { "runMode": "NovaSeq S2", - "runId": "RUTH_0214", - "flowCellId": "HJ5VNDMXY", + "runId": "SEQRUN_0009", + "flowCellId": "FCELLAAAA7", "readLength": "101/8/8/101", "runDate": "2023-04-13", "flowCellLanes": [ 2 ], "fastqs": [ - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R1_001.fastq.gz", - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R2_001.fastq.gz" + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R1_001.fastq.gz", + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R2_001.fastq.gz" ] } ] @@ -166,7 +166,7 @@ "recipe": "IMPACT505" }, "additionalProperties": { - "igoRequestId": "14269_C" + "igoRequestId": "99908_C" }, "status": { "validationStatus": true, @@ -174,12 +174,12 @@ } }, { - "primaryId": "14269_C_1", - "cmoPatientId": "C-D45N9T", + "primaryId": "99908_C_1", + "cmoPatientId": "C-PPPPP6", "investigatorSampleId": "CU0c", - "cmoSampleName": "C-D45N9T-X001-d01", + "cmoSampleName": "C-PPPPP6-X001-d01", "sampleName": "CU0c", - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "importDate": "2023-04-26", "collectionYear": "", "tubeId": "", @@ -206,26 +206,26 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "14269_C_1_1_1_1", + "libraryIgoId": "99908_C_1_1_1_1", "libraryVolume": 25.0, "libraryConcentrationNgul": 38.3, "dnaInputNg": null, "captureConcentrationNm": "5.221932115", "captureInputNg": "200.0000000045", - "captureName": "Pool-14269_C-E3_1", + "captureName": "Pool-99908_C-E3_1", "runs": [ { "runMode": "NovaSeq S2", - "runId": "RUTH_0214", - "flowCellId": "HJ5VNDMXY", + "runId": "SEQRUN_0009", + "flowCellId": "FCELLAAAA7", "readLength": "101/8/8/101", "runDate": "2023-04-13", "flowCellLanes": [ 2 ], "fastqs": [ - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R1_001_new.fastq.gz", - "/igo/delivery/FASTQ/RUTH_0214_BHJ5VNDMXY/Project_14269_C/Sample_CU0c_IGO_14269_C_1/CU0c_IGO_14269_C_1_S54_L002_R2_001_new.fastq.gz" + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R1_001_new.fastq.gz", + "/igo/delivery/FASTQ/SEQRUN_0009_BFCELLAAAA7/Project_99908_C/Sample_CU0c_IGO_99908_C_1/CU0c_IGO_99908_C_1_S54_L002_R2_001_new.fastq.gz" ] } ] @@ -238,7 +238,7 @@ "recipe": "IMPACT505" }, "additionalProperties": { - "igoRequestId": "14269_C", + "igoRequestId": "99908_C", "isCmoSample": "true" }, "status": { diff --git a/fixtures/tests/99908_C_new_request.json b/fixtures/tests/99908_C_new_request.json new file mode 100644 index 000000000..7a63baeaf --- /dev/null +++ b/fixtures/tests/99908_C_new_request.json @@ -0,0 +1,499 @@ +{ + "smileRequestId": "ab8b2cfb-c511-4cfe-9ed9-4d11d2e9650e", + "igoProjectId": "14269", + "igoRequestId": "99908_C", + "genePanel": "IMPACT505", + "projectManagerName": "", + "piEmail": "", + "labHeadName": "Lab Head E", + "labHeadEmail": "analyst8@example.org", + "investigatorName": "Investigator C", + "investigatorEmail": "analyst5@example.org", + "dataAnalystName": "", + "dataAnalystEmail": "", + "otherContactEmails": "analyst8@example.org,analyst5@example.org,analyst8@example.org,analyst5@example.org", + "dataAccessEmails": "analyst8@example.org,analyst5@example.org", + "qcAccessEmails": "analyst8@example.org,analyst5@example.org", + "strand": null, + "libraryType": null, + "isCmoRequest": true, + "bicAnalysis": true, + "status": { + "validationStatus": true, + "validationReport": "[]" + }, + "requestJson": "{\"requestId\":\"99908_C\",\"projectId\":\"14269\",\"dataAccessEmails\":\"analyst8@example.org,analyst5@example.org\",\"dataAnalystEmail\":\"\",\"dataAnalystName\":\"\",\"investigatorEmail\":\"analyst5@example.org\",\"investigatorName\":\"Investigator C\",\"labHeadEmail\":\"analyst8@example.org\",\"labHeadName\":\"Lab Head 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"samples": [ + { + "smileSampleId": "3ec2212c-30de-49e1-a447-e73bc8f7312d", + "smilePatientId": "4dec0295-6e81-47d6-8067-49de2f89f17c", + "primaryId": "99908_C_4", + "cmoPatientId": "C-PPPP16", + "cmoSampleName": "C-PPPP16-X003-d03", + "sampleName": "CV1b", + "cmoInfoIgoId": null, + "investigatorSampleId": "CV1b", + "importDate": "2023-04-19", + "sampleType": "other", + "oncotreeCode": null, + "collectionYear": "", + "tubeId": "", + "cfDNA2dBarcode": null, + "species": "Human", + "sex": "F", + "tumorOrNormal": "Normal", + "preservation": "Frozen", + "sampleClass": "PDX", + "sampleOrigin": "Tissue", + "tissueLocation": "", + "genePanel": "IMPACT505", + "baitSet": "IMPACT505_BAITS", + "datasource": "igo", + "igoComplete": true, + "status": { + "validationStatus": true, + "validationReport": "{}" + }, + "cmoSampleIdFields": { + "naToExtract": "", + "normalizedPatientId": "MRN_REDACTED", + "sampleType": "DNA", + "recipe": "IMPACT505" + }, + "qcReports": [ + { + "qcReportType": "LIBRARY", + 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"size": 2090666688, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": null, - "request_id": "16342_B", + "request_id": "99909_B", "samples": "[]", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "available": true } }, @@ -41,15 +41,15 @@ "fields": { "created_date": "2024-10-24T20:26:50.589Z", "modified_date": "2024-10-24T20:26:50.589Z", - "file_name": "MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz", + "file_name": "TEST-OBX-023_IGO_99909_B_1_S35_L001_R1_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L001_R1_001.fastq.gz", "file_type": 26, "size": 2101145526, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": null, - "request_id": "16342_B", + "request_id": "99909_B", "samples": "[]", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "available": true } }, @@ -59,15 +59,15 @@ "fields": { "created_date": "2024-10-24T20:26:50.533Z", "modified_date": "2024-10-24T20:26:50.533Z", - "file_name": "MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz", + "file_name": "TEST-OBX-023_IGO_99909_B_1_S35_L002_R2_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L002_R2_001.fastq.gz", "file_type": 26, "size": 2156189725, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": null, - "request_id": "16342_B", + "request_id": "99909_B", "samples": "[]", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "available": true } }, @@ -83,8 +83,8 @@ "metadata": { "R": "R2", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - 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"isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, @@ -205,8 +205,8 @@ "metadata": { "R": "R1", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - "runId": "DIANA_0737", + "ciTag": "s_C_PPPP18_P001_d01", + "runId": "SEQRUN_0002", "status": { "validationReport": "{}", "validationStatus": true @@ -220,7 +220,7 @@ "platform": "Illumina", "barcodeId": null, "genePanel": "HC_IMPACT", - "primaryId": "16342_B_1", + "primaryId": "99909_B_1", "qcReports": [ { "comments": "", @@ -237,26 +237,26 @@ ], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "HLYCVDSXC", + "flowCellId": "FCELLAAAA9", "importDate": "2024-10-22", "readLength": "101/8/8/101", - "sampleName": "MSK-OBX-023", + "sampleName": "TEST-OBX-023", "sampleType": "Primary", - "captureName": "Pool-09621_AX-09621_AY-16342_B-16442-A1_1", + "captureName": "Pool-99999_AX-99999_AY-99909_B-99919-A1_1", "igoComplete": true, "labHeadName": "", "sampleClass": "Non-PDX", "barcodeIndex": null, - "cmoInfoIgoId": "16342_B_1", - "cmoPatientId": "C-V5AJEY", + "cmoInfoIgoId": "99909_B_1", + "cmoPatientId": "C-PPPP18", "igoProjectId": "16342", - "igoRequestId": "16342_B", + "igoRequestId": "99909_B", "labHeadEmail": "", - "libraryIgoId": "16342_B_1", + "libraryIgoId": "99909_B_1", "oncotreeCode": "LUAD", "preservation": "FFPE", "sampleOrigin": "", - "cmoSampleName": "C-V5AJEY-P001-d01", + "cmoSampleName": "C-PPPP18-P001-d01", "flowCellLanes": [ 1, 2 @@ -264,11 +264,11 @@ "libraryVolume": null, "sampleAliases": [ { - "value": "MSK-OBX-023", + "value": "TEST-OBX-023", "namespace": "investigatorId" }, { - "value": "16342_B_1", + "value": "99909_B_1", "namespace": "igoId" } ], @@ -279,7 +279,7 @@ "collectionYear": "2024", "patientAliases": [ { - "value": "C-V5AJEY", + "value": "C-PPPP18", "namespace": "cmoId" }, { @@ -306,9 +306,9 @@ "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, @@ -327,8 +327,8 @@ "metadata": { "R": "R1", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - "runId": "DIANA_0737", + "ciTag": "s_C_PPPP18_P001_d01", + "runId": "SEQRUN_0002", "status": { "validationReport": "{}", "validationStatus": true @@ -342,7 +342,7 @@ "platform": "Illumina", "barcodeId": null, "genePanel": "HC_IMPACT", - "primaryId": "16342_B_1", + "primaryId": "99909_B_1", "qcReports": [ { "comments": "", @@ -359,26 +359,26 @@ ], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "HLYCVDSXC", + "flowCellId": "FCELLAAAA9", "importDate": "2024-10-22", "readLength": "101/8/8/101", - "sampleName": "MSK-OBX-023", + "sampleName": "TEST-OBX-023", "sampleType": "Primary", - "captureName": "Pool-09621_AX-09621_AY-16342_B-16442-A1_1", + "captureName": "Pool-99999_AX-99999_AY-99909_B-99919-A1_1", "igoComplete": true, "labHeadName": "", "sampleClass": "Non-PDX", "barcodeIndex": null, - "cmoInfoIgoId": "16342_B_1", - "cmoPatientId": "C-V5AJEY", + "cmoInfoIgoId": "99909_B_1", + "cmoPatientId": "C-PPPP18", "igoProjectId": "16342", - "igoRequestId": "16342_B", + "igoRequestId": "99909_B", "labHeadEmail": "", - "libraryIgoId": "16342_B_1", + "libraryIgoId": "99909_B_1", "oncotreeCode": "LUAD", "preservation": "FFPE", "sampleOrigin": "", - "cmoSampleName": "C-V5AJEY-P001-d01", + "cmoSampleName": "C-PPPP18-P001-d01", "flowCellLanes": [ 1, 2 @@ -386,11 +386,11 @@ "libraryVolume": null, "sampleAliases": [ { - "value": "MSK-OBX-023", + "value": "TEST-OBX-023", "namespace": "investigatorId" }, { - "value": "16342_B_1", + "value": "99909_B_1", "namespace": "igoId" } ], @@ -401,7 +401,7 @@ "collectionYear": "2024", "patientAliases": [ { - "value": "C-V5AJEY", + "value": "C-PPPP18", "namespace": "cmoId" }, { @@ -428,9 +428,9 @@ "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, @@ -449,8 +449,8 @@ "metadata": { "R": "R2", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - "runId": "DIANA_0737", + "ciTag": "s_C_PPPP18_P001_d01", + "runId": "SEQRUN_0002", "status": { "validationReport": "{}", "validationStatus": true @@ -464,7 +464,7 @@ "platform": "Illumina", "barcodeId": null, "genePanel": "HC_IMPACT", - "primaryId": "16342_B_1", + "primaryId": "99909_B_1", "qcReports": [ { "comments": "", @@ -481,26 +481,26 @@ ], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "HLYCVDSXC", + "flowCellId": "FCELLAAAA9", "importDate": "2024-10-22", "readLength": "101/8/8/101", - "sampleName": "MSK-OBX-023", + "sampleName": "TEST-OBX-023", "sampleType": "Primary", - "captureName": "Pool-09621_AX-09621_AY-16342_B-16442-A1_1", + "captureName": "Pool-99999_AX-99999_AY-99909_B-99919-A1_1", "igoComplete": true, "labHeadName": "", "sampleClass": "Non-PDX", "barcodeIndex": null, - "cmoInfoIgoId": "16342_B_1", - "cmoPatientId": "C-V5AJEY", + "cmoInfoIgoId": "99909_B_1", + "cmoPatientId": "C-PPPP18", "igoProjectId": "16342", - "igoRequestId": "16342_B", + "igoRequestId": "99909_B", "labHeadEmail": "", - "libraryIgoId": "16342_B_1", + "libraryIgoId": "99909_B_1", "oncotreeCode": "LUAD", "preservation": "FFPE", "sampleOrigin": "", - "cmoSampleName": "C-V5AJEY-P001-d01", + "cmoSampleName": "C-PPPP18-P001-d01", "flowCellLanes": [ 1, 2 @@ -508,11 +508,11 @@ "libraryVolume": null, "sampleAliases": [ { - "value": "MSK-OBX-023", + "value": "TEST-OBX-023", "namespace": "investigatorId" }, { - "value": "16342_B_1", + "value": "99909_B_1", "namespace": "igoId" } ], @@ -540,9 +540,9 @@ "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, diff --git a/fixtures/tests/16342_B.fixtures_pdx.json b/fixtures/tests/99909_B.fixtures_pdx.json similarity index 78% rename from fixtures/tests/16342_B.fixtures_pdx.json rename to fixtures/tests/99909_B.fixtures_pdx.json index cc4ee9eb7..10d1740b2 100644 --- a/fixtures/tests/16342_B.fixtures_pdx.json +++ b/fixtures/tests/99909_B.fixtures_pdx.json @@ -5,16 +5,16 @@ "fields": { "created_date": "2024-10-24T20:26:50.645Z", "modified_date": "2024-10-24T20:26:50.645Z", - "file_name": "MSK-OBX-023_IGO_16342_B_1_S35_L001_R2_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R2_001.fastq.gz", + "file_name": "TEST-OBX-023_IGO_99909_B_1_S35_L001_R2_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L001_R2_001.fastq.gz", "file_type": 26, "size": 2167712182, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": null, - "request_id": "16342_B", + "request_id": "99909_B", "samples": "[]", "samples": "[]", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "available": true } }, @@ -24,15 +24,15 @@ "fields": { "created_date": "2024-10-24T20:26:50.440Z", "modified_date": "2024-10-24T20:26:50.440Z", - "file_name": "MSK-OBX-023_IGO_16342_B_1_S35_L002_R1_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R1_001.fastq.gz", + "file_name": "TEST-OBX-023_IGO_99909_B_1_S35_L002_R1_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L002_R1_001.fastq.gz", "file_type": 26, "size": 2090666688, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": null, - "request_id": "16342_B", + "request_id": "99909_B", "samples": "[]", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "available": true } }, @@ -42,15 +42,15 @@ "fields": { "created_date": "2024-10-24T20:26:50.589Z", "modified_date": "2024-10-24T20:26:50.589Z", - "file_name": "MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz", + "file_name": "TEST-OBX-023_IGO_99909_B_1_S35_L001_R1_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L001_R1_001.fastq.gz", "file_type": 26, "size": 2101145526, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": null, - "request_id": "16342_B", + "request_id": "99909_B", "samples": "[]", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "available": true } }, @@ -60,15 +60,15 @@ "fields": { "created_date": "2024-10-24T20:26:50.533Z", "modified_date": "2024-10-24T20:26:50.533Z", - "file_name": "MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz", - "path": "/igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz", + "file_name": "TEST-OBX-023_IGO_99909_B_1_S35_L002_R2_001.fastq.gz", + "path": "/igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L002_R2_001.fastq.gz", "file_type": 26, "size": 2156189725, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": null, - "request_id": "16342_B", + "request_id": "99909_B", "samples": "[]", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "available": true } }, @@ -84,8 +84,8 @@ "metadata": { "R": "R2", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - "runId": "DIANA_0737", + "ciTag": "s_C_PPPP18_P001_d01", + "runId": "SEQRUN_0002", "status": { "validationReport": "{}", "validationStatus": true @@ -99,7 +99,7 @@ "platform": "Illumina", "barcodeId": null, "genePanel": "HC_IMPACT", - "primaryId": "16342_B_1", + "primaryId": "99909_B_1", "qcReports": [ { "comments": "", @@ -116,26 +116,26 @@ ], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "HLYCVDSXC", + "flowCellId": "FCELLAAAA9", "importDate": "2024-10-22", "readLength": "101/8/8/101", - "sampleName": "MSK-OBX-023", + "sampleName": "TEST-OBX-023", "sampleType": "Primary", - "captureName": "Pool-09621_AX-09621_AY-16342_B-16442-A1_1", + "captureName": "Pool-99999_AX-99999_AY-99909_B-99919-A1_1", "igoComplete": true, - "labHeadName": "Adam Schoenfeld", + "labHeadName": "Lab Head D", "sampleClass": "PDX", "barcodeIndex": null, - "cmoInfoIgoId": "16342_B_1", - "cmoPatientId": "C-V5AJEY", + "cmoInfoIgoId": "99909_B_1", + "cmoPatientId": "C-PPPP18", "igoProjectId": "16342", - "igoRequestId": "16342_B", + "igoRequestId": "99909_B", "labHeadEmail": "", - "libraryIgoId": "16342_B_1", + "libraryIgoId": "99909_B_1", "oncotreeCode": "LUAD", "preservation": "FFPE", "sampleOrigin": "", - "cmoSampleName": "C-V5AJEY-P001-d01", + "cmoSampleName": "C-PPPP18-P001-d01", "flowCellLanes": [ 1, 2 @@ -143,11 +143,11 @@ "libraryVolume": null, "sampleAliases": [ { - "value": "MSK-OBX-023", + "value": "TEST-OBX-023", "namespace": "investigatorId" }, { - "value": "16342_B_1", + "value": "99909_B_1", "namespace": "igoId" } ], @@ -158,7 +158,7 @@ "collectionYear": "2024", "patientAliases": [ { - "value": "C-V5AJEY", + "value": "C-PPPP18", "namespace": "cmoId" }, { @@ -172,7 +172,7 @@ "dataAnalystName": "", "dataAccessEmails": "", "dataAnalystEmail": "", - "investigatorName": "Phoebe Clark", + "investigatorName": "Investigator D", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "HC_IMPACT", @@ -185,9 +185,9 @@ "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, @@ -206,8 +206,8 @@ "metadata": { "R": "R1", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - "runId": "DIANA_0737", + "ciTag": "s_C_PPPP18_P001_d01", + "runId": "SEQRUN_0002", "status": { "validationReport": "{}", "validationStatus": true @@ -221,7 +221,7 @@ "platform": "Illumina", "barcodeId": null, "genePanel": "HC_IMPACT", - "primaryId": "16342_B_1", + "primaryId": "99909_B_1", "qcReports": [ { "comments": "", @@ -238,26 +238,26 @@ ], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "HLYCVDSXC", + "flowCellId": "FCELLAAAA9", "importDate": "2024-10-22", "readLength": "101/8/8/101", - "sampleName": "MSK-OBX-023", + "sampleName": "TEST-OBX-023", "sampleType": "Primary", - "captureName": "Pool-09621_AX-09621_AY-16342_B-16442-A1_1", + "captureName": "Pool-99999_AX-99999_AY-99909_B-99919-A1_1", "igoComplete": true, "labHeadName": "", "sampleClass": "PDX", "barcodeIndex": null, - "cmoInfoIgoId": "16342_B_1", - "cmoPatientId": "C-V5AJEY", + "cmoInfoIgoId": "99909_B_1", + "cmoPatientId": "C-PPPP18", "igoProjectId": "16342", - "igoRequestId": "16342_B", + "igoRequestId": "99909_B", "labHeadEmail": "", - "libraryIgoId": "16342_B_1", + "libraryIgoId": "99909_B_1", "oncotreeCode": "LUAD", "preservation": "FFPE", "sampleOrigin": "", - "cmoSampleName": "C-V5AJEY-P001-d01", + "cmoSampleName": "C-PPPP18-P001-d01", "flowCellLanes": [ 1, 2 @@ -265,11 +265,11 @@ "libraryVolume": null, "sampleAliases": [ { - "value": "MSK-OBX-023", + "value": "TEST-OBX-023", "namespace": "investigatorId" }, { - "value": "16342_B_1", + "value": "99909_B_1", "namespace": "igoId" } ], @@ -280,7 +280,7 @@ "collectionYear": "2024", "patientAliases": [ { - "value": "C-V5AJEY", + "value": "C-PPPP18", "namespace": "cmoId" }, { @@ -307,9 +307,9 @@ "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, @@ -328,8 +328,8 @@ "metadata": { "R": "R1", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - "runId": "DIANA_0737", + "ciTag": "s_C_PPPP18_P001_d01", + "runId": "SEQRUN_0002", "status": { "validationReport": "{}", "validationStatus": true @@ -343,7 +343,7 @@ "platform": "Illumina", "barcodeId": null, "genePanel": "HC_IMPACT", - "primaryId": "16342_B_1", + "primaryId": "99909_B_1", "qcReports": [ { "comments": "", @@ -360,26 +360,26 @@ ], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "HLYCVDSXC", + "flowCellId": "FCELLAAAA9", "importDate": "2024-10-22", "readLength": "101/8/8/101", - "sampleName": "MSK-OBX-023", + "sampleName": "TEST-OBX-023", "sampleType": "Primary", - "captureName": "Pool-09621_AX-09621_AY-16342_B-16442-A1_1", + "captureName": "Pool-99999_AX-99999_AY-99909_B-99919-A1_1", "igoComplete": true, "labHeadName": "", "sampleClass": "PDX", "barcodeIndex": null, - "cmoInfoIgoId": "16342_B_1", - "cmoPatientId": "C-V5AJEY", + "cmoInfoIgoId": "99909_B_1", + "cmoPatientId": "C-PPPP18", "igoProjectId": "16342", - "igoRequestId": "16342_B", + "igoRequestId": "99909_B", "labHeadEmail": "", - "libraryIgoId": "16342_B_1", + "libraryIgoId": "99909_B_1", "oncotreeCode": "LUAD", "preservation": "FFPE", "sampleOrigin": "", - "cmoSampleName": "C-V5AJEY-P001-d01", + "cmoSampleName": "C-PPPP18-P001-d01", "flowCellLanes": [ 1, 2 @@ -387,11 +387,11 @@ "libraryVolume": null, "sampleAliases": [ { - "value": "MSK-OBX-023", + "value": "TEST-OBX-023", "namespace": "investigatorId" }, { - "value": "16342_B_1", + "value": "99909_B_1", "namespace": "igoId" } ], @@ -402,7 +402,7 @@ "collectionYear": "2024", "patientAliases": [ { - "value": "C-V5AJEY", + "value": "C-PPPP18", "namespace": "cmoId" }, { @@ -429,9 +429,9 @@ "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, @@ -450,8 +450,8 @@ "metadata": { "R": "R2", "sex": "F", - "ciTag": "s_C_V5AJEY_P001_d01", - "runId": "DIANA_0737", + "ciTag": "s_C_PPPP18_P001_d01", + "runId": "SEQRUN_0002", "status": { "validationReport": "{}", "validationStatus": true @@ -465,7 +465,7 @@ "platform": "Illumina", "barcodeId": null, "genePanel": "HC_IMPACT", - "primaryId": "16342_B_1", + "primaryId": "99909_B_1", "qcReports": [ { "comments": "", @@ -482,26 +482,26 @@ ], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "HLYCVDSXC", + "flowCellId": "FCELLAAAA9", "importDate": "2024-10-22", "readLength": "101/8/8/101", - "sampleName": "MSK-OBX-023", + "sampleName": "TEST-OBX-023", "sampleType": "Primary", - "captureName": "Pool-09621_AX-09621_AY-16342_B-16442-A1_1", + "captureName": "Pool-99999_AX-99999_AY-99909_B-99919-A1_1", "igoComplete": true, "labHeadName": "", "sampleClass": "PDX", "barcodeIndex": null, - "cmoInfoIgoId": "16342_B_1", - "cmoPatientId": "C-V5AJEY", + "cmoInfoIgoId": "99909_B_1", + "cmoPatientId": "C-PPPP18", "igoProjectId": "16342", - "igoRequestId": "16342_B", + "igoRequestId": "99909_B", "labHeadEmail": "", - "libraryIgoId": "16342_B_1", + "libraryIgoId": "99909_B_1", "oncotreeCode": "LUAD", "preservation": "FFPE", "sampleOrigin": "", - "cmoSampleName": "C-V5AJEY-P001-d01", + "cmoSampleName": "C-PPPP18-P001-d01", "flowCellLanes": [ 1, 2 @@ -509,11 +509,11 @@ "libraryVolume": null, "sampleAliases": [ { - "value": "MSK-OBX-023", + "value": "TEST-OBX-023", "namespace": "investigatorId" }, { - "value": "16342_B_1", + "value": "99909_B_1", "namespace": "igoId" } ], @@ -541,9 +541,9 @@ "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "16342_B" + "igoRequestId": "99909_B" }, - "investigatorSampleId": "MSK-OBX-023", + "investigatorSampleId": "TEST-OBX-023", "captureConcentrationNm": "22.53521127", "libraryConcentrationNgul": null }, diff --git a/fixtures/tests/10075_D.file.json b/fixtures/tests/99990_D.file.json similarity index 60% rename from fixtures/tests/10075_D.file.json rename to fixtures/tests/99990_D.file.json index a016f2dcf..6a53111a2 100644 --- a/fixtures/tests/10075_D.file.json +++ b/fixtures/tests/99990_D.file.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.581Z", "modified_date": "2020-01-06T19:59:50.584Z", - "file_name": "31-N_IGO_10075_D_2_S14_R1_001.fastq.gz", - "path": 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"/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R2_001.fastq.gz" + ], + "tumorOrNormal": "Tumor", + "captureInputNg": "150.0", + "cmoSampleClass": "Metastasis", + "collectionYear": "2016", + "tissueLocation": "Abdominal mass", + "dataAnalystName": "", + "dataAnalystEmail": "", + "externalSampleId": "SAMPLE-T-003", + "investigatorName": "Test Scientist", + "investigatorEmail": "email2@internet.com", + "projectManagerName": "", + "investigatorSampleId": "SAMPLE-T-003", + "captureConcentrationNm": "10.344827586206897", + "libraryConcentrationNgul": 14.5, + "qcAccessEmails": "" + }, + "user": null + } + } +] diff --git a/fixtures/tests/10075_D_2.file.json b/fixtures/tests/99990_D_2.file.json similarity index 58% rename from fixtures/tests/10075_D_2.file.json rename to fixtures/tests/99990_D_2.file.json index 653a5adfe..31fd84cef 100644 --- a/fixtures/tests/10075_D_2.file.json +++ b/fixtures/tests/99990_D_2.file.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.582Z", "modified_date": "2020-01-06T19:59:50.585Z", - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.597Z", "modified_date": "2020-01-06T19:59:50.598Z", - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/fixtures/tests/10075_D_2.filemetadata.json b/fixtures/tests/99990_D_2.filemetadata.json similarity index 77% rename from fixtures/tests/10075_D_2.filemetadata.json rename to fixtures/tests/99990_D_2.filemetadata.json index 274f5ed82..478e1e774 100644 --- a/fixtures/tests/10075_D_2.filemetadata.json +++ b/fixtures/tests/99990_D_2.filemetadata.json @@ -11,27 +11,27 @@ "metadata": { "R": "R1", "sex": "F", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-12", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10075_D_2_3", + "primaryId": "99990_D_2_3", "barcodeId": null, "igoProjectId": "10075", - "libraryIgoId": "10075_D_2_3", - "cmoPatientId": "C-8VK0V7", - "igoRequestId": "10075_D_2", + "libraryIgoId": "99990_D_2_3", + "cmoPatientId": "C-PPPPP3", + "igoRequestId": "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HCYYWBBXY", + "flowCellId": "FCELLAAAA4", "readLength": "101/8/8/101", - "cmoSampleName": "C-8VK0V7-N001-d", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "cmoSampleName": "C-PPPPP3-N001-d", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": null, "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -47,14 +47,14 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "JW_MEL_007_NORM", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "otherContactEmails": "", "projectManagerName": "", "qcAccessEmails": "", "dataAccessEmails": "", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorSampleId": "SAMPLE_N_001", "captureConcentrationNm": "10.377358490566039", "libraryConcentrationNgul": 10.6, "importDate": "2022-03-23", @@ -76,27 +76,27 @@ "metadata": { "R": "R2", "sex": "F", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-12", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10075_D_2_3", + "primaryId": "99990_D_2_3", "barcodeId": null, "igoProjectId": "10075", - "libraryIgoId": "10075_D_2_3", - "cmoPatientId": "C-8VK0V7", - "igoRequestId": "10075_D_2", + "libraryIgoId": "99990_D_2_3", + "cmoPatientId": "C-PPPPP3", + "igoRequestId": "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HCYYWBBXY", + "flowCellId": "FCELLAAAA4", "readLength": "101/8/8/101", - "cmoSampleName": "C-8VK0V7-N001-d", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "cmoSampleName": "C-PPPPP3-N001-d", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": null, "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -112,14 +112,14 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "JW_MEL_007_NORM", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "otherContactEmails": "", "projectManagerName": "", "qcAccessEmails": "", "dataAccessEmails": "", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorSampleId": "SAMPLE_N_001", "captureConcentrationNm": "10.377358490566039", "libraryConcentrationNgul": 10.6, "importDate": "2022-03-23", diff --git a/fixtures/tests/10075_D_2.update_sample.json b/fixtures/tests/99990_D_2.update_sample.json similarity index 72% rename from fixtures/tests/10075_D_2.update_sample.json rename to fixtures/tests/99990_D_2.update_sample.json index f2a70ce7b..55313e1e3 100644 --- a/fixtures/tests/10075_D_2.update_sample.json +++ b/fixtures/tests/99990_D_2.update_sample.json @@ -19,19 +19,19 @@ "smileSampleList": null, "patientAliases": [ { - "value": "C-MP789JR", + "value": "C-PPPP12", "namespace": "cmoId" } ], "cmoPatientId": { - "value": "C-MP789JR", + "value": "C-PPPP12", "namespace": "cmoId" } }, "latestSampleMetadata": { "additionalProperties": { - "igoRequestId": "10075_D_2", + "igoRequestId": "99990_D_2", "isCmoSample": "true" }, "cfDNA2dBarcode": null, @@ -39,17 +39,17 @@ "baitSet": "GENESET101_BAITS", "cmoSampleIdFields": { "naToExtract": "", - "normalizedPatientId": "ALLAJV_HCISCLC002", + "normalizedPatientId": "TESTID_SAMPLEXXX002", "recipe": "IMPACT468", "sampleType": "DNA" }, "importDate": "2022-03-23", "smileSampleId": "afe750e6-8756-11eb-81b0-acde48001122", "smilePatientId": "6cc9f242-875a-11eb-ae91-acde48001122", - "primaryId": "10075_D_2_3", - "cmoPatientId": "C-MP789JR", - "cmoSampleName": "C-MP789J-X001-d", - "ciTag": "C-MP789J-X001-d", + "primaryId": "99990_D_2_3", + "cmoPatientId": "C-PPPP12", + "cmoSampleName": "C-PPPP11-X001-d", + "ciTag": "C-PPPP11-X001-d", "sampleName": "XXX002_P3_12345_L1", "sampleType": "Primary", "oncotreeCode": "CLL", @@ -58,7 +58,7 @@ "qcReports": [], "libraries": [ { - "libraryIgoId": "10075_D_2_3", + "libraryIgoId": "99990_D_2_3", "libraryVolume": 35.0, "libraryConcentrationNgul": 34.8, "captureConcentrationNm": "11.49425287356322", @@ -68,15 +68,15 @@ { "runMode": "HiSeq High Output", "runId": "RUNID_0123", - "flowCellId": "X5KL2KKAY", + "flowCellId": "FCELLBBB10", "readLength": "", "runDate": "2018-06-05", "flowCellLanes": [ 5 ], "fastqs": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ] } ] @@ -95,7 +95,7 @@ "sampleMetadataList": [ { "additionalProperties": { - "igoRequestId": "10075_D_2", + "igoRequestId": "99990_D_2", "isCmoSample": "true" }, "cfDNA2dBarcode": null, @@ -103,17 +103,17 @@ "baitSet": "GENESET101_BAITS", "cmoSampleIdFields": { "naToExtract": "", - "normalizedPatientId": "ALLAJV_HCISCLC002", + "normalizedPatientId": "TESTID_SAMPLEXXX002", "recipe": "IMPACT468", "sampleType": "DNA" }, "importDate": "2022-03-23", "smileSampleId": "afe750e6-8756-11eb-81b0-acde48001122", "smilePatientId": "6cc9f242-875a-11eb-ae91-acde48001122", - "primaryId": "10075_D_2_3", - "cmoPatientId": "C-MP789JR", - "cmoSampleName": "C-MP789J-X001-d", - "ciTag": "C-MP789J-X001-d", + "primaryId": "99990_D_2_3", + "cmoPatientId": "C-PPPP12", + "cmoSampleName": "C-PPPP11-X001-d", + "ciTag": "C-PPPP11-X001-d", "sampleName": "XXX002_P3_12345_L1", "sampleType": "Primary", "oncotreeCode": "CLL", @@ -122,7 +122,7 @@ "qcReports": [], "libraries": [ { - "libraryIgoId": "10075_D_2_3", + "libraryIgoId": "99990_D_2_3", "libraryVolume": 35.0, "libraryConcentrationNgul": 34.8, "captureConcentrationNm": "11.49425287356322", @@ -132,15 +132,15 @@ { "runMode": "HiSeq High Output", "runId": "RUNID_0123", - "flowCellId": "X5KL2KKAY", + "flowCellId": "FCELLBBB10", "readLength": "", "runDate": "2018-06-05", "flowCellLanes": [ 5 ], "fastqs": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ] } ] diff --git a/fixtures/tests/10075_D_3.file.json b/fixtures/tests/99990_D_3.file.json similarity index 58% rename from fixtures/tests/10075_D_3.file.json rename to fixtures/tests/99990_D_3.file.json index 364d9444e..197e50d2c 100644 --- a/fixtures/tests/10075_D_3.file.json +++ b/fixtures/tests/99990_D_3.file.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "SK_MEL_1091A_T_IGO_10075_D_3_5_S80_R1_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D_3/Sample_SK_MEL_1091A_T_IGO_10075_D_3_5/SK_MEL_1091A_T_IGO_10075_D_3_5_S80_R1_001.fastq.gz", + "file_name": "SAMPLE_T_001_IGO_99990_D_3_5_S80_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D_3/Sample_SAMPLE_T_001_IGO_99990_D_3_5/SAMPLE_T_001_IGO_99990_D_3_5_S80_R1_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "SK_MEL_1091A_T_IGO_10075_D_3_5_S80_R2_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D_3/Sample_SK_MEL_1091A_T_IGO_10075_D_3_5/SK_MEL_1091A_T_IGO_10075_D_3_5_S80_R2_001.fastq.gz", + "file_name": "SAMPLE_T_001_IGO_99990_D_3_5_S80_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D_3/Sample_SAMPLE_T_001_IGO_99990_D_3_5/SAMPLE_T_001_IGO_99990_D_3_5_S80_R2_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/fixtures/tests/99990_D_3.filemetadata.json b/fixtures/tests/99990_D_3.filemetadata.json new file mode 100644 index 000000000..dc32f76e3 --- /dev/null +++ b/fixtures/tests/99990_D_3.filemetadata.json @@ -0,0 +1,152 @@ +[ + { + "model": "file_system.filemetadata", + "pk": "d43f1395-cf7d-4db1-837b-eb67c7504138", + "fields": { + "created_date": "2020-01-06T19:59:50.583Z", + "modified_date": "2020-01-06T19:59:50.583Z", + "file": "d2d8ed36-d8f4-4e93-b038-d38328fad021", + "version": 0, + "latest": true, + 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"/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R2_001.fastq.gz" + ], + "tumorOrNormal": "Normal", + "captureInputNg": "110.0", + "cmoSampleClass": "Normal", + "collectionYear": "", + "tissueLocation": "", + "dataAnalystName": "", + "dataAnalystEmail": "", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", + "investigatorEmail": "email2@internet.com", + "projectManagerName": "", + "investigatorSampleId": "SAMPLE_N_001", + "captureConcentrationNm": "10.377358490566039", + "libraryConcentrationNgul": 10.6 + }, + "user": null + } + } +] diff --git a/fixtures/tests/99990_D_request_update.json b/fixtures/tests/99990_D_request_update.json new file mode 100644 index 000000000..ce7fa8ccf --- /dev/null +++ b/fixtures/tests/99990_D_request_update.json @@ -0,0 +1,20 @@ +[ + { + "igoRequestId": "99990_D_2", + "requestMetadataJson": "{\"requestId\":\"99990_D_2\",\"recipe\":\"IMPACT468\",\"projectManagerName\":\"\",\"piEmail\":\"\",\"labHeadName\":\"Lab Head C\",\"labHeadEmail\":\"analyst14@example.org\",\"investigatorName\":\"Investigator E\",\"investigatorEmail\":\"analyst10@example.org\",\"dataAnalystName\":\"\",\"dataAnalystEmail\":\"\",\"otherContactEmails\":\"\",\"dataAccessEmails\":\"analyst7@example.org,analyst4@example.org\",\"qcAccessEmails\":\"analyst7@example.org,analyst4@example.org\",\"strand\":null,\"libraryType\":null,\"isCmoRequest\":true,\"bicAnalysis\":true,\"pooledNormals\":null,\"projectId\":\"10075\"}", + "importDate": "2023-03-08", + "status": { + "validationStatus": true, + "validationReport": "" + } + }, + { + "igoRequestId": "99990_D_2", + "requestMetadataJson": "{\"requestId\":\"99990_D_2\",\"recipe\":\"IMPACT468\",\"projectManagerName\":\"\",\"piEmail\":\"\",\"labHeadName\":\"Lab Head C\",\"labHeadEmail\":\"analyst14@example.org\",\"investigatorName\":\"Investigator E\",\"investigatorEmail\":\"analyst10@example.org\",\"dataAnalystName\":\"\",\"dataAnalystEmail\":\"\",\"otherContactEmails\":\"analyst7@example.org,analyst4@example.org,analyst7@example.org,analyst4@example.org\",\"dataAccessEmails\":\"analyst7@example.org,analyst4@example.org\",\"qcAccessEmails\":\"analyst7@example.org,analyst4@example.org\",\"strand\":null,\"libraryType\":null,\"isCmoRequest\":true,\"bicAnalysis\":true,\"pooledNormals\":[],\"projectId\":\"10075\",\"status\":{\"validationReport\":[],\"validationStatus\":true}}", + "importDate": "2023-03-22", + "status": { + "validationStatus": true, + "validationReport": "[]" + } + } +] \ No newline at end of file diff --git a/fixtures/tests/10075_D_single_TN_pair.argos.input.json b/fixtures/tests/99990_D_single_TN_pair.argos.input.json similarity index 92% rename from fixtures/tests/10075_D_single_TN_pair.argos.input.json rename to fixtures/tests/99990_D_single_TN_pair.argos.input.json index 09f13e5fd..e885de7a5 100644 --- a/fixtures/tests/10075_D_single_TN_pair.argos.input.json +++ b/fixtures/tests/99990_D_single_TN_pair.argos.input.json @@ -1,71 +1,71 @@ [ { "assay": "IMPACT468_BAITS", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", "pair": [ { - "ID": "s_C_8VK0V7_R001_d", + "ID": "s_C_PPPPP3_R001_d", "CN": "MSKCC", - "LB": "10075_D_5_1_1_1", + "LB": "99990_D_5_1_1_1", "PL": "Illumina", "PU": [ - "HFTCNBBXY_GTATTGGC-TTGTCGGT" + "FCELLAAAA6_GTATTGGC-PPPP14" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R1_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D/Sample_SAMPLE_T_001_IGO_99990_D_5/SAMPLE_T_001_IGO_99990_D_5_S80_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R2_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D/Sample_SAMPLE_T_001_IGO_99990_D_5/SAMPLE_T_001_IGO_99990_D_5_S80_R2_001.fastq.gz" } ], "zR1": [], "zR2": [], "bam": [], "RG_ID": [ - "s_C_8VK0V7_R001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT" + "s_C_PPPPP3_R001_d_FCELLAAAA6_GTATTGGC-PPPP14" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_8VK0V7_R001_d.bam", - "request_id": "10075_D", + "bwa_output": "s_C_PPPPP3_R001_d.bam", + "request_id": "99990_D", "specimen_type": "Resection" }, { - "ID": "s_C_8VK0V7_N001_d", + "ID": "s_C_PPPPP3_N001_d", "CN": "MSKCC", - "LB": "10075_D_3", + "LB": "99990_D_3", "PL": "Illumina", "PU": [ - "HCYYWBBXY" + "FCELLAAAA4" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R1_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R2_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R2_001.fastq.gz" } ], "zR1": [], "zR2": [], "bam": [], "RG_ID": [ - "s_C_8VK0V7_N001_d_HCYYWBBXY" + "s_C_PPPPP3_N001_d_FCELLAAAA4" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_8VK0V7_N001_d.bam", - "request_id": "10075_D", + "bwa_output": "s_C_PPPPP3_N001_d.bam", + "request_id": "99990_D", "specimen_type": "Normal"} ], "curated_bams": [ @@ -349,7 +349,7 @@ "num_threads": 10, "assay": "IMPACT468_BAITS", "tmp_dir": "/scratch", - "project_prefix": "10075_D", + "project_prefix": "99990_D", "opt_dup_pix_dist": "2500", "delly_type": [ "DUP", @@ -364,7 +364,7 @@ "complex_tn": 0.5, "scripts_bin": "/usr/bin", "gatk_jar_path": "/usr/bin/gatk.jar", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com" } } diff --git a/fixtures/tests/10075_D_single_TN_pair.argos_1_7_0.input.json b/fixtures/tests/99990_D_single_TN_pair.argos_1_7_0.input.json similarity index 91% rename from fixtures/tests/10075_D_single_TN_pair.argos_1_7_0.input.json rename to fixtures/tests/99990_D_single_TN_pair.argos_1_7_0.input.json index 31ca6c1fe..e186d3881 100644 --- a/fixtures/tests/10075_D_single_TN_pair.argos_1_7_0.input.json +++ b/fixtures/tests/99990_D_single_TN_pair.argos_1_7_0.input.json @@ -1,23 +1,23 @@ [ { "tumor": { - "ID": "s_C_8VK0V7_R001_d", + "ID": "s_C_PPPPP3_R001_d", "CN": "MSKCC", - "LB": "10075_D_5_1_1_1", + "LB": "99990_D_5_1_1_1", "PL": "Illumina", "PU": [ - "HFTCNBBXY_GTATTGGC-TTGTCGGT" + "FCELLAAAA6_GTATTGGC-PPPP14" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R1_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D/Sample_SAMPLE_T_001_IGO_99990_D_5/SAMPLE_T_001_IGO_99990_D_5_S80_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R2_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D/Sample_SAMPLE_T_001_IGO_99990_D_5/SAMPLE_T_001_IGO_99990_D_5_S80_R2_001.fastq.gz" } ], "zR1": [], @@ -25,32 +25,32 @@ "bam": [], "zBam": [], "RG_ID": [ - "s_C_8VK0V7_R001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT" + "s_C_PPPPP3_R001_d_FCELLAAAA6_GTATTGGC-PPPP14" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_8VK0V7_R001_d.bam", - "request_id": "10075_D", + "bwa_output": "s_C_PPPPP3_R001_d.bam", + "request_id": "99990_D", "specimen_type": "Resection" }, "normal": { - "ID": "s_C_8VK0V7_N001_d", + "ID": "s_C_PPPPP3_N001_d", "CN": "MSKCC", - "LB": "10075_D_3", + "LB": "99990_D_3", "PL": "Illumina", "PU": [ - "HCYYWBBXY" + "FCELLAAAA4" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R1_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R2_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R2_001.fastq.gz" } ], "zR1": [], @@ -58,18 +58,18 @@ "bam": [], "zBam": [], "RG_ID": [ - "s_C_8VK0V7_N001_d_HCYYWBBXY" + "s_C_PPPPP3_N001_d_FCELLAAAA4" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_8VK0V7_N001_d.bam", - "request_id": "10075_D", + "bwa_output": "s_C_PPPPP3_N001_d.bam", + "request_id": "99990_D", "specimen_type": "Normal" }, "assay": "IMPACT468_BAITS", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "curated_bams": [ { "class": "File", @@ -351,7 +351,7 @@ "num_threads": 10, "assay": "IMPACT468_BAITS", "tmp_dir": "/scratch", - "project_prefix": "10075_D", + "project_prefix": "99990_D", "opt_dup_pix_dist": "2500", "delly_type": [ "DUP", @@ -366,7 +366,7 @@ "complex_tn": 0.5, "scripts_bin": "/usr/bin", "gatk_jar_path": "/usr/bin/gatk.jar", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com" } } diff --git a/fixtures/tests/10075_D_single_TN_pair.argos_bam.input.json b/fixtures/tests/99990_D_single_TN_pair.argos_bam.input.json similarity index 80% rename from fixtures/tests/10075_D_single_TN_pair.argos_bam.input.json rename to fixtures/tests/99990_D_single_TN_pair.argos_bam.input.json index 78e86cc69..4beb48cca 100644 --- a/fixtures/tests/10075_D_single_TN_pair.argos_bam.input.json +++ b/fixtures/tests/99990_D_single_TN_pair.argos_bam.input.json @@ -1,9 +1,9 @@ [ { "assay": "IMPACT468_BAITS", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "genome": "GRCh37", "intervals": [ "1", @@ -79,23 +79,23 @@ }, "conpair_markers_bed": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed", "tumor": { - "ID": "s_C_8VK0V7_R001_d", + "ID": "s_C_PPPPP3_R001_d", "CN": "MSKCC", - "LB": "10075_D_5_1_1_1", + "LB": "99990_D_5_1_1_1", "PL": "Illumina", "PU": [ - "HFTCNBBXY_GTATTGGC-TTGTCGGT" + "FCELLAAAA6_GTATTGGC-PPPP14" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R1_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D/Sample_SAMPLE_T_001_IGO_99990_D_5/SAMPLE_T_001_IGO_99990_D_5_S80_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R2_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_99990_D/Sample_SAMPLE_T_001_IGO_99990_D_5/SAMPLE_T_001_IGO_99990_D_5_S80_R2_001.fastq.gz" } ], "zR1": [], @@ -103,32 +103,32 @@ "bam": [], "zBam": [], "RG_ID": [ - "s_C_8VK0V7_R001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT" + "s_C_PPPPP3_R001_d_FCELLAAAA6_GTATTGGC-PPPP14" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_8VK0V7_R001_d.bam", - "request_id": "10075_D", + "bwa_output": "s_C_PPPPP3_R001_d.bam", + "request_id": "99990_D", "specimen_type": "Resection" }, "normal": { - "ID": "s_C_8VK0V7_N001_d", + "ID": "s_C_PPPPP3_N001_d", "CN": "MSKCC", - "LB": "10075_D_3", + "LB": "99990_D_3", "PL": "Illumina", "PU": [ - "HCYYWBBXY" + "FCELLAAAA4" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R1_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R2_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R2_001.fastq.gz" } ], "zR1": [], @@ -136,12 +136,12 @@ "bam": [], "zBam": [], "RG_ID": [ - "s_C_8VK0V7_N001_d_HCYYWBBXY" + "s_C_PPPPP3_N001_d_FCELLAAAA4" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_8VK0V7_N001_d.bam", - "request_id": "10075_D", + "bwa_output": "s_C_PPPPP3_N001_d.bam", + "request_id": "99990_D", "specimen_type": "Normal" } } diff --git a/fixtures/tests/10075_D_single_TN_pair.argos_bam_1_0_0.input.json b/fixtures/tests/99990_D_single_TN_pair.argos_bam_1_0_0.input.json similarity index 80% rename from fixtures/tests/10075_D_single_TN_pair.argos_bam_1_0_0.input.json rename to fixtures/tests/99990_D_single_TN_pair.argos_bam_1_0_0.input.json index b9099404b..fcd371950 100644 --- a/fixtures/tests/10075_D_single_TN_pair.argos_bam_1_0_0.input.json +++ b/fixtures/tests/99990_D_single_TN_pair.argos_bam_1_0_0.input.json @@ -1,9 +1,9 @@ [ { "assay": "IMPACT468_BAITS", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "genome": "GRCh37", "intervals": [ "1", @@ -79,67 +79,67 @@ }, "conpair_markers_bed": "/usr/bin/conpair/data/markers/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed", "tumor": { - "ID": "s_C_8VK0V7_R001_d", + "ID": "s_C_PPPPP3_R001_d", "CN": "MSKCC", - "LB": "10075_D_5_1_1_1", + "LB": "99990_D_5_1_1_1", "PL": "Illumina", "PU": [ - "HFTCNBBXY_GTATTGGC-TTGTCGGT" + "FCELLAAAA6_GTATTGGC-PPPP14" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_10075_D/Sample_SK_MEL_1091A_T_IGO_10075_D_5/SK_MEL_1091A_T_IGO_10075_D_5_S80_R1_001.fastq.gz" + "location": 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"Resection" }, "normal": { - "ID": "s_C_8VK0V7_N001_d", + "ID": "s_C_PPPPP3_N001_d", "CN": "MSKCC", - "LB": "10075_D_3", + "LB": "99990_D_3", "PL": "Illumina", "PU": [ - "HCYYWBBXY" + "FCELLAAAA4" ], "R1": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R1_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_JW_MEL_007_NORM_IGO_10075_D_3/JW_MEL_007_NORM_IGO_10075_D_3_S15_R2_001.fastq.gz" + "location": "juno:///ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_SAMPLE_N_001_IGO_99990_D_3/SAMPLE_N_001_IGO_99990_D_3_S15_R2_001.fastq.gz" } ], "zR1": [], "zR2": [], "bam": [], "RG_ID": [ - "s_C_8VK0V7_N001_d_HCYYWBBXY" + "s_C_PPPPP3_N001_d_FCELLAAAA4" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_8VK0V7_N001_d.bam", - "request_id": "10075_D", + "bwa_output": "s_C_PPPPP3_N001_d.bam", + "request_id": "99990_D", "specimen_type": "Normal" } } diff --git a/fixtures/tests/10075_D_single_TN_pair.file.json b/fixtures/tests/99990_D_single_TN_pair.file.json similarity index 59% rename from fixtures/tests/10075_D_single_TN_pair.file.json rename to fixtures/tests/99990_D_single_TN_pair.file.json index 4c18320c5..eb8ca6226 100644 --- a/fixtures/tests/10075_D_single_TN_pair.file.json +++ b/fixtures/tests/99990_D_single_TN_pair.file.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "SK_MEL_1091A_T_IGO_10075_D_5_S80_R1_001.fastq.gz", - "path": 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"juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX002_P3_12345_L1_IGO_99991_B_1/XXX002_P3_12345_L1_IGO_99991_B_1_S82_R2_001.fastq.gz" } ], "bam": [], "zBam": [], "RG_ID": [ - "s_C_MP76JR_X001_d_H3MV7BBXY" + "s_C_PPPP10_X001_d_FCELLAAAA1" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_MP76JR_X001_d.bam", - "request_id": "08944_B", + "bwa_output": "s_C_PPPP10_X001_d.bam", + "request_id": "99991_B", "specimen_type": "PDX" }, "normal": { - "ID": "s_C_MP76JR_N001_d", + "ID": "s_C_PPPP10_N001_d", "CN": "MSKCC", - "LB": "08944_B_2_1_1_1", + "LB": "99991_B_2_1_1_1", "PL": "Illumina", "PU": [ - "H3MV7BBXY" + "FCELLAAAA1" ], "R1": [], "R2": [], "zR1": [ { "class": "File", - "location": 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"request_id": "08944_B", + "bwa_output": "s_C_PPPP10_N001_d.bam", + "request_id": "99991_B", "specimen_type": "Blood" }, "assay": "IMPACT468_BAITS", - "pi": "John Doe", - "pi_email": "email@mskcc.org", - "patient_id": "C-MP76JR", + "pi": "Test Researcher", + "pi_email": "user@example.org", + "patient_id": "C-PPPP10", "curated_bams": [ { "class": "File", @@ -351,7 +351,7 @@ "num_threads": 10, "assay": "IMPACT468_BAITS", "tmp_dir": "/scratch", - "project_prefix": "08944_B", + "project_prefix": "99991_B", "opt_dup_pix_dist": "2500", "delly_type": [ "DUP", @@ -366,81 +366,81 @@ "complex_tn": 0.5, "scripts_bin": "/usr/bin", "gatk_jar_path": "/usr/bin/gatk.jar", - "pi": "John Doe", - "pi_email": "email@mskcc.org" + "pi": "Test Researcher", + "pi_email": "user@example.org" } }, { "tumor": { - "ID": "s_C_4LM16H_X001_d", + "ID": "s_C_PPPPP1_X001_d", "CN": "MSKCC", - "LB": "08944_B_3_1_1_1", + "LB": "99991_B_3_1_1_1", "PL": "Illumina", "PU": [ - "H3MV7BBXY" + "FCELLAAAA1" ], "R1": [], "R2": [], "zR1": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG017_P1_17095a_R_43_IGO_08944_B_3/LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R1_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R1_001.fastq.gz" } ], "zR2": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG017_P1_17095a_R_43_IGO_08944_B_3/LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R2_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R2_001.fastq.gz" } ], "bam": [], "zBam": [], "RG_ID": [ - "s_C_4LM16H_X001_d_H3MV7BBXY" + "s_C_PPPPP1_X001_d_FCELLAAAA1" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_4LM16H_X001_d.bam", - "request_id": "08944_B", + "bwa_output": "s_C_PPPPP1_X001_d.bam", + "request_id": "99991_B", "specimen_type": "PDX" }, "normal": { - "ID": "s_C_4LM16H_N001_d", + "ID": "s_C_PPPPP1_N001_d", "CN": "MSKCC", - "LB": "08944_B_4_1_1_1", + "LB": "99991_B_4_1_1_1", "PL": "Illumina", "PU": [ - "H3MV7BBXY" + "FCELLAAAA1" ], "R1": [], "R2": [], "zR1": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0010557a_IGO_08944_B_4/17-0010557a_IGO_08944_B_4_S85_R1_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R1_001.fastq.gz" } ], "zR2": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0010557a_IGO_08944_B_4/17-0010557a_IGO_08944_B_4_S85_R2_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R2_001.fastq.gz" } ], "bam": [], "zBam": [], "RG_ID": [ - "s_C_4LM16H_N001_d_H3MV7BBXY" + "s_C_PPPPP1_N001_d_FCELLAAAA1" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_4LM16H_N001_d.bam", - "request_id": "08944_B", + "bwa_output": "s_C_PPPPP1_N001_d.bam", + "request_id": "99991_B", "specimen_type": "Blood" }, "assay": "IMPACT468_BAITS", - "pi": "John Doe", - "pi_email": "email@mskcc.org", - "patient_id": "C-4LM16H", + "pi": "Test Researcher", + "pi_email": "user@example.org", + "patient_id": "C-PPPPP1", "curated_bams": [ { "class": "File", @@ -722,7 +722,7 @@ "num_threads": 10, "assay": "IMPACT468_BAITS", "tmp_dir": "/scratch", - "project_prefix": "08944_B", + "project_prefix": "99991_B", "opt_dup_pix_dist": "2500", "delly_type": [ "DUP", @@ -737,8 +737,8 @@ "complex_tn": 0.5, "scripts_bin": "/usr/bin", "gatk_jar_path": "/usr/bin/gatk.jar", - "pi": "John Doe", - "pi_email": "email@mskcc.org" + "pi": "Test Researcher", + "pi_email": "user@example.org" } } ] \ No newline at end of file diff --git a/fixtures/tests/08944_B.argos_bam.input.json b/fixtures/tests/99991_B.argos_bam.input.json similarity index 73% rename from fixtures/tests/08944_B.argos_bam.input.json rename to fixtures/tests/99991_B.argos_bam.input.json index 79cc656c1..98504113b 100644 --- a/fixtures/tests/08944_B.argos_bam.input.json +++ b/fixtures/tests/99991_B.argos_bam.input.json @@ -1,56 +1,56 @@ [ { "tumor": { - "ID": "s_C_MP76JR_X001_d", + "ID": "s_C_PPPP10_X001_d", "CN": "MSKCC", - "LB": "08944_B_1_1_1_1", + "LB": "99991_B_1_1_1_1", "PL": "Illumina", "PU": [ - "H3MV7BBXY" + "FCELLAAAA1" ], "R1": [], "R2": [], "zR1": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG002_P3_17096_L1_IGO_08944_B_1/LTG002_P3_17096_L1_IGO_08944_B_1_S82_R1_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX002_P3_12345_L1_IGO_99991_B_1/XXX002_P3_12345_L1_IGO_99991_B_1_S82_R1_001.fastq.gz" } ], "zR2": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG002_P3_17096_L1_IGO_08944_B_1/LTG002_P3_17096_L1_IGO_08944_B_1_S82_R2_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX002_P3_12345_L1_IGO_99991_B_1/XXX002_P3_12345_L1_IGO_99991_B_1_S82_R2_001.fastq.gz" } ], "bam": [], "zBam": [], "RG_ID": [ - "s_C_MP76JR_X001_d_H3MV7BBXY" + "s_C_PPPP10_X001_d_FCELLAAAA1" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_MP76JR_X001_d.bam", - "request_id": "08944_B", + "bwa_output": "s_C_PPPP10_X001_d.bam", + "request_id": "99991_B", "specimen_type": "PDX" }, "normal": { - "ID": "s_C_MP76JR_N001_d", + "ID": "s_C_PPPP10_N001_d", "CN": "MSKCC", - "LB": "08944_B_2_1_1_1", + "LB": "99991_B_2_1_1_1", "PL": "Illumina", "PU": [ - "H3MV7BBXY" + "FCELLAAAA1" ], "R1": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0001535a_IGO_08944_B_2/17-0001535a_IGO_08944_B_2_S83_R1_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000003a_IGO_99991_B_2/00-0000003a_IGO_99991_B_2_S83_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0001535a_IGO_08944_B_2/17-0001535a_IGO_08944_B_2_S83_R2_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000003a_IGO_99991_B_2/00-0000003a_IGO_99991_B_2_S83_R2_001.fastq.gz" } ], "zR1": [], @@ -58,18 +58,18 @@ "bam": [], "zBam": [], "RG_ID": [ - "s_C_MP76JR_N001_d_H3MV7BBXY" + "s_C_PPPP10_N001_d_FCELLAAAA1" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_MP76JR_N001_d.bam", - "request_id": "08944_B", + "bwa_output": "s_C_PPPP10_N001_d.bam", + "request_id": "99991_B", "specimen_type": "Blood" }, "assay": "IMPACT468_BAITS", - "pi": "John Doe", - "pi_email": "email@mskcc.org", - "patient_id": "C-MP76JR", + "pi": "Test Researcher", + "pi_email": "user@example.org", + "patient_id": "C-PPPP10", "genome": "GRCh37", "intervals": [ "1", @@ -147,56 +147,56 @@ }, { "tumor": { - "ID": "s_C_4LM16H_X001_d", + "ID": "s_C_PPPPP1_X001_d", "CN": "MSKCC", - "LB": "08944_B_3_1_1_1", + "LB": "99991_B_3_1_1_1", "PL": "Illumina", "PU": [ - "H3MV7BBXY" + "FCELLAAAA1" ], "R1": [], "R2": [], "zR1": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG017_P1_17095a_R_43_IGO_08944_B_3/LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R1_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R1_001.fastq.gz" } ], "zR2": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG017_P1_17095a_R_43_IGO_08944_B_3/LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R2_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R2_001.fastq.gz" } ], "bam": [], "zBam": [], "RG_ID": [ - "s_C_4LM16H_X001_d_H3MV7BBXY" + "s_C_PPPPP1_X001_d_FCELLAAAA1" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_4LM16H_X001_d.bam", - "request_id": "08944_B", + "bwa_output": "s_C_PPPPP1_X001_d.bam", + "request_id": "99991_B", "specimen_type": "PDX" }, "normal": { - "ID": "s_C_4LM16H_N001_d", + "ID": "s_C_PPPPP1_N001_d", "CN": "MSKCC", - "LB": "08944_B_4_1_1_1", + "LB": "99991_B_4_1_1_1", "PL": "Illumina", "PU": [ - "H3MV7BBXY" + "FCELLAAAA1" ], "R1": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0010557a_IGO_08944_B_4/17-0010557a_IGO_08944_B_4_S85_R1_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0010557a_IGO_08944_B_4/17-0010557a_IGO_08944_B_4_S85_R2_001.fastq.gz" + "location": "juno:///juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R2_001.fastq.gz" } ], "zR1": [], @@ -204,18 +204,18 @@ "bam": [], "zBam": [], "RG_ID": [ - "s_C_4LM16H_N001_d_H3MV7BBXY" + "s_C_PPPPP1_N001_d_FCELLAAAA1" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_4LM16H_N001_d.bam", - "request_id": "08944_B", + "bwa_output": "s_C_PPPPP1_N001_d.bam", + "request_id": "99991_B", "specimen_type": "Blood" }, "assay": "IMPACT468_BAITS", - "pi": "John Doe", - "pi_email": "email@mskcc.org", - "patient_id": "C-4LM16H", + "pi": "Test Researcher", + "pi_email": "user@example.org", + "patient_id": "C-PPPPP1", "genome": "GRCh37", "intervals": [ "1", diff --git a/fixtures/tests/08944_B.fixtures.json b/fixtures/tests/99991_B.fixtures.json similarity index 64% rename from fixtures/tests/08944_B.fixtures.json rename to fixtures/tests/99991_B.fixtures.json index 1b731ad3e..9f9f9e2d8 100644 --- a/fixtures/tests/08944_B.fixtures.json +++ b/fixtures/tests/99991_B.fixtures.json @@ -11,52 +11,52 @@ "metadata": { "R": "R1", "sex": "F", - "ciTag": "s_C_MP76JR_N001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPP10_N001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_2", + "primaryId": "99991_B_2", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "17-0001535a", + "sampleName": "00-0000003a", "sampleType": "Normal", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-MP76JR", + "cmoPatientId": "C-PPPP10", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_2_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_2_1_1_1", "oncotreeCode": null, "preservation": "Frozen", "sampleOrigin": "Whole Blood", - "cmoSampleName": "C-MP76JR-N001-d", + "cmoSampleName": "C-PPPP10-N001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "17-0001535a", + "value": "00-0000003a", "namespace": "investigatorId" }, { - "value": "08944_B_2", + "value": "99991_B_2", "namespace": "igoId" } ], @@ -67,32 +67,32 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-MP76JR", + "value": "C-PPPP10", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "2455a56f-f198-47db-a592-ab12137ebc17", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", "sampleType": "DNA", "naToExtract": "", - "normalizedPatientId": "ALLAJV_HCISCLC002" + "normalizedPatientId": "TESTID_SAMPLEXXX002" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "17-0001535a", + "investigatorSampleId": "00-0000003a", "captureConcentrationNm": "5.074626865671642", "libraryConcentrationNgul": 33.5 }, @@ -111,52 +111,52 @@ "metadata": { "R": "R1", "sex": "F", - "ciTag": "s_C_MP76JR_X001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPP10_X001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_1", + "primaryId": "99991_B_1", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "LTG002_P3_17096_L1", + "sampleName": "XXX002_P3_12345_L1", "sampleType": "Primary", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "PDX", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-MP76JR", + "cmoPatientId": "C-PPPP10", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_1_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_1_1_1_1", "oncotreeCode": "SCLC", "preservation": "Frozen", "sampleOrigin": "Tissue", - "cmoSampleName": "C-MP76JR-X001-d", + "cmoSampleName": "C-PPPP10-X001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "LTG002_P3_17096_L1", + "value": "XXX002_P3_12345_L1", "namespace": "investigatorId" }, { - "value": "08944_B_1", + "value": "99991_B_1", "namespace": "igoId" } ], @@ -167,32 +167,32 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-MP76JR", + "value": "C-PPPP10", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "2455a56f-f198-47db-a592-ab12137ebc17", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", "sampleType": "DNA", "naToExtract": "", - "normalizedPatientId": "ALLAJV_HCISCLC002" + "normalizedPatientId": "TESTID_SAMPLEXXX002" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "LTG002_P3_17096_L1", + "investigatorSampleId": "XXX002_P3_12345_L1", "captureConcentrationNm": "11.49425287356322", "libraryConcentrationNgul": 34.8 }, @@ -211,52 +211,52 @@ "metadata": { "R": "R2", "sex": "F", - "ciTag": "s_C_MP76JR_X001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPP10_X001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_1", + "primaryId": "99991_B_1", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "LTG002_P3_17096_L1", + "sampleName": "XXX002_P3_12345_L1", "sampleType": "Primary", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "PDX", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-MP76JR", + "cmoPatientId": "C-PPPP10", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_1_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_1_1_1_1", "oncotreeCode": "SCLC", "preservation": "Frozen", "sampleOrigin": "Tissue", - "cmoSampleName": "C-MP76JR-X001-d", + "cmoSampleName": "C-PPPP10-X001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "LTG002_P3_17096_L1", + "value": "XXX002_P3_12345_L1", "namespace": "investigatorId" }, { - "value": "08944_B_1", + "value": "99991_B_1", "namespace": "igoId" } ], @@ -267,32 +267,32 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-MP76JR", + "value": "C-PPPP10", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "2455a56f-f198-47db-a592-ab12137ebc17", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", "sampleType": "DNA", "naToExtract": "", - "normalizedPatientId": "ALLAJV_HCISCLC002" + "normalizedPatientId": "TESTID_SAMPLEXXX002" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "LTG002_P3_17096_L1", + "investigatorSampleId": "XXX002_P3_12345_L1", "captureConcentrationNm": "11.49425287356322", "libraryConcentrationNgul": 34.8 }, @@ -311,52 +311,52 @@ "metadata": { "R": "R1", "sex": "M", - "ciTag": "s_C_4LM16H_N001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPPP1_N001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_4", + "primaryId": "99991_B_4", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "17-0010557a", + "sampleName": "00-0000004a", "sampleType": "Normal", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-4LM16H", + "cmoPatientId": "C-PPPPP1", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_4_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_4_1_1_1", "oncotreeCode": null, "preservation": "Frozen", "sampleOrigin": "Whole Blood", - "cmoSampleName": "C-4LM16H-N001-d", + "cmoSampleName": "C-PPPPP1-N001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "17-0010557a", + "value": "00-0000004a", "namespace": "investigatorId" }, { - "value": "08944_B_4", + "value": "99991_B_4", "namespace": "igoId" } ], @@ -367,17 +367,17 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-4LM16H", + "value": "C-PPPPP1", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "9697e1bf-2978-44e0-aa0e-92defcc9df34", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", @@ -385,14 +385,14 @@ "naToExtract": "", "normalizedPatientId": "ALLAJV_HCISCLC017" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "17-0010557a", + "investigatorSampleId": "00-0000004a", "captureConcentrationNm": "4.9853372434017595", "libraryConcentrationNgul": 34.1 }, @@ -411,52 +411,52 @@ "metadata": { "R": "R2", "sex": "M", - "ciTag": "s_C_4LM16H_N001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPPP1_N001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_4", + "primaryId": "99991_B_4", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "17-0010557a", + "sampleName": "00-0000004a", "sampleType": "Normal", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-4LM16H", + "cmoPatientId": "C-PPPPP1", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_4_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_4_1_1_1", "oncotreeCode": null, "preservation": "Frozen", "sampleOrigin": "Whole Blood", - "cmoSampleName": "C-4LM16H-N001-d", + "cmoSampleName": "C-PPPPP1-N001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "17-0010557a", + "value": "00-0000004a", "namespace": "investigatorId" }, { - "value": "08944_B_4", + "value": "99991_B_4", "namespace": "igoId" } ], @@ -467,17 +467,17 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-4LM16H", + "value": "C-PPPPP1", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "9697e1bf-2978-44e0-aa0e-92defcc9df34", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", @@ -485,14 +485,14 @@ "naToExtract": "", "normalizedPatientId": "ALLAJV_HCISCLC017" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "17-0010557a", + "investigatorSampleId": "00-0000004a", "captureConcentrationNm": "4.9853372434017595", "libraryConcentrationNgul": 34.1 }, @@ -511,52 +511,52 @@ "metadata": { "R": "R2", "sex": "F", - "ciTag": "s_C_MP76JR_N001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPP10_N001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_2", + "primaryId": "99991_B_2", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "17-0001535a", + "sampleName": "00-0000003a", "sampleType": "Normal", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-MP76JR", + "cmoPatientId": "C-PPPP10", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_2_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_2_1_1_1", "oncotreeCode": null, "preservation": "Frozen", "sampleOrigin": "Whole Blood", - "cmoSampleName": "C-MP76JR-N001-d", + "cmoSampleName": "C-PPPP10-N001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "17-0001535a", + "value": "00-0000003a", "namespace": "investigatorId" }, { - "value": "08944_B_2", + "value": "99991_B_2", "namespace": "igoId" } ], @@ -567,32 +567,32 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-MP76JR", + "value": "C-PPPP10", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "2455a56f-f198-47db-a592-ab12137ebc17", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", "sampleType": "DNA", "naToExtract": "", - "normalizedPatientId": "ALLAJV_HCISCLC002" + "normalizedPatientId": "TESTID_SAMPLEXXX002" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "17-0001535a", + "investigatorSampleId": "00-0000003a", "captureConcentrationNm": "5.074626865671642", "libraryConcentrationNgul": 33.5 }, @@ -611,52 +611,52 @@ "metadata": { "R": "R1", "sex": "M", - "ciTag": "s_C_4LM16H_X001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPPP1_X001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_3", + "primaryId": "99991_B_3", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "LTG017_P1_17095a_R_43", + "sampleName": "XXX017_P1_12345a_R_43", "sampleType": "Primary", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "PDX", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-4LM16H", + "cmoPatientId": "C-PPPPP1", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_3_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_3_1_1_1", "oncotreeCode": "SCLC", "preservation": "Frozen", "sampleOrigin": "Tissue", - "cmoSampleName": "C-4LM16H-X001-d", + "cmoSampleName": "C-PPPPP1-X001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "LTG017_P1_17095a_R_43", + "value": "XXX017_P1_12345a_R_43", "namespace": "investigatorId" }, { - "value": "08944_B_3", + "value": "99991_B_3", "namespace": "igoId" } ], @@ -667,17 +667,17 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-4LM16H", + "value": "C-PPPPP1", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "9697e1bf-2978-44e0-aa0e-92defcc9df34", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", @@ -685,14 +685,14 @@ "naToExtract": "", "normalizedPatientId": "ALLAJV_HCISCLC017" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "LTG017_P1_17095a_R_43", + "investigatorSampleId": "XXX017_P1_12345a_R_43", "captureConcentrationNm": "11.363636363636363", "libraryConcentrationNgul": 35.2 }, @@ -711,52 +711,52 @@ "metadata": { "R": "R2", "sex": "M", - "ciTag": "s_C_4LM16H_X001_d", - "runId": "PITT_0319", + "ciTag": "s_C_PPPPP1_X001_d", + "runId": "SEQRUN_0005", "tubeId": "", "baitSet": "IMPACT468_BAITS", - "piEmail": "email@mskcc.org", + "piEmail": "user@example.org", "runDate": "2019-02-11", "runMode": "HiSeq High Output", "species": "Human", "platform": "Illumina", "barcodeId": null, "genePanel": "IMPACT468", - "primaryId": "08944_B_3", + "primaryId": "99991_B_3", "qcReports": [], "datasource": "igo", "dnaInputNg": null, - "flowCellId": "H3MV7BBXY", + "flowCellId": "FCELLAAAA1", "importDate": "2022-11-28", "readLength": "", - "sampleName": "LTG017_P1_17095a_R_43", + "sampleName": "XXX017_P1_12345a_R_43", "sampleType": "Primary", - "captureName": "Pool-08944_B-Tube7_1", + "captureName": "Pool-99991_B-Tube7_1", "igoComplete": true, - "labHeadName": "John Doe", + "labHeadName": "Test Researcher", "sampleClass": "PDX", "barcodeIndex": null, "cmoInfoIgoId": null, - "cmoPatientId": "C-4LM16H", + "cmoPatientId": "C-PPPPP1", "igoProjectId": "08944", - "igoRequestId": "08944_B", - "labHeadEmail": "email@mskcc.org", - "libraryIgoId": "08944_B_3_1_1_1", + "igoRequestId": "99991_B", + "labHeadEmail": "user@example.org", + "libraryIgoId": "99991_B_3_1_1_1", "oncotreeCode": "SCLC", "preservation": "Frozen", "sampleOrigin": "Tissue", - "cmoSampleName": "C-4LM16H-X001-d", + "cmoSampleName": "C-PPPPP1-X001-d", "flowCellLanes": [ 5 ], "libraryVolume": 35.0, "sampleAliases": [ { - "value": "LTG017_P1_17095a_R_43", + "value": "XXX017_P1_12345a_R_43", "namespace": "investigatorId" }, { - "value": "08944_B_3", + "value": "99991_B_3", "namespace": "igoId" } ], @@ -767,17 +767,17 @@ "collectionYear": "", "patientAliases": [ { - "value": "C-4LM16H", + "value": "C-PPPPP1", "namespace": "cmoId" } ], - "qcAccessEmails": ",email@mskcc.org", + "qcAccessEmails": ",user@example.org", "smilePatientId": "9697e1bf-2978-44e0-aa0e-92defcc9df34", "tissueLocation": "", - "dataAnalystName": "John Doe", + "dataAnalystName": "Test Researcher", "dataAccessEmails": "", - "dataAnalystEmail": "email@mskcc.org", - "investigatorName": "John Doe", + "dataAnalystEmail": "user@example.org", + "investigatorName": "Test Researcher", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "IMPACT468", @@ -785,14 +785,14 @@ "naToExtract": "", "normalizedPatientId": "ALLAJV_HCISCLC017" }, - "investigatorEmail": "email@mskcc.org", - "otherContactEmails": "email@mskcc.org", - "projectManagerName": "John Doe", + "investigatorEmail": "user@example.org", + "otherContactEmails": "user@example.org", + "projectManagerName": "Test Researcher", "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "08944_B" + "igoRequestId": "99991_B" }, - "investigatorSampleId": "LTG017_P1_17095a_R_43", + "investigatorSampleId": "XXX017_P1_12345a_R_43", "captureConcentrationNm": "11.363636363636363", "libraryConcentrationNgul": 35.2 }, @@ -805,15 +805,15 @@ "fields": { "created_date": "2021-03-15T16:42:54.092Z", "modified_date": "2024-06-12T17:04:28.167Z", - "file_name": "17-0001535a_IGO_08944_B_2_S83_R1_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0001535a_IGO_08944_B_2/17-0001535a_IGO_08944_B_2_S83_R1_001.fastq.gz", + "file_name": "00-0000003a_IGO_99991_B_2_S83_R1_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000003a_IGO_99991_B_2/00-0000003a_IGO_99991_B_2_S83_R1_001.fastq.gz", "file_type": 1, "size": 390343219, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$25ce76ddbdc98420e9db765b91febc87e727617c", - "request_id": "08944_B", - "samples": "[\"08944_B_2\"]", - "patient_id": "C-MP76JR", + "request_id": "99991_B", + "samples": "[\"99991_B_2\"]", + "patient_id": "C-PPPP10", "available": true } }, @@ -823,15 +823,15 @@ "fields": { "created_date": "2021-03-15T16:42:54.048Z", "modified_date": "2024-06-12T17:04:28.131Z", - "file_name": "LTG002_P3_17096_L1_IGO_08944_B_1_S82_R1_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG002_P3_17096_L1_IGO_08944_B_1/LTG002_P3_17096_L1_IGO_08944_B_1_S82_R1_001.fastq.gz", + "file_name": "XXX002_P3_12345_L1_IGO_99991_B_1_S82_R1_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX002_P3_12345_L1_IGO_99991_B_1/XXX002_P3_12345_L1_IGO_99991_B_1_S82_R1_001.fastq.gz", "file_type": 1, "size": 933098209, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$828da3499a01e62c844a2d9d916e2990baca8d81", - "request_id": "08944_B", - "samples": "[\"08944_B_1\"]", - "patient_id": "C-MP76JR", + "request_id": "99991_B", + "samples": "[\"99991_B_1\"]", + "patient_id": "C-PPPP10", "available": true } }, @@ -841,15 +841,15 @@ "fields": { "created_date": "2021-03-15T16:42:55.529Z", "modified_date": "2024-06-12T17:04:28.217Z", - "file_name": "LTG002_P3_17096_L1_IGO_08944_B_1_S82_R2_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG002_P3_17096_L1_IGO_08944_B_1/LTG002_P3_17096_L1_IGO_08944_B_1_S82_R2_001.fastq.gz", + "file_name": "XXX002_P3_12345_L1_IGO_99991_B_1_S82_R2_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX002_P3_12345_L1_IGO_99991_B_1/XXX002_P3_12345_L1_IGO_99991_B_1_S82_R2_001.fastq.gz", "file_type": 1, "size": 1063798887, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$29780618e4107c54aea4a05361ded4dd35f3a34f", - "request_id": "08944_B", - "samples": "[\"08944_B_1\"]", - "patient_id": "C-MP76JR", + "request_id": "99991_B", + "samples": "[\"99991_B_1\"]", + "patient_id": "C-PPPP10", "available": true } }, @@ -859,15 +859,15 @@ "fields": { "created_date": "2021-03-15T16:42:53.209Z", "modified_date": "2024-06-12T17:04:28.231Z", - "file_name": "17-0010557a_IGO_08944_B_4_S85_R1_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0010557a_IGO_08944_B_4/17-0010557a_IGO_08944_B_4_S85_R1_001.fastq.gz", + "file_name": "00-0000004a_IGO_99991_B_4_S85_R1_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R1_001.fastq.gz", "file_type": 1, "size": 447094784, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$70dd62c2e3439bace690a965dce18bb99e0b82ff", - "request_id": "08944_B", - "samples": "[\"08944_B_4\"]", - "patient_id": "C-4LM16H", + "request_id": "99991_B", + "samples": "[\"99991_B_4\"]", + "patient_id": "C-PPPPP1", "available": true } }, @@ -877,15 +877,15 @@ "fields": { "created_date": "2021-03-15T16:42:54.252Z", "modified_date": "2024-06-12T17:04:28.248Z", - "file_name": "17-0010557a_IGO_08944_B_4_S85_R2_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0010557a_IGO_08944_B_4/17-0010557a_IGO_08944_B_4_S85_R2_001.fastq.gz", + "file_name": "00-0000004a_IGO_99991_B_4_S85_R2_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R2_001.fastq.gz", "file_type": 1, "size": 508780796, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$3c6c251afae505cecaffe29205a5d75cae45fd04", - "request_id": "08944_B", - "samples": "[\"08944_B_4\"]", - "patient_id": "C-4LM16H", + "request_id": "99991_B", + "samples": "[\"99991_B_4\"]", + "patient_id": "C-PPPPP1", "available": true } }, @@ -895,15 +895,15 @@ "fields": { "created_date": "2021-03-15T16:42:53.224Z", "modified_date": "2024-06-12T17:04:28.264Z", - "file_name": "17-0001535a_IGO_08944_B_2_S83_R2_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_17-0001535a_IGO_08944_B_2/17-0001535a_IGO_08944_B_2_S83_R2_001.fastq.gz", + "file_name": "00-0000003a_IGO_99991_B_2_S83_R2_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000003a_IGO_99991_B_2/00-0000003a_IGO_99991_B_2_S83_R2_001.fastq.gz", "file_type": 1, "size": 434118132, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$cea4a479dbbe8cb5bf7c304b7871fb8a25057019", - "request_id": "08944_B", - "samples": "[\"08944_B_2\"]", - "patient_id": "C-MP76JR", + "request_id": "99991_B", + "samples": "[\"99991_B_2\"]", + "patient_id": "C-PPPP10", "available": true } }, @@ -913,15 +913,15 @@ "fields": { "created_date": "2021-03-15T16:42:54.065Z", "modified_date": "2024-06-12T17:04:28.187Z", - "file_name": "LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R1_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG017_P1_17095a_R_43_IGO_08944_B_3/LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R1_001.fastq.gz", + "file_name": "XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R1_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R1_001.fastq.gz", "file_type": 1, "size": 952360556, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$e3b7d1ef35084d4f6e8e9e096d15ccfa33956f0e", - "request_id": "08944_B", - "samples": "[\"08944_B_3\"]", - "patient_id": "C-4LM16H", + "request_id": "99991_B", + "samples": "[\"99991_B_3\"]", + "patient_id": "C-PPPPP1", "available": true } }, @@ -931,15 +931,15 @@ "fields": { "created_date": "2021-03-15T16:42:55.535Z", "modified_date": "2024-06-12T17:04:28.204Z", - "file_name": "LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R2_001.fastq.gz", - "path": "/juno/archive/msk/cmo/FASTQ/PITT_0319_BH3MV7BBXY/Project_08944_B/Sample_LTG017_P1_17095a_R_43_IGO_08944_B_3/LTG017_P1_17095a_R_43_IGO_08944_B_3_S84_R2_001.fastq.gz", + "file_name": "XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R2_001.fastq.gz", + "path": "/juno/archive/msk/cmo/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R2_001.fastq.gz", "file_type": 1, "size": 1082701694, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a", "checksum": "sha1$3aba8adb1b77fd1b76533584588a67dcff63d6dd", - "request_id": "08944_B", - "samples": "[\"08944_B_3\"]", - "patient_id": "C-4LM16H", + "request_id": "99991_B", + "samples": "[\"99991_B_3\"]", + "patient_id": "C-PPPPP1", "available": true } } diff --git a/fixtures/tests/99991_B_new_request.json b/fixtures/tests/99991_B_new_request.json new file mode 100644 index 000000000..a642caf42 --- /dev/null +++ b/fixtures/tests/99991_B_new_request.json @@ -0,0 +1,368 @@ +{ + "smileRequestId": "7203e4e8-ab74-4928-b31f-5089908ab051", + "igoProjectId": "08944", + "igoRequestId": "99991_B", + "genePanel": "IMPACT468", + "projectManagerName": "Manager, Test", + "piEmail": "analyst11@example.org", + "labHeadName": "Lab Head B", + "labHeadEmail": "analyst11@example.org", + "investigatorName": "Investigator B", + "investigatorEmail": "analyst1@example.org", + "dataAnalystName": "Analyst A", + "dataAnalystEmail": "analyst9@example.org", + "otherContactEmails": "analyst9@example.org", + "dataAccessEmails": "", + "qcAccessEmails": ",pdxteam@example.org", + "strand": null, + "libraryType": null, + "isCmoRequest": true, + "bicAnalysis": true, + "requestJson": "{\"requestId\":\"99991_B\",\"projectId\":\"08944\",\"dataAccessEmails\":\"\",\"dataAnalystEmail\":\"analyst9@example.org\",\"dataAnalystName\":\"Analyst A\",\"investigatorEmail\":\"analyst1@example.org\",\"investigatorName\":\"Investigator B\",\"labHeadEmail\":\"analyst11@example.org\",\"labHeadName\":\"Lab Head B\",\"libraryType\":null,\"otherContactEmails\":\"analyst9@example.org\",\"piEmail\":\"analyst11@example.org\",\"projectManagerName\":\"Manager, Test\",\"qcAccessEmails\":\",pdxteam@example.org\",\"recipe\":\"IMPACT468\",\"strand\":null,\"deliveryDate\":null,\"bicAnalysis\":true,\"isCmoRequest\":true,\"samples\":[{\"igoId\":\"99991_B_3\",\"cmoPatientId\":\"C-PPPPP1\",\"cmoSampleName\":\"C-PPPPP1-X001-d\",\"sampleName\":\"XXX017_P1_12345a_R_43\",\"baitSet\":\"IMPACT468_BAITS\",\"cfDNA2dBarcode\":null,\"cmoInfoIgoId\":null,\"cmoSampleClass\":\"Primary\",\"collectionYear\":\"\",\"investigatorSampleId\":\"XXX017_P1_12345a_R_43\",\"oncoTreeCode\":\"SCLC\",\"preservation\":\"Frozen\",\"sampleOrigin\":\"Tissue\",\"sex\":\"M\",\"species\":\"Human\",\"specimenType\":\"PDX\",\"tissueLocation\":\"\",\"tubeId\":\"\",\"tumorOrNormal\":\"Tumor\",\"igoComplete\":true,\"qcReports\":[],\"libraries\":[{\"barcodeId\":null,\"barcodeIndex\":null,\"libraryIgoId\":\"99991_B_3_1_1_1\",\"libraryVolume\":35.0,\"libraryConcentrationNgul\":35.2,\"dnaInputNg\":null,\"captureConcentrationNm\":\"11.363636363636363\",\"captureInputNg\":\"400.0\",\"captureName\":\"Pool-99991_B-Tube7_1\",\"runs\":[{\"runMode\":\"HiSeq High Output\",\"runId\":\"SEQRUN_0005\",\"flowCellId\":\"FCELLAAAA1\",\"readLength\":\"\",\"runDate\":\"2019-02-11\",\"flowCellLanes\":[5],\"fastqs\":[\"/igo/delivery/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R1_001.fastq.gz\",\"/igo/delivery/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_XXX017_P1_12345a_R_43_IGO_99991_B_3/XXX017_P1_12345a_R_43_IGO_99991_B_3_S84_R2_001.fastq.gz\"]}]}],\"cmoSampleIdFields\":{\"naToExtract\":\"\",\"normalizedPatientId\":\"ALLAJV_HCISCLC017\",\"sampleType\":\"DNA\",\"recipe\":\"IMPACT468\"}},{\"igoId\":\"99991_B_4\",\"cmoPatientId\":\"C-PPPPP1\",\"cmoSampleName\":\"C-PPPPP1-N001-d\",\"sampleName\":\"00-0000004a\",\"baitSet\":\"IMPACT468_BAITS\",\"cfDNA2dBarcode\":null,\"cmoInfoIgoId\":null,\"cmoSampleClass\":\"Normal\",\"collectionYear\":\"\",\"investigatorSampleId\":\"00-0000004a\",\"oncoTreeCode\":null,\"preservation\":\"Frozen\",\"sampleOrigin\":\"Whole Blood\",\"sex\":\"M\",\"species\":\"Human\",\"specimenType\":\"Blood\",\"tissueLocation\":\"\",\"tubeId\":\"\",\"tumorOrNormal\":\"Normal\",\"igoComplete\":true,\"qcReports\":[],\"libraries\":[{\"barcodeId\":null,\"barcodeIndex\":null,\"libraryIgoId\":\"99991_B_4_1_1_1\",\"libraryVolume\":35.0,\"libraryConcentrationNgul\":34.1,\"dnaInputNg\":null,\"captureConcentrationNm\":\"4.9853372434017595\",\"captureInputNg\":\"170.0\",\"captureName\":\"Pool-99991_B-Tube7_1\",\"runs\":[{\"runMode\":\"HiSeq High Output\",\"runId\":\"SEQRUN_0005\",\"flowCellId\":\"FCELLAAAA1\",\"readLength\":\"\",\"runDate\":\"2019-02-11\",\"flowCellLanes\":[5],\"fastqs\":[\"/igo/delivery/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R1_001.fastq.gz\",\"/igo/delivery/FASTQ/SEQRUN_0005_BFCELLAAAA1/Project_99991_B/Sample_00-0000004a_IGO_99991_B_4/00-0000004a_IGO_99991_B_4_S85_R2_001.fastq.gz\"]}]}],\"cmoSampleIdFields\":{\"naToExtract\":\"\",\"normalizedPatientId\":\"ALLAJV_HCISCLC017\",\"sampleType\":\"DNA\",\"recipe\":\"IMPACT468\"}},{\"igoId\":\"99991_B_1\",\"cmoPatientId\":\"C-PPPP10\",\"cmoSampleName\":\"C-PPPP10-X001-d\",\"sampleName\":\"XXX002_P3_12345_L1\",\"baitSet\":\"IMPACT468_BAITS\",\"cfDNA2dBarcode\":null,\"cmoInfoIgoId\":null,\"cmoSampleClass\":\"Primary\",\"collectionYear\":\"\",\"investigatorSampleId\":\"XXX002_P3_12345_L1\",\"oncoTreeCode\":\"SCLC\",\"preservation\":\"Frozen\",\"sampleOrigin\":\"Tissue\",\"sex\":\"F\",\"species\":\"Human\",\"specimenType\":\"PDX\",\"tissueLocation\":\"\",\"tubeId\":\"\",\"tumorOrNormal\":\"Tumor\",\"igoComplete\":true,\"qcReports\":[],\"libraries\":[{\"barcodeId\":null,\"barcodeIndex\":null,\"libraryIgoId\":\"99991_B_1_1_1_1\",\"libraryVolume\":35.0,\"libraryConcentrationNgul\":34.8,\"dnaInputNg\":null,\"captureConcentrationNm\":\"11.49425287356322\",\"captureInputNg\":\"400.0\",\"captureName\":\"Pool-99991_B-Tube7_1\",\"runs\":[{\"runMode\":\"HiSeq 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"file_name": "SAMPLE-PDX-T_IGO_99992_C_1_S16_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_99992_C/Sample_SAMPLE-PDX-T_IGO_99992_C_1/SAMPLE-PDX-T_IGO_99992_C_1_S16_R2_001.fastq.gz", "file_type": 1, "size": 1513545923, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -96,8 +96,8 @@ "fields": { "created_date": "2019-11-30T16:40:13.992Z", "modified_date": "2020-01-09T16:49:14.302Z", - "file_name": "DS-puma-1708-T_IGO_05257_CB_1_S16_R2_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_05257_CB/Sample_DS-puma-1708-T_IGO_05257_CB_1/DS-puma-1708-T_IGO_05257_CB_1_S16_R2_001.fastq.gz", + "file_name": "SAMPLE-PDX-T_IGO_99992_C_1_S16_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_99992_C/Sample_SAMPLE-PDX-T_IGO_99992_C_1/SAMPLE-PDX-T_IGO_99992_C_1_S16_R2_001.fastq.gz", "file_type": 1, "size": 1513545923, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/fixtures/tests/05257_CB.filemetadata.json b/fixtures/tests/99992_C.filemetadata.json similarity index 57% rename from fixtures/tests/05257_CB.filemetadata.json rename to fixtures/tests/99992_C.filemetadata.json index 082248719..75cd3712c 100644 --- a/fixtures/tests/05257_CB.filemetadata.json +++ b/fixtures/tests/99992_C.filemetadata.json @@ -10,63 +10,63 @@ "latest": false, "metadata": { "sex": "F", - "igoId": "05257_CB_2", + "igoId": "99992_C_2", "baitSet": "IMPACT468_BAITS", "species": "Human", "libraries": { "runs": { - "runId": "JAX_0389", + "runId": "SEQRUN_0003", "runDate": "2019-11-25", "runMode": "HiSeq High Output", - "flowCellId": "HFJGCBBXY", + "flowCellId": "FCELLAAAA5", "readLength": "101/8/8/101", "flowCellLanes": [ 5 ] }, "barcodeId": "DUAL_IDT_LIB_287", - "captureName": "Pool-05257_CB-05604_V-10396-Tube1_1", + "captureName": "Pool-99992_C-99993_V-99994-Tube1_1", "barcodeIndex": "TCGTGGAT-GTCTAGGT", - "libraryIgoId": "05257_CB_2_1_1_1", + "libraryIgoId": 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"externalSampleId": "SAMPLE-PDX-N", + "investigatorName": "Test Investigator", "investigatorEmail": "email@internet.com", "projectManagerName": "", - "investigatorSampleId": "DS-puma-1708-N", + "investigatorSampleId": "SAMPLE-PDX-N", "captureConcentrationNm": "4.149377593360995", "libraryConcentrationNgul": 24.1 }, @@ -425,24 +425,24 @@ "metadata": { "R": "R2", "sex": "F", - "runId": "JAX_0389", + "runId": "SEQRUN_0003", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-11-25", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "05257_CB_1", + "primaryId": "99992_C_1", "barcodeId": "DUAL_IDT_LIB_275", "libraryIgoId": null, - "patientId": "C-A0D0WK", - "igoRequestId": "05257_CB", - "flowCellId": "HFJGCBBXY", + "patientId": "C-PPPPP5", + "igoRequestId": "99992_C", + "flowCellId": "FCELLAAAA5", "readLength": "101/8/8/101", - "sampleName": "C-A0D0WK-T001-d", - "captureName": "Pool-05257_CB-05604_V-10396-Tube1_1", + "sampleName": "C-PPPPP5-T001-d", + "captureName": "Pool-99992_C-99993_V-99994-Tube1_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": "TCCGAGTT-ACGGTCTT", "labHeadEmail": "email@internet.com", "oncotreeCode": "BREAST", @@ -454,12 +454,12 @@ ], "libraryVolume": 35.0, "pooledNormals": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R2_001.fastq.gz" ], "tumorOrNormal": "Tumor", "captureInputNg": "350.0", @@ -468,11 +468,11 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "DS-puma-1708-T", - "investigatorName": "John Smith", + "externalSampleId": "SAMPLE-PDX-T", + "investigatorName": "Test Investigator", "investigatorEmail": "email@internet.com", "projectManagerName": "", - "investigatorSampleId": "DS-puma-1708-T", + "investigatorSampleId": "SAMPLE-PDX-T", "captureConcentrationNm": "21.21212121212121", "libraryConcentrationNgul": 16.5 }, @@ -491,24 +491,24 @@ "metadata": { "R": "R2", "sex": "F", - "runId": "JAX_0389", + "runId": "SEQRUN_0003", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-11-25", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "05257_CB_2", + "primaryId": "99992_C_2", "barcodeId": "DUAL_IDT_LIB_287", "libraryIgoId": null, - "patientId": "C-A0D0WK", - "igoRequestId": "05257_CB", - "flowCellId": "HFJGCBBXY", + "patientId": "C-PPPPP5", + "igoRequestId": "99992_C", + "flowCellId": "FCELLAAAA5", "readLength": "101/8/8/101", - "sampleName": "C-A0D0WK-N001-d", - "captureName": "Pool-05257_CB-05604_V-10396-Tube1_1", + "sampleName": "C-PPPPP5-N001-d", + "captureName": "Pool-99992_C-99993_V-99994-Tube1_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": "TCGTGGAT-GTCTAGGT", "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -520,12 +520,12 @@ ], "libraryVolume": 35.0, "pooledNormals": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0389_AHFJGCBBXY/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S18_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S19_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0003_AFCELLAAAA5/Project_POOLEDNORMALS/Sample_MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC/MOUSEPOOLEDNORMAL_IGO_M-IMPACT_v1_TGCGTACC_S33_R2_001.fastq.gz" ], "tumorOrNormal": "Normal", "captureInputNg": "100.0", @@ -534,11 +534,11 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "DS-puma-1708-N", - "investigatorName": "John Smith", + "externalSampleId": "SAMPLE-PDX-N", + "investigatorName": "Test Investigator", "investigatorEmail": "email@internet.com", "projectManagerName": "", - "investigatorSampleId": "DS-puma-1708-N", + "investigatorSampleId": "SAMPLE-PDX-N", "captureConcentrationNm": "4.149377593360995", "libraryConcentrationNgul": 24.1 }, diff --git a/fixtures/tests/access_fastq_to_bam/10151_F.file.json b/fixtures/tests/access_fastq_to_bam/99996_F.file.json similarity index 100% rename from fixtures/tests/access_fastq_to_bam/10151_F.file.json rename to fixtures/tests/access_fastq_to_bam/99996_F.file.json diff --git a/fixtures/tests/access_fastq_to_bam/10151_F.filemetadata.json b/fixtures/tests/access_fastq_to_bam/99996_F.filemetadata.json similarity index 74% rename from fixtures/tests/access_fastq_to_bam/10151_F.filemetadata.json rename to fixtures/tests/access_fastq_to_bam/99996_F.filemetadata.json index 43fda59ac..cb0eef3f3 100644 --- a/fixtures/tests/access_fastq_to_bam/10151_F.filemetadata.json +++ b/fixtures/tests/access_fastq_to_bam/99996_F.filemetadata.json @@ -10,9 +10,9 @@ "version": 0, "metadata": { "barcodeId": "DUAL_IDT_LIB_255", - "cmoSampleName": "C-DRKHP7-M002-d", - "investigatorSampleId": "SK_MEL_1091A_T", - "cmoPatientId": "C-8VK0V7", + "cmoSampleName": "C-PPPPP7-M002-d", + "investigatorSampleId": "SAMPLE_T_001", + "cmoPatientId": "C-PPPPP3", "tumorOrNormal": "Normal", "sampleOrigin": "Plasma", "dnaInputNg": null, @@ -21,11 +21,11 @@ "sex": "F", "barcodeIndex": null, "libraryVolume": 35.0, - "captureName": "Pool-09483_R-10151_F-Tube7_1", + "captureName": "Pool-99998_R-99996_F-Tube7_1", "libraryConcentrationNgul": 10.6, "captureConcentrationNm": 10.377358490566039, - "primaryId": "10151_F_13", - "igoRequestId": "10151_F" + "primaryId": "99996_F_13", + "igoRequestId": "99996_F" }, "user": null } @@ -41,9 +41,9 @@ "latest": true, "metadata": { "barcodeId": "DUAL_IDT_LIB_255", - "cmoSampleName": "C-DRKHP7-M002-d", - "investigatorSampleId": "SK_MEL_1091A_T", - "cmoPatientId": "C-8VK0V7", + "cmoSampleName": "C-PPPPP7-M002-d", + "investigatorSampleId": "SAMPLE_T_001", + "cmoPatientId": "C-PPPPP3", "tumorOrNormal": "Normal", "sampleOrigin": "Plasma", "dnaInputNg": null, @@ -52,11 +52,11 @@ "sex": "F", "barcodeIndex": null, "libraryVolume": 35.0, - "captureName": "Pool-09483_R-10151_F-Tube7_1", + "captureName": "Pool-99998_R-99996_F-Tube7_1", "libraryConcentrationNgul": 10.6, "captureConcentrationNm": 10.377358490566039, - "primaryId": "10151_F_13", - "igoRequestId": "10151_F" + "primaryId": "99996_F_13", + "igoRequestId": "99996_F" }, "user": null } diff --git a/fixtures/tests/access_fastq_to_bam/10151_F.port.json b/fixtures/tests/access_fastq_to_bam/99996_F.port.json similarity index 100% rename from fixtures/tests/access_fastq_to_bam/10151_F.port.json rename to fixtures/tests/access_fastq_to_bam/99996_F.port.json diff --git a/fixtures/tests/access_fastq_to_bam/10151_F.run.json b/fixtures/tests/access_fastq_to_bam/99996_F.run.json similarity index 100% rename from fixtures/tests/access_fastq_to_bam/10151_F.run.json rename to fixtures/tests/access_fastq_to_bam/99996_F.run.json diff --git a/fixtures/tests/access_snv/files.json b/fixtures/tests/access_snv/files.json index 1f638dbff..2eabe34f1 100644 --- a/fixtures/tests/access_snv/files.json +++ b/fixtures/tests/access_snv/files.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", - "path": "/test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "file_name": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "path": "/test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", - "path": "/test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", + "file_name": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", + "path": "/test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -31,8 +31,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-000884-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", - "path": "/test/path/C-000884-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "file_name": "C-PPPP19-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "path": "/test/path/C-PPPP19-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -44,8 +44,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", - "path": "/test/path/C-000884-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", + "file_name": "C-PPPP19-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", + "path": "/test/path/C-PPPP19-L010-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -57,8 +57,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-L010-d.fastq.gz", - "path": "/test/path/C-000884-L010-d.fastq.gz", + "file_name": "C-PPPP19-L010-d.fastq.gz", + "path": "/test/path/C-PPPP19-L010-d.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -70,8 +70,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -83,8 +83,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", - "path": "/test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", + "file_name": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", + "path": "/test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -96,8 +96,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", - "path": "/test/path/C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", + "file_name": "C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", + "path": "/test/path/C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -109,8 +109,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/test/path/C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/test/path/C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -148,8 +148,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-L011-d.fastq.gz", - "path": "/test/path/JAR31-Buffy_IGO_10151_F_10_S21_R1_001.fastq.gz", + "file_name": "C-PPPP19-L011-d.fastq.gz", + "path": "/test/path/JAR31-Buffy_IGO_99996_F_10_S21_R1_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -200,8 +200,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-N004-d.fastq.gz", - "path": "/test/path/JAR31-Buffy_IGO_10151_F_11_S21_R1_001.fastq.gz", + "file_name": "C-PPPP19-N004-d.fastq.gz", + "path": "/test/path/JAR31-Buffy_IGO_99996_F_11_S21_R1_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -213,8 +213,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", - "path": "/test/path/C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", + "file_name": "C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", + "path": "/test/path/C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -226,8 +226,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", - "path": "/test/path/C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "file_name": "C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "path": "/test/path/C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/fixtures/tests/access_snv/files_metadata.json b/fixtures/tests/access_snv/files_metadata.json index 0cc9fba7f..82dd23865 100644 --- a/fixtures/tests/access_snv/files_metadata.json +++ b/fixtures/tests/access_snv/files_metadata.json @@ -115,9 +115,9 @@ "file": "2f77f3ac-ab25-4a02-90bd-86542401ac82", "version": 0, "metadata": { - "primaryId": "06302_AG_2", + "primaryId": "99907_AG_2", "cmoPatientId": "DONOR22-TP", - "igoRequestId": "06302_AB", + "igoRequestId": "99907_AB", "cmoSampleName": "DONOR22-TP", "genePanel": "-", "dataAnalystName": "-", @@ -146,9 +146,9 @@ "file": "2f77f3ac-ab25-4a02-90bd-86542401ac99", "version": 0, "metadata": { - "primaryId": "06302_AG_2", + "primaryId": "99907_AG_2", "cmoPatientId": "DONOR22-TP", - "igoRequestId": "06302_AB", + "igoRequestId": "99907_AB", "cmoSampleName": "DONOR22-TP", "genePanel": "-", "dataAnalystName": "-", @@ -177,11 +177,11 @@ "file": "2f77f3ac-ab25-4a02-90bd-86542401ac2d", "version": 0, "metadata": { - "primaryId": "06302_AB_1", - "cmoPatientId": "C-000884", - "cmoSampleName": "C-000884-L011-d", - "igoRequestId": "06302_AB", - "captureName": "Pool-06302_AH-D1_1", + "primaryId": "99907_AB_1", + "cmoPatientId": "C-PPPP19", + "cmoSampleName": "C-PPPP19-L011-d", + "igoRequestId": "99907_AB", + "captureName": "Pool-99997_AH-D1_1", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -212,7 +212,7 @@ "metadata": { "type": "T", "patient": { - "cmo": "000884", + "cmo": "PPPP19", "dmp": "P-0021500" }, "cmo_assay": "ACCESS_V1_0" @@ -232,7 +232,7 @@ "metadata": { "type": "T", "patient": { - "cmo": "000884", + "cmo": "PPPP19", "dmp": "P-0021500" }, "cmo_assay": "ACCESS_V1_0" @@ -252,7 +252,7 @@ "metadata": { "type": "N", "patient": { - "cmo": "000884", + "cmo": "PPPP19", "dmp": "P-0021500" }, "cmo_assay": "ACCESS_V1_0" @@ -270,11 +270,11 @@ "file": "2f77f3ac-ab25-4a02-90bd-86542401ac8e", "version": 0, "metadata": { - "primaryId": "06302_AB_2", - "cmoPatientId": "C-000884", - "cmoSampleName": "C-000884-N004-d", - "igoRequestId": "06302_AB", - "captureName": "Pool-06302_AH-D1_1", + "primaryId": "99907_AB_2", + "cmoPatientId": "C-PPPP19", + "cmoSampleName": "C-PPPP19-N004-d", + "igoRequestId": "99907_AB", + "captureName": "Pool-99997_AH-D1_1", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -329,11 +329,11 @@ "file": "2f77f3ac-ab25-4a02-90bd-86542401ac37", "version": 0, "metadata": { - "primaryId": "06302_AB_1", - "cmoPatientId": "C-000884", - "cmoSampleName": "C-000884-L010-d", - "igoRequestId": "06302_AB", - "captureName": "Pool-06302_AH-D1_1", + "primaryId": "99907_AB_1", + "cmoPatientId": "C-PPPP19", + "cmoSampleName": "C-PPPP19-L010-d", + "igoRequestId": "99907_AB", + "captureName": "Pool-99997_AH-D1_1", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", diff --git a/fixtures/tests/access_snv/ports.json b/fixtures/tests/access_snv/ports.json index adfc58a07..92aabad00 100644 --- a/fixtures/tests/access_snv/ports.json +++ b/fixtures/tests/access_snv/ports.json @@ -22,12 +22,12 @@ }], "value": [{ "file": { - "location": "juno:///test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", + "location": "juno:///test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-simplex.bam", "size": 7313069069, "class": "File" }, - "primaryId": "C-000884-L011-d", - "cmoPatientId": "C-000884", + "primaryId": "C-PPPP19-L011-d", + "cmoPatientId": "C-PPPP19", "tumorOrNormal": "Tumor" }], "files": [ @@ -60,18 +60,18 @@ "size": 8308038181, "class": "File", "nameext": ".bam", - "basename": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", + "basename": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", "checksum": "sha1$a39f15ee6ee1d35b7ea24a0431597f4279e152bb", - "location": "file:///juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/C-000884-L011-d/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", - "nameroot": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR", + "location": "file:///juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/C-PPPP19-L011-d/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR.bam", + "nameroot": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR", "secondaryFiles": [{ "size": 6151720, "class": "File", "nameext": ".bai", - "basename": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR.bai", + "basename": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR.bai", "checksum": "sha1$4d222b65996d1c0841333f75f942717fce96f7bd", - "location": "file:///juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/C-000884-L011-d/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR.bai", - "nameroot": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR"} + "location": "file:///juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/C-PPPP19-L011-d/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR.bai", + "nameroot": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR"} ]} ], "files": [ @@ -108,12 +108,12 @@ "value": [{ "file": { "class": "File", - "location": "juno:///test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", - "basename": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "location": "juno:///test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "basename": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", "size": 7313069069 }, - "primaryId": "C-000884-L011-d", - "cmoPatientId": "C-000884", + "primaryId": "C-PPPP19-L011-d", + "cmoPatientId": "C-PPPP19", "tumorOrNormal": "Tumor" }], "files": [ @@ -145,8 +145,8 @@ "value": [ { "class": "File", - "location": "juno:///test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", - "basename": "C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "location": "juno:///test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", + "basename": "C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam", "size": 7313069069 } ], @@ -184,11 +184,11 @@ "value": [{ "class": "File", "size": 7313069069, - "location": "juno:///test/path/C-000884-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" + "location": "juno:///test/path/C-PPPP19-L011-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" },{ "class": "File", "size": 7313069069, - "location": "juno:///test/path/C-000884-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" + "location": "juno:///test/path/C-PPPP19-N004-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" }], "files": [ "2f77f3ac-ab25-4a02-90bd-86542401acbb", @@ -212,8 +212,8 @@ ], "items": "string" }, - "db_value": ["C-000884"], - "value": ["C-000884"], + "db_value": ["C-PPPP19"], + "value": ["C-PPPP19"], "files": [] } }, @@ -233,8 +233,8 @@ ], "items": "string" }, - "db_value": ["C-000884-L011-d"], - "value": ["C-000884-L011-d"], + "db_value": ["C-PPPP19-L011-d"], + "value": ["C-PPPP19-L011-d"], "files": [] } }, diff --git a/fixtures/tests/access_snv/sv_bams/files.json b/fixtures/tests/access_snv/sv_bams/files.json index b9704a51e..3b149c0cd 100644 --- a/fixtures/tests/access_snv/sv_bams/files.json +++ b/fixtures/tests/access_snv/sv_bams/files.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-TU65EU-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-TU65EU-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP15-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPP15-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-MEL3YF-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-MEL3YF-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPPP9-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPPP9-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -31,8 +31,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-MEL3YF-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-MEL3YF-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPPP9-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPPP9-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -44,8 +44,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-P073CR-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-P073CR-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP13-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPP13-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -57,8 +57,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-P073CR-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-P073CR-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP13-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPP13-L004-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -70,8 +70,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-P073CR-L006-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-P073CR-L006-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP13-L006-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPP13-L006-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -83,8 +83,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-000884-L012-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-000884-L012-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP19-L012-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPP19-L012-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -96,8 +96,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-MEL3YF-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-MEL3YF-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPPP9-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPPP9-L003-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -109,8 +109,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-9FHC4R-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-9FHC4R-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPPP4-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPPP4-L002-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -122,8 +122,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-MEL3YF-L001-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-MEL3YF-L001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPPP9-L001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/juno/work/access/production/runs/Project_06302_AD/bam_qc/TDM/06302_AD_group_3-1.2.9/standard_bams/C-PPPPP9-L001-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/fixtures/tests/access_snv/sv_bams/files_metadata.json b/fixtures/tests/access_snv/sv_bams/files_metadata.json index 1bcbdf05c..1e1a76743 100644 --- a/fixtures/tests/access_snv/sv_bams/files_metadata.json +++ b/fixtures/tests/access_snv/sv_bams/files_metadata.json @@ -9,10 +9,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44aaa", "version": 0, "metadata": { - "primaryId": "C-TU65EU-L002-d", - "cmoPatientId": "C-TU65EU", + "primaryId": "C-PPPP15-L002-d", + "cmoPatientId": "C-PPPP15", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-TU65EU-L002-d", + "cmoSampleName": "C-PPPP15-L002-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -40,10 +40,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44abb", "version": 0, "metadata": { - "primaryId": "C-MEL3YF-L002-d", - "cmoPatientId": "C-MEL3YF", + "primaryId": "C-PPPPP9-L002-d", + "cmoPatientId": "C-PPPPP9", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-MEL3YF-L002-d", + "cmoSampleName": "C-PPPPP9-L002-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -71,10 +71,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44acc", "version": 0, "metadata": { - "primaryId": "C-MEL3YF-L004-d", - "cmoPatientId": "C-MEL3YF", + "primaryId": "C-PPPPP9-L004-d", + "cmoPatientId": "C-PPPPP9", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-MEL3YF-L004-d", + "cmoSampleName": "C-PPPPP9-L004-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -102,10 +102,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44add", "version": 0, "metadata": { - "primaryId": "C-P073CR-L003-d", - "cmoPatientId": "C-P073CR", + "primaryId": "C-PPPP13-L003-d", + "cmoPatientId": "C-PPPP13", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-P073CR-L003-d", + "cmoSampleName": "C-PPPP13-L003-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -133,10 +133,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44aee", "version": 0, "metadata": { - "primaryId": "C-P073CR-L004-d", - "cmoPatientId": "C-P073CR", + "primaryId": "C-PPPP13-L004-d", + "cmoPatientId": "C-PPPP13", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-P073CR-L004-d", + "cmoSampleName": "C-PPPP13-L004-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -164,10 +164,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44aff", "version": 0, "metadata": { - "primaryId": "C-P073CR-L006-d", - "cmoPatientId": "C-P073CR", + "primaryId": "C-PPPP13-L006-d", + "cmoPatientId": "C-PPPP13", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-P073CR-L006-d", + "cmoSampleName": "C-PPPP13-L006-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -195,10 +195,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44a11", "version": 0, "metadata": { - "primaryId": "C-000884-L012-d", - "cmoPatientId": "C-000884", + "primaryId": "C-PPPP19-L012-d", + "cmoPatientId": "C-PPPP19", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-000884-L012-d", + "cmoSampleName": "C-PPPP19-L012-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -226,10 +226,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44a22", "version": 0, "metadata": { - "primaryId": "C-MEL3YF-L003-d", - "cmoPatientId": "C-MEL3YF", + "primaryId": "C-PPPPP9-L003-d", + "cmoPatientId": "C-PPPPP9", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-MEL3YF-L003-d", + "cmoSampleName": "C-PPPPP9-L003-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -257,10 +257,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44a33", "version": 0, "metadata": { - "primaryId": "C-9FHC4R-L002-d", - "cmoPatientId": "C-9FHC4R", + "primaryId": "C-PPPPP4-L002-d", + "cmoPatientId": "C-PPPPP4", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-9FHC4R-L002-d", + "cmoSampleName": "C-PPPPP4-L002-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -288,10 +288,10 @@ "file": "fffff52a-0696-48d4-9ca5-6580daa44a44", "version": 0, "metadata": { - "primaryId": "C-MEL3YF-L001-d", - "cmoPatientId": "C-MEL3YF", + "primaryId": "C-PPPPP9-L001-d", + "cmoPatientId": "C-PPPPP9", "igoRequestId": "ACCESS_SV_TEST", - "cmoSampleName": "C-MEL3YF-L001-d", + "cmoSampleName": "C-PPPPP9-L001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", diff --git a/fixtures/tests/argos_non_pdx.inputs.json b/fixtures/tests/argos_non_pdx.inputs.json index 9be0a1b41..bf4f717f7 100644 --- a/fixtures/tests/argos_non_pdx.inputs.json +++ b/fixtures/tests/argos_non_pdx.inputs.json @@ -1,32 +1,32 @@ [ { "tumor": { - "ID": "s_C_V5AJEY_P001_d01", + "ID": "s_C_PPPP18_P001_d01", "CN": "MSKCC", - "LB": "16342_B_1", + "LB": "99909_B_1", "PL": "Illumina", "PU": [ - "HLYCVDSXC", - "HLYCVDSXC" + "FCELLAAAA9", + "FCELLAAAA9" ], "R1": [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L002_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L001_R1_001.fastq.gz" } ], "R2": [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L002_R2_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L001_R2_001.fastq.gz" } ], "zR1": [], @@ -34,19 +34,19 @@ "bam": [], "zBam": [], "RG_ID": [ - "s_C_V5AJEY_P001_d01_HLYCVDSXC", - "s_C_V5AJEY_P001_d01_HLYCVDSXC" + "s_C_PPPP18_P001_d01_FCELLAAAA9", + "s_C_PPPP18_P001_d01_FCELLAAAA9" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_V5AJEY_P001_d01.bam", - "request_id": "16342_B", + "bwa_output": "s_C_PPPP18_P001_d01.bam", + "request_id": "99909_B", "specimen_type": "Non-PDX" }, "normal": { - "ID": "s_C_V5AJEY_N901_dZ_IM7", + "ID": "s_C_PPPP18_N901_dZ_IM7", "CN": "MSKCC", - "LB": "C-V5AJEY-N901-dZ-IM7_1", + "LB": "C-PPPP18-N901-dZ-IM7_1", "PL": "Illumina", "PU": [ "DMP_FCID_DMP_BARCODEIDX" @@ -63,18 +63,18 @@ ], "zBam": [], "RG_ID": [ - "s_C_V5AJEY_N901_dZ_IM7_DMP_FCID_DMP_BARCODEIDX" + "s_C_PPPP18_N901_dZ_IM7_DMP_FCID_DMP_BARCODEIDX" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_V5AJEY_N901_dZ_IM7.bam", + "bwa_output": "s_C_PPPP18_N901_dZ_IM7.bam", "request_id": null, "specimen_type": "DMP" }, "assay": "IMPACT505_BAITS", - "pi": "Adam Schoenfeld", + "pi": "Lab Head D", "pi_email": "", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "curated_bams": [ { "class": "File", @@ -356,7 +356,7 @@ "num_threads": 10, "assay": "IMPACT505_BAITS", "tmp_dir": "/scratch", - "project_prefix": "16342_B", + "project_prefix": "99909_B", "opt_dup_pix_dist": "2500", "delly_type": [ "DUP", @@ -371,7 +371,7 @@ "complex_tn": 0.5, "scripts_bin": "/usr/bin", "gatk_jar_path": "/usr/bin/gatk.jar", - "pi": "Adam Schoenfeld", + "pi": "Lab Head D", "pi_email": "" } } diff --git a/fixtures/tests/argos_pdx.inputs.json b/fixtures/tests/argos_pdx.inputs.json index 7cafe2002..024ecf043 100644 --- a/fixtures/tests/argos_pdx.inputs.json +++ b/fixtures/tests/argos_pdx.inputs.json @@ -1,52 +1,52 @@ [ { "tumor": { - "ID": "s_C_V5AJEY_P001_d01", + "ID": "s_C_PPPP18_P001_d01", "CN": "MSKCC", - "LB": "16342_B_1", + "LB": "99909_B_1", "PL": "Illumina", "PU": [ - "HLYCVDSXC", - "HLYCVDSXC" + "FCELLAAAA9", + "FCELLAAAA9" ], "R1": [], "R2": [], "zR1": [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L002_R1_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R1_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L001_R1_001.fastq.gz" } ], "zR2": [ { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L002_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L002_R2_001.fastq.gz" }, { "class": "File", - "location": "juno:///igo/delivery/FASTQ/DIANA_0737_BHLYCVDSXC/Project_16342_B/Sample_MSK-OBX-023_IGO_16342_B_1/MSK-OBX-023_IGO_16342_B_1_S35_L001_R2_001.fastq.gz" + "location": "juno:///igo/delivery/FASTQ/SEQRUN_0002_BFCELLAAAA9/Project_99909_B/Sample_TEST-OBX-023_IGO_99909_B_1/TEST-OBX-023_IGO_99909_B_1_S35_L001_R2_001.fastq.gz" } ], "bam": [], "zBam": [], "RG_ID": [ - "s_C_V5AJEY_P001_d01_HLYCVDSXC", - "s_C_V5AJEY_P001_d01_HLYCVDSXC" + "s_C_PPPP18_P001_d01_FCELLAAAA9", + "s_C_PPPP18_P001_d01_FCELLAAAA9" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_V5AJEY_P001_d01.bam", - "request_id": "16342_B", + "bwa_output": "s_C_PPPP18_P001_d01.bam", + "request_id": "99909_B", "specimen_type": "PDX" }, "normal": { - "ID": "s_C_V5AJEY_N901_dZ_IM7", + "ID": "s_C_PPPP18_N901_dZ_IM7", "CN": "MSKCC", - "LB": "C-V5AJEY-N901-dZ-IM7_1", + "LB": "C-PPPP18-N901-dZ-IM7_1", "PL": "Illumina", "PU": [ "DMP_FCID_DMP_BARCODEIDX" @@ -63,18 +63,18 @@ } ], "RG_ID": [ - "s_C_V5AJEY_N901_dZ_IM7_DMP_FCID_DMP_BARCODEIDX" + "s_C_PPPP18_N901_dZ_IM7_DMP_FCID_DMP_BARCODEIDX" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_V5AJEY_N901_dZ_IM7.bam", + "bwa_output": "s_C_PPPP18_N901_dZ_IM7.bam", "request_id": null, "specimen_type": "DMP" }, "assay": "IMPACT505_BAITS", - "pi": "Adam Schoenfeld", + "pi": "Lab Head D", "pi_email": "", - "patient_id": "C-V5AJEY", + "patient_id": "C-PPPP18", "curated_bams": [ { "class": "File", @@ -356,7 +356,7 @@ "num_threads": 10, "assay": "IMPACT505_BAITS", "tmp_dir": "/scratch", - "project_prefix": "16342_B", + "project_prefix": "99909_B", "opt_dup_pix_dist": "2500", "delly_type": [ "DUP", @@ -371,7 +371,7 @@ "complex_tn": 0.5, "scripts_bin": "/usr/bin", "gatk_jar_path": "/usr/bin/gatk.jar", - "pi": "Adam Schoenfeld", + "pi": "Lab Head D", "pi_email": "" } } diff --git a/fixtures/tests/argos_pdx.json b/fixtures/tests/argos_pdx.json index 5631c9d6a..3ab66c088 100644 --- a/fixtures/tests/argos_pdx.json +++ b/fixtures/tests/argos_pdx.json @@ -31,7 +31,7 @@ "sample": "P-0112838-N01-IM7", "anon_id": "REDACTED", "patient": { - "cmo": "V5AJEY", + "cmo": "PPPP18", "dmp": "P-0000001" }, "updated": "2024-09-26 05:04:16.056479+00:00", @@ -40,7 +40,7 @@ "imported": "2024-09-26 05:04:16.056467+00:00", "cmo_assay": "IMPACT505", "tumor_type": null, - "external_id": "C-V5AJEY-N901-dZ-IM7", + "external_id": "C-PPPP18-N901-dZ-IM7", "sample_type": null, "tissue_type": null, "primary_site": null, diff --git a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json index 41a0b9233..e67c12f02 100644 --- a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json +++ b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.json @@ -5,7 +5,7 @@ "fields": { "created_date": "2019-12-11T22:53:02.012Z", "modified_date": "2020-01-14T23:03:35.530Z", - "name": "ARGOS 09670_D, 22 of 54 (12/11/2019, 22:53:02)", + "name": "ARGOS 99906_D, 22 of 54 (12/11/2019, 22:53:02)", "app": "cb5d793b-e650-4b7d-bfcd-882858e29cc5", "status": 4, "execution_id": "df43cc77-bed4-4233-9817-6d12e25d9e1c", @@ -14,7 +14,7 @@ "assay": "IDT_Exome_v1_FP_b37" }, "tags": { - "igoRequestId": "09670_D" + "igoRequestId": "99906_D" }, "notify_for_outputs": "[\"qc_pdf\"]" } @@ -1156,7 +1156,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1219,7 +1219,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1245,11 +1245,11 @@ "db_value": [ { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { @@ -1267,19 +1267,19 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { @@ -1297,32 +1297,32 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" } ], "value": [ { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R1_001.fastq.gz", "size": 5966546453, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R2_001.fastq.gz", "size": 5832468368, "class": "File" } @@ -1331,30 +1331,30 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R1_001.fastq.gz", "size": 3576965127, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", "size": 3592299152, "class": "File" } @@ -1363,11 +1363,11 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" } ], "files": [ @@ -1399,19 +1399,19 @@ "size": 65612975, "class": "File", "nameext": ".vcf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "checksum": 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"nameroot": "s_C_K2902H_P001_d.rg.md.abra.printreads" + "nameroot": "s_C_PPPPP8_P001_d.rg.md.abra.printreads" } ] }, @@ -1502,19 +1502,19 @@ "size": 14961505727, "class": "File", "nameext": ".bam", - "basename": "s_C_K2902H_N001_d.rg.md.abra.printreads.bam", + "basename": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.bam", "checksum": "sha1$45f52cc5db96a9d90784ddcee324cedbe1ac5618", "location": "bid://f6d0fd8d-cae6-469d-ab57-f22ab55178c9", - "nameroot": "s_C_K2902H_N001_d.rg.md.abra.printreads", + "nameroot": "s_C_PPPPP8_N001_d.rg.md.abra.printreads", "secondaryFiles": [ { "size": 6010352, "class": "File", "nameext": ".bai", - "basename": "s_C_K2902H_N001_d.rg.md.abra.printreads.bai", + "basename": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.bai", "checksum": "sha1$67a9aff1f1cd7be0240b7fefe740f7852dee4933", "location": "bid://12ffa7a4-b853-452d-8076-fde5bac09aec", - "nameroot": "s_C_K2902H_N001_d.rg.md.abra.printreads" + "nameroot": "s_C_PPPPP8_N001_d.rg.md.abra.printreads" } ] } @@ -1524,19 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"P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", "file_type": 1, "size": 3592299152, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -5146,25 +5146,25 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "PITT_0390", + "runId": "SEQRUN_0006", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-15", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_1", + "primaryId": "99906_D_1", "barcodeId": "IDT366", "libraryIgoId": null, - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7HCTBBXY", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA3", "readLength": "101/8/101", - "sampleName": "C-K2902H-P001-d", + "sampleName": "C-PPPPP8-P001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5188,15 +5188,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5213,25 +5213,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0390", + "runId": "SEQRUN_0006", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-15", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_1", + "primaryId": "99906_D_1", "barcodeId": "IDT366", - "libraryIgoId": "09670_D_1_1_1_1_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7HCTBBXY", + "libraryIgoId": "99906_D_1_1_1_1_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA3", "readLength": "101/8/101", - "sampleName": "C-K2902H-P001-d", + "sampleName": "C-PPPPP8-P001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5255,15 +5255,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5280,25 +5280,25 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5320,15 +5320,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5345,25 +5345,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, - "libraryIgoId": "09670_D_46_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "libraryIgoId": "99906_D_46_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5385,15 +5385,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5405,8 +5405,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.368Z", "modified_date": "2019-12-14T12:08:14.368Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "file_type": 11, "size": 65612975, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5418,8 +5418,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.539Z", "modified_date": "2019-12-14T12:08:13.539Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", "file_type": 24, "size": 181310718, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5431,8 +5431,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.575Z", "modified_date": "2019-12-14T12:08:13.575Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.bam", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.bam", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bam", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.bam", "file_type": 3, "size": 22899967017, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5444,8 +5444,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.614Z", "modified_date": "2019-12-14T12:08:13.614Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.bam", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.bam", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.bam", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.bam", "file_type": 3, "size": 14961505727, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5457,8 +5457,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.658Z", "modified_date": "2019-12-14T12:08:13.658Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2641, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5470,8 +5470,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.676Z", "modified_date": "2019-12-14T12:08:13.676Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2611, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5483,8 +5483,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.695Z", "modified_date": "2019-12-14T12:08:13.695Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", "file_type": 21, "size": 2576, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5496,8 +5496,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.713Z", "modified_date": "2019-12-14T12:08:13.713Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2764, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5509,8 +5509,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.731Z", "modified_date": "2019-12-14T12:08:13.731Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2714, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5522,8 +5522,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.754Z", "modified_date": "2019-12-14T12:08:13.754Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2818, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5535,8 +5535,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.778Z", "modified_date": "2019-12-14T12:08:13.778Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2815, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5548,8 +5548,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.803Z", "modified_date": "2019-12-14T12:08:13.803Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", "file_type": 21, "size": 2775, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5561,8 +5561,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.820Z", "modified_date": "2019-12-14T12:08:13.820Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2873, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5574,8 +5574,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.836Z", "modified_date": "2019-12-14T12:08:13.836Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2826, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5587,8 +5587,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.858Z", "modified_date": "2019-12-14T12:08:13.858Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", "file_type": 24, "size": 59073, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5600,8 +5600,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.880Z", "modified_date": "2019-12-14T12:08:13.880Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8189, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5613,8 +5613,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.896Z", "modified_date": "2019-12-14T12:08:13.896Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8219, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5626,8 +5626,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.930Z", "modified_date": "2019-12-14T12:08:13.930Z", - "file_name": "s_C_K2902H_P001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.asmetrics", "file_type": 21, "size": 2171, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5639,8 +5639,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.947Z", "modified_date": "2019-12-14T12:08:13.947Z", - "file_name": "s_C_K2902H_N001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.asmetrics", "file_type": 21, "size": 2134, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5652,8 +5652,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.969Z", "modified_date": "2019-12-14T12:08:13.969Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", "file_type": 21, "size": 603, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5665,8 +5665,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.986Z", "modified_date": "2019-12-14T12:08:13.986Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", "file_type": 21, "size": 602, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5678,8 +5678,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.009Z", "modified_date": "2019-12-14T12:08:14.009Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", "file_type": 21, "size": 124853, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5691,8 +5691,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.027Z", "modified_date": "2019-12-14T12:08:14.027Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", "file_type": 21, "size": 111084, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5704,8 +5704,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.050Z", "modified_date": "2019-12-14T12:08:14.050Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", "file_type": 21, "size": 4777, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5717,8 +5717,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.068Z", "modified_date": "2019-12-14T12:08:14.068Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", "file_type": 21, "size": 3222, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5730,8 +5730,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.092Z", "modified_date": "2019-12-14T12:08:14.092Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6784, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5743,8 +5743,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.108Z", "modified_date": "2019-12-14T12:08:14.108Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6794, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5756,8 +5756,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.131Z", "modified_date": "2019-12-14T12:08:14.131Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hsmetrics", "file_type": 21, "size": 5016, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5769,8 +5769,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.147Z", "modified_date": "2019-12-14T12:08:14.147Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hsmetrics", "file_type": 21, "size": 5029, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5782,8 +5782,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.168Z", "modified_date": "2019-12-14T12:08:14.168Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 13994, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5795,8 +5795,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.183Z", "modified_date": "2019-12-14T12:08:14.183Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 12712, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5808,8 +5808,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.203Z", "modified_date": "2019-12-14T12:08:14.203Z", - "file_name": "s_C_K2902H_P001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_metrics", "file_type": 21, "size": 2900, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5821,8 +5821,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.219Z", "modified_date": "2019-12-14T12:08:14.219Z", - "file_name": "s_C_K2902H_N001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_metrics", "file_type": 21, "size": 2866, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5834,8 +5834,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.242Z", "modified_date": "2019-12-14T12:08:14.242Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", "file_type": 11, "size": 24213327, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5847,8 +5847,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.263Z", "modified_date": "2019-12-14T12:08:14.263Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", "file_type": 21, "size": 13440159, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5860,8 +5860,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.302Z", "modified_date": "2019-12-14T12:08:14.302Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", "file_type": 11, "size": 19739, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5873,8 +5873,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.324Z", "modified_date": "2019-12-14T12:08:14.324Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", "file_type": 10, "size": 5795, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5886,8 +5886,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.346Z", "modified_date": "2019-12-14T12:08:14.346Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", "file_type": 11, "size": 403491742, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5899,8 +5899,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.390Z", "modified_date": "2019-12-14T12:08:14.390Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", "file_type": 21, "size": 8622126, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5912,8 +5912,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.406Z", "modified_date": "2019-12-14T12:08:14.406Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", "file_type": 21, "size": 8618530, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5925,8 +5925,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.428Z", "modified_date": "2019-12-14T12:08:14.428Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5494, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5938,8 +5938,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.445Z", "modified_date": "2019-12-14T12:08:14.445Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5508, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5951,8 +5951,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.466Z", "modified_date": "2019-12-14T12:08:14.466Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", "file_type": 21, "size": 32693698, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5964,8 +5964,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.488Z", "modified_date": "2019-12-14T12:08:14.488Z", - "file_name": "s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13779990, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5977,8 +5977,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.504Z", "modified_date": "2019-12-14T12:08:14.504Z", - "file_name": "s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13586169, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5990,8 +5990,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.527Z", "modified_date": "2019-12-14T12:08:14.527Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6648, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6003,8 +6003,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.544Z", "modified_date": "2019-12-14T12:08:14.544Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6632, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6016,8 +6016,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.574Z", "modified_date": "2019-12-14T12:08:14.575Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1201, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6029,8 +6029,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.593Z", "modified_date": "2019-12-14T12:08:14.593Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1199, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6042,8 +6042,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.616Z", "modified_date": "2019-12-14T12:08:14.616Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics", "file_type": 21, "size": 7754, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6055,8 +6055,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.635Z", "modified_date": "2019-12-14T12:08:14.635Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics", "file_type": 21, "size": 7041, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6068,8 +6068,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.658Z", "modified_date": "2019-12-14T12:08:14.658Z", - "file_name": "s_C_K2902H_P001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_P001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.pileup", "file_type": 21, "size": 55203868, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6081,8 +6081,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.675Z", "modified_date": "2019-12-14T12:08:14.675Z", - "file_name": "s_C_K2902H_N001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_N001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.pileup", "file_type": 21, "size": 33915095, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6094,8 +6094,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.697Z", "modified_date": "2019-12-14T12:08:14.697Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", "file_type": 21, "size": 129554, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6107,8 +6107,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.738Z", "modified_date": "2019-12-14T12:08:14.738Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", "file_type": 10, "size": 172715192, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6120,8 +6120,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.762Z", "modified_date": "2019-12-14T12:08:14.762Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", "file_type": 21, "size": 13247144, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6133,8 +6133,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.800Z", "modified_date": "2019-12-14T12:08:14.800Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", "file_type": 10, "size": 11388, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6146,8 +6146,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.822Z", "modified_date": "2019-12-14T12:08:14.822Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", "file_type": 10, "size": 7525, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6159,8 +6159,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.844Z", "modified_date": "2019-12-14T12:08:14.844Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hstmetrics", "file_type": 21, "size": 19302184, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6172,8 +6172,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.860Z", "modified_date": "2019-12-14T12:08:14.860Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hstmetrics", "file_type": 21, "size": 19114455, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6185,8 +6185,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.883Z", "modified_date": "2019-12-14T12:08:14.883Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", "file_type": 11, "size": 2741838, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" diff --git a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_bed.json b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_bed.json index 83702d30f..93988d7fb 100644 --- a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_bed.json +++ b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_bed.json @@ -5,7 +5,7 @@ "fields": { "created_date": "2019-12-11T22:53:02.012Z", "modified_date": "2020-01-14T23:03:35.530Z", - "name": "ARGOS 09670_D, 22 of 54 (12/11/2019, 22:53:02)", + "name": "ARGOS 99906_D, 22 of 54 (12/11/2019, 22:53:02)", "app": "cb5d793b-e650-4b7d-bfcd-882858e29cc5", "status": 4, "execution_id": "df43cc77-bed4-4233-9817-6d12e25d9e1c", @@ -14,7 +14,7 @@ "assay": "IDT_Exome_v1_FP_b37" }, "tags": { - "igoRequestId": "09670_D" + "igoRequestId": "99906_D" }, "notify_for_outputs": "[\"qc_pdf\"]" } @@ -1156,7 +1156,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1219,7 +1219,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1244,11 +1244,11 @@ "secondary_files": [], "db_value": { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { @@ -1266,30 +1266,30 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, "value": { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R1_001.fastq.gz", "size": 5966546453, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R2_001.fastq.gz", "size": 5832468368, "class": "File" } @@ -1298,11 +1298,11 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, "files": [ "02cfb077-f61c-4659-9877-752c456e8f80", @@ -1326,11 +1326,11 @@ "secondary_files": [], "db_value": { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { @@ -1348,30 +1348,30 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" }, "value": { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R1_001.fastq.gz", "size": 3576965127, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", "size": 3592299152, "class": "File" } @@ -1380,11 +1380,11 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" }, "files": [ "47be3848-e16b-4126-9e64-1d3f5a67b927", @@ -1413,19 +1413,19 @@ "size": 65612975, "class": "File", "nameext": ".vcf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "checksum": "sha1$0201d57f5fd370615df7ce8b78f49ae512692e0e", "location": "bid://b835c33c-d241-42fc-beb2-e1ce1c41a77d", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants" + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants" }, "value": { "size": 65612975, "class": "File", "nameext": ".vcf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "checksum": "sha1$0201d57f5fd370615df7ce8b78f49ae512692e0e", - "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants" + "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", + "nameroot": 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+ "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts" }, "files": [ "f9f55509-fcae-45f7-bdd2-72aebb59178e" @@ -1496,19 +1496,19 @@ "size": 22899967017, "class": "File", "nameext": ".bam", - "basename": "s_C_K2902H_P001_d.rg.md.abra.printreads.bam", + "basename": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bam", "checksum": "sha1$d67cf2c24cacfeaa222893c5d4303aed55556457", "location": "bid://e528ce76-0c6f-4088-8e22-38ece693bcdd", - "nameroot": "s_C_K2902H_P001_d.rg.md.abra.printreads", + "nameroot": "s_C_PPPPP8_P001_d.rg.md.abra.printreads", "secondaryFiles": [ { "size": 6252264, "class": "File", "nameext": ".bai", - "basename": "s_C_K2902H_P001_d.rg.md.abra.printreads.bai", + "basename": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bai", "checksum": "sha1$776fc843bcdbd215452e611f03d7d9b42ad05a09", "location": 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"captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5271,15 +5271,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5296,25 +5296,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0390", + "runId": "SEQRUN_0006", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-15", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_1", + "primaryId": "99906_D_1", "barcodeId": "IDT366", - "libraryIgoId": "09670_D_1_1_1_1_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7HCTBBXY", + "libraryIgoId": "99906_D_1_1_1_1_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA3", "readLength": "101/8/101", - "sampleName": "C-K2902H-P001-d", + "sampleName": "C-PPPPP8-P001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5338,15 +5338,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5363,25 +5363,25 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5403,15 +5403,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5428,25 +5428,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, - "libraryIgoId": "09670_D_46_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "libraryIgoId": "99906_D_46_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5468,15 +5468,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5488,8 +5488,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.368Z", "modified_date": "2019-12-14T12:08:14.368Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "file_type": 11, "size": 65612975, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5501,8 +5501,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.539Z", "modified_date": "2019-12-14T12:08:13.539Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", "file_type": 24, "size": 181310718, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5514,8 +5514,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.575Z", "modified_date": "2019-12-14T12:08:13.575Z", - "file_name": 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14961505727, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5540,8 +5540,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.658Z", "modified_date": "2019-12-14T12:08:13.658Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2641, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5553,8 +5553,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.676Z", "modified_date": "2019-12-14T12:08:13.676Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2611, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5566,8 +5566,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.695Z", "modified_date": "2019-12-14T12:08:13.695Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", "file_type": 21, "size": 2576, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5579,8 +5579,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.713Z", "modified_date": "2019-12-14T12:08:13.713Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2764, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5592,8 +5592,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.731Z", "modified_date": "2019-12-14T12:08:13.731Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2714, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5605,8 +5605,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.754Z", "modified_date": "2019-12-14T12:08:13.754Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2818, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5618,8 +5618,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.778Z", "modified_date": "2019-12-14T12:08:13.778Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2815, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5631,8 +5631,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.803Z", "modified_date": "2019-12-14T12:08:13.803Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", "file_type": 21, "size": 2775, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5644,8 +5644,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.820Z", "modified_date": "2019-12-14T12:08:13.820Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2873, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5657,8 +5657,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.836Z", "modified_date": "2019-12-14T12:08:13.836Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2826, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5670,8 +5670,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.858Z", "modified_date": "2019-12-14T12:08:13.858Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", "file_type": 24, "size": 59073, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5683,8 +5683,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.880Z", "modified_date": "2019-12-14T12:08:13.880Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8189, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5696,8 +5696,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.896Z", "modified_date": "2019-12-14T12:08:13.896Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8219, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5709,8 +5709,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.930Z", "modified_date": "2019-12-14T12:08:13.930Z", - "file_name": "s_C_K2902H_P001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.asmetrics", "file_type": 21, "size": 2171, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5722,8 +5722,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.947Z", "modified_date": "2019-12-14T12:08:13.947Z", - "file_name": "s_C_K2902H_N001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.asmetrics", "file_type": 21, "size": 2134, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5735,8 +5735,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.969Z", "modified_date": "2019-12-14T12:08:13.969Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", "file_type": 21, "size": 603, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5748,8 +5748,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.986Z", "modified_date": "2019-12-14T12:08:13.986Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", "file_type": 21, "size": 602, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5761,8 +5761,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.009Z", "modified_date": "2019-12-14T12:08:14.009Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", "file_type": 21, "size": 124853, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5774,8 +5774,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.009Z", "modified_date": "2019-12-14T12:08:14.009Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.bed", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.bed", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.bed", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.bed", "file_type": 4, "size": 124853, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5787,8 +5787,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.027Z", "modified_date": "2019-12-14T12:08:14.027Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", "file_type": 21, "size": 111084, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5800,8 +5800,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.050Z", "modified_date": "2019-12-14T12:08:14.050Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", "file_type": 21, "size": 4777, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5813,8 +5813,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.068Z", "modified_date": "2019-12-14T12:08:14.068Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", "file_type": 21, "size": 3222, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5826,8 +5826,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.092Z", "modified_date": "2019-12-14T12:08:14.092Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6784, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5839,8 +5839,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.108Z", "modified_date": "2019-12-14T12:08:14.108Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6794, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5852,8 +5852,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.131Z", "modified_date": "2019-12-14T12:08:14.131Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hsmetrics", "file_type": 21, "size": 5016, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5865,8 +5865,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.147Z", "modified_date": "2019-12-14T12:08:14.147Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hsmetrics", "file_type": 21, "size": 5029, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5878,8 +5878,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.168Z", "modified_date": "2019-12-14T12:08:14.168Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 13994, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5891,8 +5891,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.183Z", "modified_date": "2019-12-14T12:08:14.183Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 12712, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5904,8 +5904,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.203Z", "modified_date": "2019-12-14T12:08:14.203Z", - "file_name": "s_C_K2902H_P001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_metrics", "file_type": 21, "size": 2900, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5917,8 +5917,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.219Z", "modified_date": "2019-12-14T12:08:14.219Z", - "file_name": "s_C_K2902H_N001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_metrics", "file_type": 21, "size": 2866, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5930,8 +5930,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.242Z", "modified_date": "2019-12-14T12:08:14.242Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", "file_type": 11, "size": 24213327, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5943,8 +5943,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.263Z", "modified_date": "2019-12-14T12:08:14.263Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", "file_type": 21, "size": 13440159, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5956,8 +5956,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.302Z", "modified_date": "2019-12-14T12:08:14.302Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", "file_type": 11, "size": 19739, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5969,8 +5969,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.324Z", "modified_date": "2019-12-14T12:08:14.324Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", "file_type": 10, "size": 5795, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5982,8 +5982,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.346Z", "modified_date": "2019-12-14T12:08:14.346Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", "file_type": 11, "size": 403491742, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5995,8 +5995,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.390Z", "modified_date": "2019-12-14T12:08:14.390Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", "file_type": 21, "size": 8622126, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6008,8 +6008,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.406Z", "modified_date": "2019-12-14T12:08:14.406Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", "file_type": 21, "size": 8618530, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6021,8 +6021,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.428Z", "modified_date": "2019-12-14T12:08:14.428Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5494, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6034,8 +6034,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.445Z", "modified_date": "2019-12-14T12:08:14.445Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5508, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6047,8 +6047,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.466Z", "modified_date": "2019-12-14T12:08:14.466Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", "file_type": 21, "size": 32693698, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6060,8 +6060,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.488Z", "modified_date": "2019-12-14T12:08:14.488Z", - "file_name": "s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13779990, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6073,8 +6073,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.504Z", "modified_date": "2019-12-14T12:08:14.504Z", - "file_name": "s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13586169, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6086,8 +6086,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.527Z", "modified_date": "2019-12-14T12:08:14.527Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6648, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6099,8 +6099,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.544Z", "modified_date": "2019-12-14T12:08:14.544Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6632, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6112,8 +6112,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.574Z", "modified_date": "2019-12-14T12:08:14.575Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1201, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6125,8 +6125,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.593Z", "modified_date": "2019-12-14T12:08:14.593Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1199, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6138,8 +6138,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.616Z", "modified_date": "2019-12-14T12:08:14.616Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics", "file_type": 21, "size": 7754, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6151,8 +6151,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.635Z", "modified_date": "2019-12-14T12:08:14.635Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics", "file_type": 21, "size": 7041, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6164,8 +6164,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.658Z", "modified_date": "2019-12-14T12:08:14.658Z", - "file_name": "s_C_K2902H_P001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_P001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.pileup", "file_type": 21, "size": 55203868, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6177,8 +6177,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.675Z", "modified_date": "2019-12-14T12:08:14.675Z", - "file_name": "s_C_K2902H_N001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_N001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.pileup", "file_type": 21, "size": 33915095, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6190,8 +6190,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.697Z", "modified_date": "2019-12-14T12:08:14.697Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", "file_type": 21, "size": 129554, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6203,8 +6203,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.738Z", "modified_date": "2019-12-14T12:08:14.738Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", "file_type": 10, "size": 172715192, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6216,8 +6216,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.762Z", "modified_date": "2019-12-14T12:08:14.762Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", "file_type": 21, "size": 13247144, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6229,8 +6229,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.800Z", "modified_date": "2019-12-14T12:08:14.800Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", "file_type": 10, "size": 11388, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6242,8 +6242,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.822Z", "modified_date": "2019-12-14T12:08:14.822Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", "file_type": 10, "size": 7525, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6255,8 +6255,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.844Z", "modified_date": "2019-12-14T12:08:14.844Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hstmetrics", "file_type": 21, "size": 19302184, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6268,8 +6268,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.860Z", "modified_date": "2019-12-14T12:08:14.860Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hstmetrics", "file_type": 21, "size": 19114455, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6281,8 +6281,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.883Z", "modified_date": "2019-12-14T12:08:14.883Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", "file_type": 11, "size": 2741838, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" diff --git a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_disambiguate.json b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_disambiguate.json index 1894877b2..a5d80faf0 100644 --- a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_disambiguate.json +++ b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.with_disambiguate.json @@ -5,7 +5,7 @@ "fields": { "created_date": "2019-12-11T22:53:02.012Z", "modified_date": "2020-01-14T23:03:35.530Z", - "name": "ARGOS 09670_D, 22 of 54 (12/11/2019, 22:53:02)", + "name": "ARGOS 99906_D, 22 of 54 (12/11/2019, 22:53:02)", "app": "cb5d793b-e650-4b7d-bfcd-882858e29cc5", "status": 4, "execution_id": "df43cc77-bed4-4233-9817-6d12e25d9e1c", @@ -14,7 +14,7 @@ "assay": "IDT_Exome_v1_FP_b37" }, "tags": { - "igoRequestId": "09670_D" + "igoRequestId": "99906_D" }, "notify_for_outputs": "[\"qc_pdf\"]" } @@ -1156,7 +1156,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1219,7 +1219,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1244,11 +1244,11 @@ "secondary_files": [], "db_value": { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { @@ -1266,30 +1266,30 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, "value": { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R1_001.fastq.gz", "size": 5966546453, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R2_001.fastq.gz", "size": 5832468368, "class": "File" } @@ -1298,11 +1298,11 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, "files": [ "02cfb077-f61c-4659-9877-752c456e8f80", @@ -1326,11 +1326,11 @@ "secondary_files": [], "db_value": { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { @@ -1348,30 +1348,30 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" }, "value": { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R1_001.fastq.gz", "size": 3576965127, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", "size": 3592299152, "class": "File" } @@ -1380,11 +1380,11 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" }, "files": [ "47be3848-e16b-4126-9e64-1d3f5a67b927", @@ -1413,19 +1413,19 @@ "size": 65612975, "class": "File", "nameext": ".vcf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "checksum": "sha1$0201d57f5fd370615df7ce8b78f49ae512692e0e", "location": "bid://b835c33c-d241-42fc-beb2-e1ce1c41a77d", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants" + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants" }, "value": { "size": 65612975, "class": "File", "nameext": ".vcf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "checksum": "sha1$0201d57f5fd370615df7ce8b78f49ae512692e0e", - "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants" + "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants" }, "files": [ "b835c33c-d241-42fc-beb2-e1ce1c41a77d" @@ -1453,19 +1453,19 @@ "size": 181310718, "class": "File", "nameext": ".maf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", "checksum": "sha1$15db27138a1586bf4f017b572154875c5ff129db", "location": "bid://f9f55509-fcae-45f7-bdd2-72aebb59178e", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts" + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts" }, "value": { "size": 181310718, "class": "File", "nameext": ".maf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", "checksum": "sha1$15db27138a1586bf4f017b572154875c5ff129db", - "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts" + "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts" }, "files": [ "f9f55509-fcae-45f7-bdd2-72aebb59178e" @@ -1496,19 +1496,19 @@ "size": 22899967017, "class": "File", "nameext": ".bam", - "basename": "s_C_K2902H_P001_d.rg.md.abra.printreads.bam", + "basename": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bam", "checksum": "sha1$d67cf2c24cacfeaa222893c5d4303aed55556457", "location": "bid://e528ce76-0c6f-4088-8e22-38ece693bcdd", - "nameroot": "s_C_K2902H_P001_d.rg.md.abra.printreads", + "nameroot": "s_C_PPPPP8_P001_d.rg.md.abra.printreads", "secondaryFiles": [ { "size": 6252264, "class": "File", "nameext": ".bai", - "basename": "s_C_K2902H_P001_d.rg.md.abra.printreads.bai", + "basename": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bai", "checksum": "sha1$776fc843bcdbd215452e611f03d7d9b42ad05a09", "location": "bid://a0184edc-0a1c-40e7-9d41-69dda2e1e23e", - "nameroot": "s_C_K2902H_P001_d.rg.md.abra.printreads" + "nameroot": "s_C_PPPPP8_P001_d.rg.md.abra.printreads" } ] }, @@ -1516,19 +1516,19 @@ "size": 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"P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", "file_type": 1, "size": 3592299152, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -5370,25 +5370,25 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "PITT_0390", + "runId": "SEQRUN_0006", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-15", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_1", + "primaryId": "99906_D_1", "barcodeId": "IDT366", "libraryIgoId": null, - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7HCTBBXY", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA3", "readLength": "101/8/101", - "sampleName": "C-K2902H-P001-d", + "sampleName": "C-PPPPP8-P001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5412,15 +5412,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5437,25 +5437,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0390", + "runId": "SEQRUN_0006", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-15", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_1", + "primaryId": "99906_D_1", "barcodeId": "IDT366", - "libraryIgoId": "09670_D_1_1_1_1_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7HCTBBXY", + "libraryIgoId": "99906_D_1_1_1_1_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA3", "readLength": "101/8/101", - "sampleName": "C-K2902H-P001-d", + "sampleName": "C-PPPPP8-P001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5479,15 +5479,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5504,25 +5504,25 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5544,15 +5544,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5569,25 +5569,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, - "libraryIgoId": "09670_D_46_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "libraryIgoId": "99906_D_46_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5609,15 +5609,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5629,8 +5629,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.368Z", "modified_date": "2019-12-14T12:08:14.368Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "file_type": 11, "size": 65612975, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5642,8 +5642,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.539Z", "modified_date": "2019-12-14T12:08:13.539Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.muts.maf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", "file_type": 24, "size": 181310718, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5655,8 +5655,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.575Z", "modified_date": "2019-12-14T12:08:13.575Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.bam", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.bam", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bam", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.bam", "file_type": 3, "size": 22899967017, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5668,8 +5668,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.614Z", "modified_date": "2019-12-14T12:08:13.614Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.bam", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.bam", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.bam", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.bam", "file_type": 3, "size": 14961505727, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5681,8 +5681,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.658Z", "modified_date": "2019-12-14T12:08:13.658Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2641, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5694,8 +5694,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.676Z", "modified_date": "2019-12-14T12:08:13.676Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2611, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5707,8 +5707,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.695Z", "modified_date": "2019-12-14T12:08:13.695Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", "file_type": 21, "size": 2576, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5720,8 +5720,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.713Z", "modified_date": "2019-12-14T12:08:13.713Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2764, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5733,8 +5733,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.731Z", "modified_date": "2019-12-14T12:08:13.731Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2714, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5746,8 +5746,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.754Z", "modified_date": "2019-12-14T12:08:13.754Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2818, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5759,8 +5759,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.778Z", "modified_date": "2019-12-14T12:08:13.778Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2815, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5772,8 +5772,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.803Z", "modified_date": "2019-12-14T12:08:13.803Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", "file_type": 21, "size": 2775, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5785,8 +5785,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.820Z", "modified_date": "2019-12-14T12:08:13.820Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2873, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5798,8 +5798,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.836Z", "modified_date": "2019-12-14T12:08:13.836Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2826, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5811,8 +5811,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.858Z", "modified_date": "2019-12-14T12:08:13.858Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", "file_type": 24, "size": 59073, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5824,8 +5824,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.880Z", "modified_date": "2019-12-14T12:08:13.880Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8189, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5837,8 +5837,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.896Z", "modified_date": "2019-12-14T12:08:13.896Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8219, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5850,8 +5850,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.930Z", "modified_date": "2019-12-14T12:08:13.930Z", - "file_name": "s_C_K2902H_P001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.asmetrics", "file_type": 21, "size": 2171, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5863,8 +5863,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.947Z", "modified_date": "2019-12-14T12:08:13.947Z", - "file_name": "s_C_K2902H_N001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.asmetrics", "file_type": 21, "size": 2134, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5876,8 +5876,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.969Z", "modified_date": "2019-12-14T12:08:13.969Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", "file_type": 21, "size": 603, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5889,8 +5889,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.986Z", "modified_date": "2019-12-14T12:08:13.986Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", "file_type": 21, "size": 602, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5902,8 +5902,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.009Z", "modified_date": "2019-12-14T12:08:14.009Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", "file_type": 21, "size": 124853, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5915,8 +5915,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.027Z", "modified_date": "2019-12-14T12:08:14.027Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", "file_type": 21, "size": 111084, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5928,8 +5928,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.050Z", "modified_date": "2019-12-14T12:08:14.050Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", "file_type": 21, "size": 4777, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5941,8 +5941,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.068Z", "modified_date": "2019-12-14T12:08:14.068Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", "file_type": 21, "size": 3222, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5954,8 +5954,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.092Z", "modified_date": "2019-12-14T12:08:14.092Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6784, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5967,8 +5967,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.108Z", "modified_date": "2019-12-14T12:08:14.108Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6794, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5980,8 +5980,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.131Z", "modified_date": "2019-12-14T12:08:14.131Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hsmetrics", "file_type": 21, "size": 5016, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5993,8 +5993,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.147Z", "modified_date": "2019-12-14T12:08:14.147Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hsmetrics", "file_type": 21, "size": 5029, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6006,8 +6006,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.168Z", "modified_date": "2019-12-14T12:08:14.168Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 13994, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6019,8 +6019,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.183Z", "modified_date": "2019-12-14T12:08:14.183Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 12712, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6032,8 +6032,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.203Z", "modified_date": "2019-12-14T12:08:14.203Z", - "file_name": "s_C_K2902H_P001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_metrics", "file_type": 21, "size": 2900, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6045,8 +6045,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.219Z", "modified_date": "2019-12-14T12:08:14.219Z", - "file_name": "s_C_K2902H_N001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_metrics", "file_type": 21, "size": 2866, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6058,8 +6058,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.242Z", "modified_date": "2019-12-14T12:08:14.242Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", "file_type": 11, "size": 24213327, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6071,8 +6071,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.263Z", "modified_date": "2019-12-14T12:08:14.263Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", "file_type": 21, "size": 13440159, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6084,8 +6084,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.302Z", "modified_date": "2019-12-14T12:08:14.302Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", "file_type": 11, "size": 19739, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6097,8 +6097,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.324Z", "modified_date": "2019-12-14T12:08:14.324Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", "file_type": 10, "size": 5795, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6110,8 +6110,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.346Z", "modified_date": "2019-12-14T12:08:14.346Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", "file_type": 11, "size": 403491742, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6123,8 +6123,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.390Z", "modified_date": "2019-12-14T12:08:14.390Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", "file_type": 21, "size": 8622126, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6136,8 +6136,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.406Z", "modified_date": "2019-12-14T12:08:14.406Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", "file_type": 21, "size": 8618530, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6149,8 +6149,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.428Z", "modified_date": "2019-12-14T12:08:14.428Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5494, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6162,8 +6162,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.445Z", "modified_date": "2019-12-14T12:08:14.445Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5508, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6175,8 +6175,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.466Z", "modified_date": "2019-12-14T12:08:14.466Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", "file_type": 21, "size": 32693698, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6188,8 +6188,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.488Z", "modified_date": "2019-12-14T12:08:14.488Z", - "file_name": "s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13779990, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6201,8 +6201,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.504Z", "modified_date": "2019-12-14T12:08:14.504Z", - "file_name": "s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13586169, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6214,8 +6214,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.527Z", "modified_date": "2019-12-14T12:08:14.527Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6648, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6227,8 +6227,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.544Z", "modified_date": "2019-12-14T12:08:14.544Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6632, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6240,8 +6240,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.574Z", "modified_date": "2019-12-14T12:08:14.575Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1201, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6253,8 +6253,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.593Z", "modified_date": "2019-12-14T12:08:14.593Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1199, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6266,8 +6266,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.616Z", "modified_date": "2019-12-14T12:08:14.616Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics", "file_type": 21, "size": 7754, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6279,8 +6279,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.635Z", "modified_date": "2019-12-14T12:08:14.635Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics", "file_type": 21, "size": 7041, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6292,8 +6292,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.658Z", "modified_date": "2019-12-14T12:08:14.658Z", - "file_name": "s_C_K2902H_P001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_P001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.pileup", "file_type": 21, "size": 55203868, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6305,8 +6305,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.675Z", "modified_date": "2019-12-14T12:08:14.675Z", - "file_name": "s_C_K2902H_N001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_N001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.pileup", "file_type": 21, "size": 33915095, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6318,8 +6318,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.697Z", "modified_date": "2019-12-14T12:08:14.697Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", "file_type": 21, "size": 129554, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6331,8 +6331,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.738Z", "modified_date": "2019-12-14T12:08:14.738Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", "file_type": 10, "size": 172715192, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6344,8 +6344,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.762Z", "modified_date": "2019-12-14T12:08:14.762Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", "file_type": 21, "size": 13247144, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6357,8 +6357,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.800Z", "modified_date": "2019-12-14T12:08:14.800Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", "file_type": 10, "size": 11388, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6370,8 +6370,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.822Z", "modified_date": "2019-12-14T12:08:14.822Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", "file_type": 10, "size": 7525, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6383,8 +6383,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.844Z", "modified_date": "2019-12-14T12:08:14.844Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hstmetrics", "file_type": 21, "size": 19302184, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6396,8 +6396,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.860Z", "modified_date": "2019-12-14T12:08:14.860Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hstmetrics", "file_type": 21, "size": 19114455, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6409,8 +6409,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.883Z", "modified_date": "2019-12-14T12:08:14.883Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", "file_type": 11, "size": 2741838, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" diff --git a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.without_disambiguate.json b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.without_disambiguate.json index 2520b8bf9..d65ed3af4 100644 --- a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.without_disambiguate.json +++ b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.full.without_disambiguate.json @@ -5,7 +5,7 @@ "fields": { "created_date": "2019-12-11T22:53:02.012Z", "modified_date": "2020-01-14T23:03:35.530Z", - "name": "ARGOS 09670_D, 22 of 54 (12/11/2019, 22:53:02)", + "name": "ARGOS 99906_D, 22 of 54 (12/11/2019, 22:53:02)", "app": "cb5d793b-e650-4b7d-bfcd-882858e29cc5", "status": 4, "execution_id": "df43cc77-bed4-4233-9817-6d12e25d9e1c", @@ -14,7 +14,7 @@ "assay": "IDT_Exome_v1_FP_b37" }, "tags": { - "igoRequestId": "09670_D" + "igoRequestId": "99906_D" }, "notify_for_outputs": "[\"qc_pdf\"]" } @@ -1156,7 +1156,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1219,7 +1219,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -1244,11 +1244,11 @@ "secondary_files": [], "db_value": { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { @@ -1266,30 +1266,30 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, "value": { "CN": "MSKCC", - "ID": "s_C_K2902H_P001_d", - "LB": "09670_D_1_1_1_1_1", + "ID": "s_C_PPPPP8_P001_d", + "LB": "99906_D_1_1_1_1_1", "PL": "Illumina", "PU": [ - "H7HCTBBXY_ACATACGG" + "FCELLAAAA3_ACATACGG" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R1_001.fastq.gz", "size": 5966546453, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0390_BH7HCTBBXY/Project_09670_D/Sample_S16-68609_IGO_09670_D_1/S16-68609_IGO_09670_D_1_S11_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0006_BFCELLAAAA3/Project_99906_D/Sample_S00-00000_IGO_99906_D_1/S00-00000_IGO_99906_D_1_S11_R2_001.fastq.gz", "size": 5832468368, "class": "File" } @@ -1298,11 +1298,11 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_P001_d_H7HCTBBXY_ACATACGG" + "s_C_PPPPP8_P001_d_FCELLAAAA3_ACATACGG" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_P001_d.bam" + "bwa_output": "s_C_PPPPP8_P001_d.bam" }, "files": [ "02cfb077-f61c-4659-9877-752c456e8f80", @@ -1326,11 +1326,11 @@ "secondary_files": [], "db_value": { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { @@ -1348,30 +1348,30 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" }, "value": { "CN": "MSKCC", - "ID": "s_C_K2902H_N001_d", - "LB": "09670_D_46_1", + "ID": "s_C_PPPPP8_N001_d", + "LB": "99906_D_46_1", "PL": "Illumina", "PU": [ - "H7FKJBBXY" + "FCELLAAAA2" ], "R1": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R1_001.fastq.gz", "size": 3576965127, "class": "File" } ], "R2": [ { - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R2_001.fastq.gz", "size": 3592299152, "class": "File" } @@ -1380,11 +1380,11 @@ "zR1": [], "zR2": [], "RG_ID": [ - "s_C_K2902H_N001_d_H7FKJBBXY" + "s_C_PPPPP8_N001_d_FCELLAAAA2" ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "s_C_K2902H_N001_d.bam" + "bwa_output": "s_C_PPPPP8_N001_d.bam" }, "files": [ "47be3848-e16b-4126-9e64-1d3f5a67b927", @@ -1413,19 +1413,19 @@ "size": 65612975, "class": "File", "nameext": ".vcf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "checksum": "sha1$0201d57f5fd370615df7ce8b78f49ae512692e0e", "location": "bid://b835c33c-d241-42fc-beb2-e1ce1c41a77d", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants" + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants" }, "value": { "size": 65612975, "class": "File", "nameext": ".vcf", - "basename": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "basename": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", "checksum": "sha1$0201d57f5fd370615df7ce8b78f49ae512692e0e", - "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", - "nameroot": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants" + "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", + "nameroot": 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+ "location": "file:///juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts.maf", + "nameroot": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.muts" }, "files": [ "f9f55509-fcae-45f7-bdd2-72aebb59178e" @@ -1496,19 +1496,19 @@ "size": 22899967017, "class": "File", "nameext": ".bam", - "basename": "s_C_K2902H_P001_d.rg.md.abra.printreads.bam", + "basename": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bam", "checksum": "sha1$d67cf2c24cacfeaa222893c5d4303aed55556457", "location": "bid://e528ce76-0c6f-4088-8e22-38ece693bcdd", - "nameroot": "s_C_K2902H_P001_d.rg.md.abra.printreads", + "nameroot": "s_C_PPPPP8_P001_d.rg.md.abra.printreads", "secondaryFiles": [ { "size": 6252264, "class": "File", "nameext": ".bai", - "basename": "s_C_K2902H_P001_d.rg.md.abra.printreads.bai", + "basename": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.bai", "checksum": "sha1$776fc843bcdbd215452e611f03d7d9b42ad05a09", "location": 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"2020-02-03T22:05:10.138Z", - "file_name": "P-0017035-N01-WES_IGO_09670_D_46_S12_R1_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R1_001.fastq.gz", + "file_name": "P-0000000-N01-WES_IGO_99906_D_46_S12_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0007_AFCELLAAAA2/Project_99906_D/Sample_P-0000000-N01-WES_IGO_99906_D_46/P-0000000-N01-WES_IGO_99906_D_46_S12_R1_001.fastq.gz", "file_type": 1, "size": 3576965127, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -4292,8 +4292,8 @@ "fields": { "created_date": "2019-11-29T21:15:50.983Z", "modified_date": "2020-02-03T22:05:10.112Z", - "file_name": "P-0017035-N01-WES_IGO_09670_D_46_S12_R2_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/PITT_0391_AH7FKJBBXY/Project_09670_D/Sample_P-0017035-N01-WES_IGO_09670_D_46/P-0017035-N01-WES_IGO_09670_D_46_S12_R2_001.fastq.gz", + "file_name": 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"captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5227,15 +5227,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5252,25 +5252,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0390", + "runId": "SEQRUN_0006", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-15", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_1", + "primaryId": "99906_D_1", "barcodeId": "IDT366", - "libraryIgoId": "09670_D_1_1_1_1_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7HCTBBXY", + "libraryIgoId": "99906_D_1_1_1_1_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA3", "readLength": "101/8/101", - "sampleName": "C-K2902H-P001-d", + "sampleName": "C-PPPPP8-P001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Primary", "barcodeIndex": "ACATACGG", "labHeadEmail": "user@internet.com", @@ -5294,15 +5294,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "S16-68609", + "externalSampleId": "S00-00000", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "S16-68609", + "investigatorSampleId": "S00-00000", "captureConcentrationNm": null, "libraryConcentrationNgul": 40.03237153464453, - "ciTag": "s_C_K2902H_P001_d", - "cmoSampleName": "s_C_K2902H_P001_d" + "ciTag": "s_C_PPPPP8_P001_d", + "cmoSampleName": "s_C_PPPPP8_P001_d" }, "user": null, "latest": true @@ -5319,25 +5319,25 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5359,15 +5359,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5384,25 +5384,25 @@ "metadata": { "R": "R2", "sex": "M", - "runId": "PITT_0391", + "runId": "SEQRUN_0007", "genePanel": "WholeExomeSequencing", "baitSet": "IDT_Exome_v1_FP_BAITS", "piEmail": "", "runDate": "2019-08-19", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "09670_D_46", + "primaryId": "99906_D_46", "barcodeId": null, - "libraryIgoId": "09670_D_46_1", - "cmoPatientId": "C-K2902H", - "igoRequestId": "09670_D", - "flowCellId": "H7FKJBBXY", + "libraryIgoId": "99906_D_46_1", + "cmoPatientId": "C-PPPPP8", + "igoRequestId": "99906_D", + "flowCellId": "FCELLAAAA2", "readLength": "101/8/101", - "sampleName": "C-K2902H-N001-d", + "sampleName": "C-PPPPP8-N001-d", "sampleType": "Primary", "captureName": null, "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "sampleClass": "Normal", "barcodeIndex": null, "labHeadEmail": "user@internet.com", @@ -5424,15 +5424,15 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "P-0017035-N01-WES", + "externalSampleId": "P-0000000-N01-WES", "investigatorName": "Bob Sagat", "investigatorEmail": "user2@internet.com", "projectManagerName": "Franklin, Rosalind", - "investigatorSampleId": "P-0017035-N01-WES", + "investigatorSampleId": "P-0000000-N01-WES", "captureConcentrationNm": null, "libraryConcentrationNgul": 32.135796910139796, - "ciTag": "s_C_K2902H_N001_d", - "cmoSampleName": "s_C_K2902H_N001_d" + "ciTag": "s_C_PPPPP8_N001_d", + "cmoSampleName": "s_C_PPPPP8_N001_d" }, "user": null, "latest": true @@ -5444,8 +5444,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.368Z", "modified_date": "2019-12-14T12:08:14.368Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.annotate-variants.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.annotate-variants.vcf", + "path": 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14961505727, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5496,8 +5496,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.658Z", "modified_date": "2019-12-14T12:08:13.658Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2641, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5509,8 +5509,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.676Z", "modified_date": "2019-12-14T12:08:13.676Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2611, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5522,8 +5522,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.695Z", "modified_date": "2019-12-14T12:08:13.695Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R1-001.chunk002_cl.stats", "file_type": 21, "size": 2576, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5535,8 +5535,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.713Z", "modified_date": "2019-12-14T12:08:13.713Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk000_cl.stats", "file_type": 21, "size": 2764, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5548,8 +5548,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.731Z", "modified_date": "2019-12-14T12:08:13.731Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R1-001.chunk001_cl.stats", "file_type": 21, "size": 2714, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5561,8 +5561,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.754Z", "modified_date": "2019-12-14T12:08:13.754Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2818, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5574,8 +5574,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.778Z", "modified_date": "2019-12-14T12:08:13.778Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2815, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5587,8 +5587,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.803Z", "modified_date": "2019-12-14T12:08:13.803Z", - "file_name": "H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7HCTBBXY_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "file_name": "FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA3_ACATACGG-IGO-09670-D-1-S11-R2-001.chunk002_cl.stats", "file_type": 21, "size": 2775, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5600,8 +5600,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.820Z", "modified_date": "2019-12-14T12:08:13.820Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk000_cl.stats", "file_type": 21, "size": 2873, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5613,8 +5613,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.836Z", "modified_date": "2019-12-14T12:08:13.836Z", - "file_name": "H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/H7FKJBBXY-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "file_name": "FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/FCELLAAAA2-IGO-09670-D-46-S12-R2-001.chunk001_cl.stats", "file_type": 21, "size": 2826, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5626,8 +5626,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.858Z", "modified_date": "2019-12-14T12:08:13.858Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.maf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.maf", "file_type": 24, "size": 59073, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5639,8 +5639,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.880Z", "modified_date": "2019-12-14T12:08:13.880Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8189, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5652,8 +5652,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.896Z", "modified_date": "2019-12-14T12:08:13.896Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle.pdf", "file_type": 21, "size": 8219, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5665,8 +5665,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.930Z", "modified_date": "2019-12-14T12:08:13.930Z", - "file_name": "s_C_K2902H_P001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.asmetrics", "file_type": 21, "size": 2171, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5678,8 +5678,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.947Z", "modified_date": "2019-12-14T12:08:13.947Z", - "file_name": "s_C_K2902H_N001_d.rg.md.asmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.asmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.asmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.asmetrics", "file_type": 21, "size": 2134, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5691,8 +5691,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.969Z", "modified_date": "2019-12-14T12:08:13.969Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.out", "file_type": 21, "size": 603, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5704,8 +5704,8 @@ "fields": { "created_date": "2019-12-14T12:08:13.986Z", "modified_date": "2019-12-14T12:08:13.986Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.out", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.out", "file_type": 21, "size": 602, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5717,8 +5717,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.009Z", "modified_date": "2019-12-14T12:08:14.009Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.CNCF.png", "file_type": 21, "size": 124853, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5730,8 +5730,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.027Z", "modified_date": "2019-12-14T12:08:14.027Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.CNCF.png", "file_type": 21, "size": 111084, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5743,8 +5743,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.050Z", "modified_date": "2019-12-14T12:08:14.050Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.seg", "file_type": 21, "size": 4777, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5756,8 +5756,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.068Z", "modified_date": "2019-12-14T12:08:14.068Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.seg", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.seg", "file_type": 21, "size": 3222, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5769,8 +5769,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.092Z", "modified_date": "2019-12-14T12:08:14.092Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6784, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5782,8 +5782,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.108Z", "modified_date": "2019-12-14T12:08:14.108Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.pdf", "file_type": 21, "size": 6794, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5795,8 +5795,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.131Z", "modified_date": "2019-12-14T12:08:14.131Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hsmetrics", "file_type": 21, "size": 5016, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5808,8 +5808,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.147Z", "modified_date": "2019-12-14T12:08:14.147Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hsmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hsmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hsmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hsmetrics", "file_type": 21, "size": 5029, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5821,8 +5821,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.168Z", "modified_date": "2019-12-14T12:08:14.168Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 13994, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5834,8 +5834,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.183Z", "modified_date": "2019-12-14T12:08:14.183Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics.pdf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics.pdf", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics.pdf", "file_type": 21, "size": 12712, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5847,8 +5847,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.203Z", "modified_date": "2019-12-14T12:08:14.203Z", - "file_name": "s_C_K2902H_P001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_metrics", "file_type": 21, "size": 2900, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5860,8 +5860,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.219Z", "modified_date": "2019-12-14T12:08:14.219Z", - "file_name": "s_C_K2902H_N001_d.rg.md_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_metrics", "file_type": 21, "size": 2866, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5873,8 +5873,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.242Z", "modified_date": "2019-12-14T12:08:14.242Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.vcf", "file_type": 11, "size": 24213327, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5886,8 +5886,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.263Z", "modified_date": "2019-12-14T12:08:14.263Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.combined-variants.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.combined-variants.vcf.gz", "file_type": 21, "size": 13440159, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5899,8 +5899,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.302Z", "modified_date": "2019-12-14T12:08:14.302Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vcf", "file_type": 11, "size": 19739, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5912,8 +5912,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.324Z", "modified_date": "2019-12-14T12:08:14.324Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.pass.vep.portal.txt", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.pass.vep.portal.txt", "file_type": 10, "size": 5795, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5925,8 +5925,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.346Z", "modified_date": "2019-12-14T12:08:14.346Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.vcf", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.vcf", "file_type": 11, "size": 403491742, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5938,8 +5938,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.390Z", "modified_date": "2019-12-14T12:08:14.390Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.Rdata", "file_type": 21, "size": 8622126, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5951,8 +5951,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.406Z", "modified_date": "2019-12-14T12:08:14.406Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.Rdata", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.Rdata", "file_type": 21, "size": 8618530, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5964,8 +5964,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.428Z", "modified_date": "2019-12-14T12:08:14.428Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5494, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5977,8 +5977,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.445Z", "modified_date": "2019-12-14T12:08:14.445Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads.qmetrics.quality_by_cycle_metrics", "file_type": 21, "size": 5508, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -5990,8 +5990,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.466Z", "modified_date": "2019-12-14T12:08:14.466Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads.dat.gz", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads.dat.gz", "file_type": 21, "size": 32693698, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6003,8 +6003,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.488Z", "modified_date": "2019-12-14T12:08:14.488Z", - "file_name": "s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13779990, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6016,8 +6016,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.504Z", "modified_date": "2019-12-14T12:08:14.504Z", - "file_name": "s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md_FP_base_counts.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md_FP_base_counts.txt", "file_type": 10, "size": 13586169, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6029,8 +6029,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.527Z", "modified_date": "2019-12-14T12:08:14.527Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6648, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6042,8 +6042,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.544Z", "modified_date": "2019-12-14T12:08:14.544Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbiasmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbiasmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbiasmetrics", "file_type": 21, "size": 6632, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6055,8 +6055,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.574Z", "modified_date": "2019-12-14T12:08:14.575Z", - "file_name": "s_C_K2902H_P001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_P001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1201, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6068,8 +6068,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.593Z", "modified_date": "2019-12-14T12:08:14.593Z", - "file_name": "s_C_K2902H_N001_d.rg.md.gcbias.summary", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.gcbias.summary", + "file_name": "s_C_PPPPP8_N001_d.rg.md.gcbias.summary", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.gcbias.summary", "file_type": 21, "size": 1199, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6081,8 +6081,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.616Z", "modified_date": "2019-12-14T12:08:14.616Z", - "file_name": "s_C_K2902H_P001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.ismetrics", "file_type": 21, "size": 7754, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6094,8 +6094,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.635Z", "modified_date": "2019-12-14T12:08:14.635Z", - "file_name": "s_C_K2902H_N001_d.rg.md.ismetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.ismetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.ismetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.ismetrics", "file_type": 21, "size": 7041, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6107,8 +6107,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.658Z", "modified_date": "2019-12-14T12:08:14.658Z", - "file_name": "s_C_K2902H_P001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_P001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.pileup", "file_type": 21, "size": 55203868, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6120,8 +6120,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.675Z", "modified_date": "2019-12-14T12:08:14.675Z", - "file_name": "s_C_K2902H_N001_d.rg.md.pileup", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.pileup", + "file_name": "s_C_PPPPP8_N001_d.rg.md.pileup", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.pileup", "file_type": 21, "size": 33915095, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6133,8 +6133,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.697Z", "modified_date": "2019-12-14T12:08:14.697Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect_STDfilter.norm.vcf.gz", "file_type": 21, "size": 129554, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6146,8 +6146,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.738Z", "modified_date": "2019-12-14T12:08:14.738Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.mutect.txt", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.mutect.txt", "file_type": 10, "size": 172715192, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6159,8 +6159,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.762Z", "modified_date": "2019-12-14T12:08:14.762Z", - "file_name": "s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.abra.printreads.s_C_K2902H_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "file_name": "s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.abra.printreads.s_C_PPPPP8_N001_d.rg.md.abra.printreads.vardict.complex_filtered_STDfilter.norm.vcf.gz", "file_type": 21, "size": 13247144, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6172,8 +6172,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.800Z", "modified_date": "2019-12-14T12:08:14.800Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_hisens.cncf.txt", "file_type": 10, "size": 11388, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6185,8 +6185,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.822Z", "modified_date": "2019-12-14T12:08:14.822Z", - "file_name": "s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.abra.printreads__s_C_K2902H_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "file_name": "s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.abra.printreads__s_C_PPPPP8_P001_d.rg.md.abra.printreads_purity.cncf.txt", "file_type": 10, "size": 7525, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6198,8 +6198,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.844Z", "modified_date": "2019-12-14T12:08:14.844Z", - "file_name": "s_C_K2902H_P001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_P001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.rg.md.hstmetrics", "file_type": 21, "size": 19302184, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6211,8 +6211,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.860Z", "modified_date": "2019-12-14T12:08:14.860Z", - "file_name": "s_C_K2902H_N001_d.rg.md.hstmetrics", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_N001_d.rg.md.hstmetrics", + "file_name": "s_C_PPPPP8_N001_d.rg.md.hstmetrics", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_N001_d.rg.md.hstmetrics", "file_type": 21, "size": 19114455, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" @@ -6224,8 +6224,8 @@ "fields": { "created_date": "2019-12-14T12:08:14.883Z", "modified_date": "2019-12-14T12:08:14.883Z", - "file_name": "s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", - "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_K2902H_P001_d.s_C_K2902H_N001_d.svs.vcf", + "file_name": "s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", + "path": "/juno/work/ci/argos-test/data/ca18b090-03ad-4bef-acd3-52600f8e62eb/outputs/s_C_PPPPP8_P001_d.s_C_PPPPP8_N001_d.svs.vcf", "file_type": 11, "size": 2741838, "file_group": "a975f490-1b02-4575-abae-a4f8e3667733" diff --git a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.json b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.json index 9680beeec..7997fd334 100644 --- a/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.json +++ b/fixtures/tests/ca18b090-03ad-4bef-acd3-52600f8e62eb.run.json @@ -5,14 +5,14 @@ "fields": { "created_date": "2019-12-11T22:53:02.012Z", "modified_date": "2020-01-14T16:44:31.649Z", - "name": "ARGOS 09670_D, 22 of 54 (12/11/2019, 22:53:02)", + "name": "ARGOS 99906_D, 22 of 54 (12/11/2019, 22:53:02)", "app": "cb5d793b-e650-4b7d-bfcd-882858e29cc5", "status": 4, "execution_id": "df43cc77-bed4-4233-9817-6d12e25d9e1c", "job_statuses": {}, "output_metadata": {}, "tags": { - "igoRequestId": "09670_D" + "igoRequestId": "99906_D" } } } diff --git a/fixtures/tests/etl/10075_D_2.file.json b/fixtures/tests/etl/99990_D_2.file.json similarity index 63% rename from fixtures/tests/etl/10075_D_2.file.json rename to fixtures/tests/etl/99990_D_2.file.json index 1508bc2d1..f7a1d637d 100644 --- a/fixtures/tests/etl/10075_D_2.file.json +++ b/fixtures/tests/etl/99990_D_2.file.json @@ -5,9 +5,9 @@ "fields": { "created_date": "2020-01-06T19:59:50.582Z", "modified_date": "2020-01-06T19:59:50.585Z", - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", - "original_path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R1_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R1_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", + "original_path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R1_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -19,9 +19,9 @@ "fields": { "created_date": "2020-01-06T19:59:50.597Z", "modified_date": "2020-01-06T19:59:50.598Z", - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", - "original_path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R2_001.fastq.gz", - "path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R2_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", + "original_path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R2_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/fixtures/tests/etl/10075_D_2.filemetadata.json b/fixtures/tests/etl/99990_D_2.filemetadata.json similarity index 78% rename from fixtures/tests/etl/10075_D_2.filemetadata.json rename to fixtures/tests/etl/99990_D_2.filemetadata.json index 58e1df82a..04ae1785b 100644 --- a/fixtures/tests/etl/10075_D_2.filemetadata.json +++ b/fixtures/tests/etl/99990_D_2.filemetadata.json @@ -11,28 +11,28 @@ "metadata": { "R": "R1", "sex": "F", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-12", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10075_D_2", + "primaryId": "99990_D_2", "sampleName": "TestSample001", "barcodeId": null, "igoProjectId": "10075", - "libraryIgoId": "10075_D_2_3", - "cmoPatientId": "C-8VK0V7", - "igoRequestId": "10075_D", + "libraryIgoId": "99990_D_2_3", + "cmoPatientId": "C-PPPPP3", + "igoRequestId": "99990_D", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HCYYWBBXY", + "flowCellId": "FCELLAAAA4", "readLength": "101/8/8/101", - "cmoSampleName": "C-8VK0V7-N001-d", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "cmoSampleName": "C-PPPPP3-N001-d", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": null, "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -48,14 +48,14 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "JW_MEL_007_NORM", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "otherContactEmails": "", "projectManagerName": "", "qcAccessEmails": "", "dataAccessEmails": "", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorSampleId": "SAMPLE_N_001", "captureConcentrationNm": "10.377358490566039", "libraryConcentrationNgul": 10.6, "importDate": "2022-03-23", @@ -77,28 +77,28 @@ "metadata": { "R": "R2", "sex": "F", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-12", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10075_D_2", + "primaryId": "99990_D_2", "sampleName": "TestSample001", "barcodeId": null, "igoProjectId": "10075", - "libraryIgoId": "10075_D_2_3", - "cmoPatientId": "C-8VK0V7", - "igoRequestId": "10075_D", + "libraryIgoId": "99990_D_2_3", + "cmoPatientId": "C-PPPPP3", + "igoRequestId": "99990_D", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HCYYWBBXY", + "flowCellId": "FCELLAAAA4", "readLength": "101/8/8/101", - "cmoSampleName": "C-8VK0V7-N001-d", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "cmoSampleName": "C-PPPPP3-N001-d", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": null, "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -114,14 +114,14 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "JW_MEL_007_NORM", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "otherContactEmails": "", "projectManagerName": "", "qcAccessEmails": "", "dataAccessEmails": "", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorSampleId": "SAMPLE_N_001", "captureConcentrationNm": "10.377358490566039", "libraryConcentrationNgul": 10.6, "importDate": "2022-03-23", diff --git a/fixtures/tests/etl/10075_D_2.update.json b/fixtures/tests/etl/99990_D_2.update.json similarity index 83% rename from fixtures/tests/etl/10075_D_2.update.json rename to fixtures/tests/etl/99990_D_2.update.json index 5f7961710..938d3dc72 100644 --- a/fixtures/tests/etl/10075_D_2.update.json +++ b/fixtures/tests/etl/99990_D_2.update.json @@ -1,16 +1,16 @@ [{ "metaDbRequestId": "6cc9f987-875a-11eb-ada3-acde48001122", - "igoRequestId": "10075_D_2", + "igoRequestId": "99990_D_2", "genePanel": "GENESET101_BAITS", "projectManagerName": "Bar, Foo", - "piEmail": "request1pi@mskcc.org", + "piEmail": "pi1@example.org", "labHeadName": "Foo Bar", - "labHeadEmail": "request1pi@mskcc.org", - "investigatorName": "John Smith", - "investigatorEmail": "smithj@mskcc.org", + "labHeadEmail": "pi1@example.org", + "investigatorName": "Test Investigator", + "investigatorEmail": "analyst12@example.org", "dataAnalystName": "Poin Dexter", - "dataAnalystEmail": "dexterp@mskcc.org", - "otherContactEmails": "dexterp@mskcc.org", + "dataAnalystEmail": "analyst3@example.org", + "otherContactEmails": "analyst3@example.org", "dataAccessEmails": "", "qcAccessEmails": "", "isCmoRequest": true, @@ -19,8 +19,8 @@ { "metaDbSampleId": "afe750e6-8756-11eb-81b0-acde48001122", "metaDbPatientId": "6cc9f242-875a-11eb-ae91-acde48001122", - "cmoSampleName": "C-MP789J-X001-d", - "ciTag": "C-MP789J-X001-d", + "cmoSampleName": "C-PPPP11-X001-d", + "ciTag": "C-PPPP11-X001-d", "sampleName": "XXX002_P3_12345_L1", "sampleType": "Primary", "oncotreeCode": "CLL", @@ -41,7 +41,7 @@ { "runMode": "HiSeq High Output", "runId": "RUNID_0123", - "flowCellId": "X5KL2KKAY", + "flowCellId": "FCELLBBB10", "readLength": "", "runDate": "2018-06-05", "flowCellLanes": [5], @@ -53,7 +53,7 @@ ] } ], - "cmoPatientId": "C-MP789JR", + "cmoPatientId": "C-PPPP12", "primaryId": "MOCKREQUEST1_B_1", "investigatorSampleId": "XXX002_P3_12345_L1", "species": "Human", @@ -69,7 +69,7 @@ "patientAliases": [ { "namespace": "cmo", - "value": "C-MP789JR" + "value": "C-PPPP12" } ], "sampleAliases": [ @@ -86,9 +86,9 @@ { "metaDbSampleId": "afe75123-8756-11eb-8f14-acde48001122", "metaDbPatientId": "6cc9f242-875a-11eb-ae91-acde48001122", - "cmoSampleName": "C-MP789J-N001-d", - "ciTag": "C-MP789J-N001-d", - "sampleName": "01-0012345a", + "cmoSampleName": "C-PPPP11-N001-d", + "ciTag": "C-PPPP11-N001-d", + "sampleName": "00-0000001a", "sampleType": "Normal", "oncotreeCode": "CLL", "collectionYear": "", @@ -108,21 +108,21 @@ { "runMode": "HiSeq High Output", "runId": "RUNID_0123", - "flowCellId": "X5KL2KKAY", + "flowCellId": "FCELLBBB10", "readLength": "", "runDate": "2018-06-05", "flowCellLanes": [5], "fastqs": [ - "/FASTQ/Project_MOCKREQUEST1_B/Sample_01-0012345a_IGO_MOCKREQUEST1_B_2/01-0012345a_IGO_MOCKREQUEST1_B_2_S83_R2_001.fastq.gz", - "/FASTQ/Project_MOCKREQUEST1_B/Sample_01-0012345a_IGO_MOCKREQUEST1_B_2/01-0012345a_IGO_MOCKREQUEST1_B_2_S83_R1_001.fastq.gz" + "/FASTQ/Project_MOCKREQUEST1_B/Sample_00-0000001a_IGO_MOCKREQUEST1_B_2/00-0000001a_IGO_MOCKREQUEST1_B_2_S83_R2_001.fastq.gz", + "/FASTQ/Project_MOCKREQUEST1_B/Sample_00-0000001a_IGO_MOCKREQUEST1_B_2/00-0000001a_IGO_MOCKREQUEST1_B_2_S83_R1_001.fastq.gz" ] } ] } ], - "cmoPatientId": "C-MP789JR", + "cmoPatientId": "C-PPPP12", "primaryId": "MOCKREQUEST1_B_2", - "investigatorSampleId": "01-0012345a", + "investigatorSampleId": "00-0000001a", "species": "Human", "sex": "F", "tumorOrNormal": "Normal", @@ -136,13 +136,13 @@ "patientAliases": [ { "namespace": "cmo", - "value": "C-MP789JR" + "value": "C-PPPP12" } ], "sampleAliases": [ { "namespace": "investigatorId", - "value": "01-0012345a" + "value": "00-0000001a" }, { "namespace": "igoId", @@ -153,8 +153,8 @@ { "metaDbSampleId": "afe75161-8756-11eb-96c5-acde48001122", "metaDbPatientId": "6cc9f745-875a-11eb-a134-acde48001122", - "cmoSampleName": "C-8DH24X-X001-d", - "ciTag": "C-8DH24X-X001-d", + "cmoSampleName": "C-PPPPP2-X001-d", + "ciTag": "C-PPPPP2-X001-d", "sampleName": "XXX002_P1_12348a_R_43", "sampleType": "Primary", "oncotreeCode": "COAD", @@ -175,7 +175,7 @@ { "runMode": "HiSeq High Output", "runId": "RUNID_0123", - "flowCellId": "X5KL2KKAY", + "flowCellId": "FCELLBBB10", "readLength": "", "runDate": "2018-06-05", "flowCellLanes": [5], @@ -187,7 +187,7 @@ ] } ], - "cmoPatientId": "C-8DH24X", + "cmoPatientId": "C-PPPPP2", "primaryId": "MOCKREQUEST1_B_3", "investigatorSampleId": "XXX002_P1_12348a_R_43", "species": "Human", @@ -203,7 +203,7 @@ "patientAliases": [ { "namespace": "cmo", - "value": "C-8DH24X" + "value": "C-PPPPP2" } ], "sampleAliases": [ @@ -220,9 +220,9 @@ { "metaDbSampleId": "afe7519c-8756-11eb-ac58-acde48001122", "metaDbPatientId": "6cc9f745-875a-11eb-a134-acde48001122", - "cmoSampleName": "C-8DH24X-N001-d", - "ciTag": "C-8DH24X-N001-d", - "sampleName": "01-XXXXXXXa", + "cmoSampleName": "C-PPPPP2-N001-d", + "ciTag": "C-PPPPP2-N001-d", + "sampleName": "00-0000002a", "sampleType": "Normal", "oncotreeCode": "COAD", "collectionYear": "", @@ -242,21 +242,21 @@ { "runMode": "HiSeq High Output", "runId": "RUNID_0123", - "flowCellId": "X5KL2KKAY", + "flowCellId": "FCELLBBB10", "readLength": "", "runDate": "2018-06-05", "flowCellLanes": [5], "fastqs": [ - "/FASTQ/Project_MOCKREQUEST1_B/Sample_01-XXXXXXXa_IGO_MOCKREQUEST1_B_4/01-XXXXXXXa_IGO_MOCKREQUEST1_B_4_S85_R1_001.fastq.gz", - "/FASTQ/Project_MOCKREQUEST1_B/Sample_01-XXXXXXXa_IGO_MOCKREQUEST1_B_4/01-XXXXXXXa_IGO_MOCKREQUEST1_B_4_S85_R2_001.fastq.gz" + "/FASTQ/Project_MOCKREQUEST1_B/Sample_00-0000002a_IGO_MOCKREQUEST1_B_4/00-0000002a_IGO_MOCKREQUEST1_B_4_S85_R1_001.fastq.gz", + "/FASTQ/Project_MOCKREQUEST1_B/Sample_00-0000002a_IGO_MOCKREQUEST1_B_4/00-0000002a_IGO_MOCKREQUEST1_B_4_S85_R2_001.fastq.gz" ] } ] } ], - "cmoPatientId": "C-8DH24X", + "cmoPatientId": "C-PPPPP2", "primaryId": "MOCKREQUEST1_B_4", - "investigatorSampleId": "01-XXXXXXXa", + "investigatorSampleId": "00-0000002a", "species": "Human", "sex": "M", "tumorOrNormal": "Normal", @@ -270,13 +270,13 @@ "patientAliases": [ { "namespace": "cmo", - "value": "C-8DH24X" + "value": "C-PPPPP2" } ], "sampleAliases": [ { "namespace": "investigatorId", - "value": "01-XXXXXXXa" + "value": "00-0000002a" }, { "namespace": "igoId", diff --git a/fixtures/tests/etl/10075_D_2.update_sample.json b/fixtures/tests/etl/99990_D_2.update_sample.json similarity index 82% rename from fixtures/tests/etl/10075_D_2.update_sample.json rename to fixtures/tests/etl/99990_D_2.update_sample.json index 18176f407..cecbdb3b6 100644 --- a/fixtures/tests/etl/10075_D_2.update_sample.json +++ b/fixtures/tests/etl/99990_D_2.update_sample.json @@ -1,6 +1,6 @@ { "smileSampleId": "5fe2dc20-92f4-4763-b437-fa1e2fb1b93f", - "primarySampleAlias": "10075_D_2", + "primarySampleAlias": "99990_D_2", "sampleClass": "Normal", "sampleCategory": "research", "datasource": "igo", @@ -11,7 +11,7 @@ "namespace": "investigatorId" }, { - "value": "10075_D_2", + "value": "99990_D_2", "namespace": "igoId" } ], @@ -29,14 +29,14 @@ } }, "latestSampleMetadata": { - "primaryId": "10075_D_2", + "primaryId": "99990_D_2", "cmoPatientId": "C-TEST001", "investigatorSampleId": "TestSample001", "cmoSampleName": "C-TEST001-X001-d", "sampleName": "TestSample001", - "igoRequestId": "10075_D", + "igoRequestId": "99990_D", "importDate": "2022-03-23", - "cmoInfoIgoId": "10075_D_2", + "cmoInfoIgoId": "99990_D_2", "oncotreeCode": "CLL", "collectionYear": "", "tubeId": "", @@ -57,13 +57,13 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "10075_D_2", + "libraryIgoId": "99990_D_2", "libraryVolume": 35.0, "libraryConcentrationNgul": 34.8, "dnaInputNg": null, "captureConcentrationNm": "11.49425287356322", "captureInputNg": "400.0", - "captureName": "Pool-10075_D-Tube1_1", + "captureName": "Pool-99990_D-Tube1_1", "runs": [ { "runMode": "HiSeq High Output", @@ -73,8 +73,8 @@ "runDate": "2022-03-20", "flowCellLanes": [5], "fastqs": [ - "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R2_001.fastq.gz" ] } ] @@ -88,7 +88,7 @@ }, "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "10075_D" + "igoRequestId": "99990_D" }, "status": { "validationStatus": true, @@ -97,14 +97,14 @@ }, "sampleMetadataList": [ { - "primaryId": "10075_D_2", + "primaryId": "99990_D_2", "cmoPatientId": "C-TEST001", "investigatorSampleId": "TestSample001", "cmoSampleName": "C-TEST001-X001-d", "sampleName": "TestSample001", - "igoRequestId": "10075_D", + "igoRequestId": "99990_D", "importDate": "2022-03-23", - "cmoInfoIgoId": "10075_D_2", + "cmoInfoIgoId": "99990_D_2", "oncotreeCode": "CLL", "collectionYear": "", "tubeId": "", @@ -125,13 +125,13 @@ { "barcodeId": null, "barcodeIndex": null, - "libraryIgoId": "10075_D_2", + "libraryIgoId": "99990_D_2", "libraryVolume": 35.0, "libraryConcentrationNgul": 34.8, "dnaInputNg": null, "captureConcentrationNm": "11.49425287356322", "captureInputNg": "400.0", - "captureName": "Pool-10075_D-Tube1_1", + "captureName": "Pool-99990_D-Tube1_1", "runs": [ { "runMode": "HiSeq High Output", @@ -141,8 +141,8 @@ "runDate": "2022-03-20", "flowCellLanes": [5], "fastqs": [ - "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_10075_D/Sample_TestSample001_IGO_10075_D_2/TestSample001_IGO_10075_D_2_S1_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/TEST_RUN_001/Project_99990_D/Sample_TestSample001_IGO_99990_D_2/TestSample001_IGO_99990_D_2_S1_R2_001.fastq.gz" ] } ] @@ -156,7 +156,7 @@ }, "additionalProperties": { "isCmoSample": "true", - "igoRequestId": "10075_D" + "igoRequestId": "99990_D" }, "status": { "validationStatus": true, diff --git a/fixtures/tests/etl/10075_D_request_update.json b/fixtures/tests/etl/99990_D_request_update.json similarity index 90% rename from fixtures/tests/etl/10075_D_request_update.json rename to fixtures/tests/etl/99990_D_request_update.json index cbc26737a..86b020c72 100644 --- a/fixtures/tests/etl/10075_D_request_update.json +++ b/fixtures/tests/etl/99990_D_request_update.json @@ -1,7 +1,7 @@ [ { - "igoRequestId": "10075_D", - "requestMetadataJson": "{\"ilabRequestId\":\"IGO-TEST001\",\"requestId\":\"10075_D\",\"requestName\":\"HybridCapture\",\"recipe\":\"IMPACT468\",\"projectManagerName\":\"\",\"piEmail\":\"\",\"labHeadName\":\"Test Researcher\",\"labHeadEmail\":\"researcher@example.org\",\"investigatorName\":\"Test Investigator\",\"investigatorEmail\":\"investigator@example.org\",\"dataAnalystName\":\"\",\"dataAnalystEmail\":\"\",\"otherContactEmails\":\"investigator@example.org\",\"dataAccessEmails\":\"investigator@example.org\",\"qcAccessEmails\":\"investigator@example.org\",\"isCmoRequest\":true,\"bicAnalysis\":true,\"neoAg\":false,\"deliveryPath\":\"/ifs/datadelivery/test/share\",\"pooledNormals\":[],\"projectId\":\"10075\",\"status\":{\"validationReport\":\"{\\\"samples (failed)\\\":\\\"Some request samples failed validation\\\"}\",\"validationStatus\":false}}", + "igoRequestId": "99990_D", + "requestMetadataJson": "{\"ilabRequestId\":\"IGO-TEST001\",\"requestId\":\"99990_D\",\"requestName\":\"HybridCapture\",\"recipe\":\"IMPACT468\",\"projectManagerName\":\"\",\"piEmail\":\"\",\"labHeadName\":\"Test Researcher\",\"labHeadEmail\":\"researcher@example.org\",\"investigatorName\":\"Test Investigator\",\"investigatorEmail\":\"investigator@example.org\",\"dataAnalystName\":\"\",\"dataAnalystEmail\":\"\",\"otherContactEmails\":\"investigator@example.org\",\"dataAccessEmails\":\"investigator@example.org\",\"qcAccessEmails\":\"investigator@example.org\",\"isCmoRequest\":true,\"bicAnalysis\":true,\"neoAg\":false,\"deliveryPath\":\"/ifs/datadelivery/test/share\",\"pooledNormals\":[],\"projectId\":\"10075\",\"status\":{\"validationReport\":\"{\\\"samples (failed)\\\":\\\"Some request samples failed validation\\\"}\",\"validationStatus\":false}}", "importDate": "2023-03-08", "status": { "validationStatus": false, @@ -9,8 +9,8 @@ } }, { - "igoRequestId": "10075_D", - "requestMetadataJson": "{\"ilabRequestId\":\"IGO-TEST001\",\"requestId\":\"10075_D\",\"requestName\":\"HybridCapture\",\"recipe\":\"IMPACT468\",\"projectManagerName\":\"\",\"piEmail\":\"\",\"labHeadName\":\"Test Researcher\",\"labHeadEmail\":\"researcher@example.org\",\"investigatorName\":\"Test Investigator\",\"investigatorEmail\":\"investigator@example.org\",\"dataAnalystName\":\"\",\"dataAnalystEmail\":\"\",\"otherContactEmails\":\"investigator@example.org\",\"dataAccessEmails\":\"investigator@example.org\",\"qcAccessEmails\":\"investigator@example.org\",\"isCmoRequest\":true,\"bicAnalysis\":true,\"neoAg\":false,\"deliveryDate\":1.704067200000E12,\"deliveryPath\":\"/ifs/datadelivery/test/share\",\"pooledNormals\":[],\"projectId\":\"10075\",\"status\":{\"validationReport\":\"{}\",\"validationStatus\":true}}", + "igoRequestId": "99990_D", + "requestMetadataJson": "{\"ilabRequestId\":\"IGO-TEST001\",\"requestId\":\"99990_D\",\"requestName\":\"HybridCapture\",\"recipe\":\"IMPACT468\",\"projectManagerName\":\"\",\"piEmail\":\"\",\"labHeadName\":\"Test Researcher\",\"labHeadEmail\":\"researcher@example.org\",\"investigatorName\":\"Test Investigator\",\"investigatorEmail\":\"investigator@example.org\",\"dataAnalystName\":\"\",\"dataAnalystEmail\":\"\",\"otherContactEmails\":\"investigator@example.org\",\"dataAccessEmails\":\"investigator@example.org\",\"qcAccessEmails\":\"investigator@example.org\",\"isCmoRequest\":true,\"bicAnalysis\":true,\"neoAg\":false,\"deliveryDate\":1.704067200000E12,\"deliveryPath\":\"/ifs/datadelivery/test/share\",\"pooledNormals\":[],\"projectId\":\"10075\",\"status\":{\"validationReport\":\"{}\",\"validationStatus\":true}}", "importDate": "2023-03-22", "status": { "validationStatus": true, diff --git a/fixtures/tests/juno_argos_demo2.filemetadata.json b/fixtures/tests/juno_argos_demo2.filemetadata.json index c3da80efa..09101b162 100644 --- a/fixtures/tests/juno_argos_demo2.filemetadata.json +++ b/fixtures/tests/juno_argos_demo2.filemetadata.json @@ -11,27 +11,27 @@ "metadata": { "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-17", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10075_D_5", + "primaryId": "99990_D_5", "barcodeId": "DUAL_IDT_LIB_267", - "libraryIgoId": "10075_D_5_1_1_1", - "cmoPatientId": "C-8VK0V7", + "libraryIgoId": "99990_D_5_1_1_1", + "cmoPatientId": "C-PPPPP3", "igoRequestId": "DemoRequest1", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "readLength": "101/8/8/101", - "sampleName": "C-8VK0V7-R001-d", - "captureName": "Pool-09483_R-10075_D-Tube7_1", + "sampleName": "C-PPPPP3-R001-d", + "captureName": "Pool-99998_R-99990_D-Tube7_1", "igoComplete": true, - "labHeadName": "John Smith", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "labHeadName": "Test Investigator", + "barcodeIndex": "GTATTGGC-PPPP14", "labHeadEmail": "email@internet.com", "oncotreeCode": "MEL", "preservation": "Frozen", @@ -43,18 +43,18 @@ ], "libraryVolume": 35.0, "pooledNormals": [ - 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"/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S12_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S12_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R2_001.fastq.gz" ], "tumorOrNormal": "Normal", "captureInputNg": "110.0", @@ -214,11 +214,11 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "JW_MEL_007_NORM", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "projectManagerName": "", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorSampleId": "SAMPLE_N_001", "captureConcentrationNm": "10.377358490566039", "libraryConcentrationNgul": 10.6 }, @@ -237,26 +237,26 @@ "metadata": { "R": "R2", "sex": "F", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-12", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10075_D_3", + "primaryId": "99990_D_3", "barcodeId": null, "libraryIgoId": null, - "cmoPatientId": "C-8VK0V7", + "cmoPatientId": "C-PPPPP3", "igoRequestId": "DemoRequest1", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HCYYWBBXY", + "flowCellId": "FCELLAAAA4", "readLength": "101/8/8/101", - "sampleName": "C-8VK0V7-N001-d", - "captureName": "Pool-05257_CD-06287_AY-10075_D-Tube2_1", + "sampleName": "C-PPPPP3-N001-d", + "captureName": "Pool-99992_D-99995_AY-99990_D-Tube2_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": null, "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -270,18 +270,18 @@ ], "libraryVolume": null, "pooledNormals": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S5_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S5_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA_S27_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA_S27_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S12_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S12_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R2_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R1_001.fastq.gz", - "/ifs/archive/GCL/hiseq/FASTQ/PITT_0439_BHFTCNBBXY/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S5_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG/FFPEPOOLEDNORMAL_IGO_IMPACT468_GTGAAGTG_S5_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA_S27_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_GTTACGCA_S27_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S12_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA/FROZENPOOLEDNORMAL_IGO_IMPACT468_GTTACGCA_S12_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC/FFPEPOOLEDNORMAL_IGO_IMPACT468_CAGTCTTC_S16_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG/FROZENPOOLEDNORMAL_IGO_HemePACT_v4_CTAACTCG_S95_R2_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R1_001.fastq.gz", + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0008_BFCELLAAAA6/Project_POOLEDNORMALS/Sample_FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG/FROZENPOOLEDNORMAL_IGO_IMPACT468_CTAACTCG_S7_R2_001.fastq.gz" ], "tumorOrNormal": "Normal", "captureInputNg": "110.0", @@ -290,11 +290,11 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "JW_MEL_007_NORM", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "projectManagerName": "", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorSampleId": "SAMPLE_N_001", "captureConcentrationNm": "10.377358490566039", "libraryConcentrationNgul": 10.6 }, diff --git a/fixtures/tests/juno_argos_demo2.pipeline_input.json b/fixtures/tests/juno_argos_demo2.pipeline_input.json index 81c9a7e26..1afb44fcd 100644 --- a/fixtures/tests/juno_argos_demo2.pipeline_input.json +++ b/fixtures/tests/juno_argos_demo2.pipeline_input.json @@ -295,7 +295,7 @@ "facets_pcval": 500, "gatk_jar_path": "/usr/bin/gatk.jar", "project_prefix": [ - "09670_D" + "99906_D" ], "opt_dup_pix_dist": "2500", "emit_original_quals": true, @@ -304,8 +304,8 @@ "pair": [ { "CN": "MSKCC", - "ID": "10075_D_5", - "LB": "10075_D_5_1_1_1", + "ID": "99990_D_5", + "LB": "99990_D_5_1_1_1", "PL": "Illumina", "PU": [ ], @@ -322,12 +322,12 @@ ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "10075_D_5.bam" + "bwa_output": "99990_D_5.bam" }, { "CN": "MSKCC", - "ID": "10075_D_3", - "LB": "10075_D_3", + "ID": "99990_D_3", + "LB": "99990_D_3", "PL": "Illumina", "PU": [ ], @@ -344,7 +344,7 @@ ], "adapter": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG", "adapter2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", - "bwa_output": "10075_D_3.bam" + "bwa_output": "99990_D_3.bam" } ] } diff --git a/fixtures/tests/merge_fastqs/10151_F_13.file.json b/fixtures/tests/merge_fastqs/99996_F_13.file.json similarity index 75% rename from fixtures/tests/merge_fastqs/10151_F_13.file.json rename to fixtures/tests/merge_fastqs/99996_F_13.file.json index 4b01a23ec..af78a1cec 100644 --- a/fixtures/tests/merge_fastqs/10151_F_13.file.json +++ b/fixtures/tests/merge_fastqs/99996_F_13.file.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-07T19:59:50.582Z", "modified_date": "2020-01-07T19:59:50.585Z", - "file_name": "JAR34-Buffy_IGO_10151_F_13_S54_R1_001.fastq.gz", - "path": "/test/JAR34-Buffy_IGO_10151_F_13_S54_R1_001.fastq.gz", + "file_name": "JAR34-Buffy_IGO_99996_F_13_S54_R1_001.fastq.gz", + "path": "/test/JAR34-Buffy_IGO_99996_F_13_S54_R1_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-07T19:59:50.597Z", "modified_date": "2020-01-07T19:59:50.598Z", - "file_name": "JAR34-Buffy_IGO_10151_F_13_S298_R2_001.fastq.gz", - "path": "/test/JAR34-Buffy_IGO_10151_F_13_S298_R2_001.fastq.gz", + "file_name": "JAR34-Buffy_IGO_99996_F_13_S298_R2_001.fastq.gz", + "path": "/test/JAR34-Buffy_IGO_99996_F_13_S298_R2_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -31,8 +31,8 @@ "fields": { "created_date": "2020-01-07T19:59:50.597Z", "modified_date": "2020-01-07T19:59:50.598Z", - "file_name": "JAR34-Buffy_IGO_10151_F_13_S298_R1_001.fastq.gz", - "path": "/test/JAR34-Buffy_IGO_10151_F_13_S298_R1_001.fastq.gz", + "file_name": "JAR34-Buffy_IGO_99996_F_13_S298_R1_001.fastq.gz", + "path": "/test/JAR34-Buffy_IGO_99996_F_13_S298_R1_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -44,8 +44,8 @@ "fields": { "created_date": "2020-01-07T19:59:50.597Z", "modified_date": "2020-01-07T19:59:50.598Z", - "file_name": "JAR34-Buffy_IGO_10151_F_13_S54_R2_001.fastq.gz", - "path": "/test/JAR34-Buffy_IGO_10151_F_13_S54_R2_001.fastq.gz", + "file_name": "JAR34-Buffy_IGO_99996_F_13_S54_R2_001.fastq.gz", + "path": "/test/JAR34-Buffy_IGO_99996_F_13_S54_R2_001.fastq.gz", "file_type": 1, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json b/fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json similarity index 75% rename from fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json rename to fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json index dd118dd20..4dd4c7fe5 100644 --- a/fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json +++ b/fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json @@ -11,27 +11,27 @@ "metadata": { "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-17", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10151_F_13", + "primaryId": "99996_F_13", "barcodeId": "DUAL_IDT_LIB_267", - "libraryIgoId": "10151_F_5_1_1_1", - "cmoPatientId": "C-8VK0V7", - "igoRequestId": "10151_F", + "libraryIgoId": "99996_F_5_1_1_1", + "cmoPatientId": "C-PPPPP3", + "igoRequestId": "99996_F", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "readLength": "101/8/8/101", - "cmoSampleName": "C-8VK0V7-R001-d", - "captureName": "Pool-09483_R-10151_F-Tube7_1", + "cmoSampleName": "C-PPPPP3-R001-d", + "captureName": "Pool-99998_R-99996_F-Tube7_1", "igoComplete": true, - "labHeadName": "John Smith", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "labHeadName": "Test Investigator", + "barcodeIndex": "GTATTGGC-PPPP14", "labHeadEmail": "email@internet.com", "oncotreeCode": "MEL", "preservation": "Frozen", @@ -46,11 +46,11 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "SK_MEL_1091A_T", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_T_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "projectManagerName": "", - "investigatorSampleId": "SK_MEL_1091A_T", + "investigatorSampleId": "SAMPLE_T_001", "captureConcentrationNm": "8.333333333333334", "libraryConcentrationNgul": 13.2, "qcAccessEmails": "" @@ -70,26 +70,26 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-17", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10151_F_13", + "primaryId": "99996_F_13", "barcodeId": "DUAL_IDT_LIB_255", - "libraryIgoId": "10151_F_4_1_1_1", - "cmoPatientId": "C-DRKHP7", - "igoRequestId": "10151_F", + "libraryIgoId": "99996_F_4_1_1_1", + "cmoPatientId": "C-PPPPP7", + "igoRequestId": "99996_F", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "readLength": "101/8/8/101", - "cmoSampleName": "C-DRKHP7-M002-d", - "captureName": "Pool-09483_R-10151_F-Tube7_1", + "cmoSampleName": "C-PPPPP7-M002-d", + "captureName": "Pool-99998_R-99996_F-Tube7_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": "AGGATGGT-CGGAATAC", "labHeadEmail": "email@internet.com", "oncotreeCode": "MUP", @@ -105,11 +105,11 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "SK_MEL_919B_T", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_T_002", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "projectManagerName": "", - "investigatorSampleId": "SK_MEL_919B_T", + "investigatorSampleId": "SAMPLE_T_002", "captureConcentrationNm": "8.870967741935484", "libraryConcentrationNgul": 12.4, "qcAccessEmails": "" @@ -129,26 +129,26 @@ "metadata": { "R": "R1", "sex": "M", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-12", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10151_F_13", + "primaryId": "99996_F_13", "barcodeId": null, - "libraryIgoId": "10151_F_2", - "cmoPatientId": "C-DRKHP7", - "igoRequestId": "10151_F", + "libraryIgoId": "99996_F_2", + "cmoPatientId": "C-PPPPP7", + "igoRequestId": "99996_F", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HCYYWBBXY", + "flowCellId": "FCELLAAAA4", "readLength": "101/8/8/101", - "cmoSampleName": "C-DRKHP7-N001-d", - "captureName": "Pool-05257_CD-06287_AY-10151_F-Tube2_1", + "cmoSampleName": "C-PPPPP7-N001-d", + "captureName": "Pool-99992_D-99995_AY-99996_F-Tube2_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": null, "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -165,7 +165,7 @@ "dataAnalystName": "", "dataAnalystEmail": "", "externalSampleId": "31-N", - "investigatorName": "Jane Doe", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "projectManagerName": "", "investigatorSampleId": "31-N", @@ -188,26 +188,26 @@ "metadata": { "R": "R1", "sex": "F", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "genePanel": "IMPACT468", "baitSet": "IMPACT468_BAITS", "piEmail": "", "runDate": "2019-12-12", "runMode": "HiSeq High Output", "species": "Human", - "primaryId": "10151_F_13", + "primaryId": "99996_F_13", "barcodeId": null, - "libraryIgoId": "10151_F_3", - "cmoPatientId": "C-8VK0V7", - "igoRequestId": "10151_F", + "libraryIgoId": "99996_F_3", + "cmoPatientId": "C-PPPPP3", + "igoRequestId": "99996_F", "sequencingCenter": "MSKCC", "platform": "Illumina", - "flowCellId": "HCYYWBBXY", + "flowCellId": "FCELLAAAA4", "readLength": "101/8/8/101", - "cmoSampleName": "C-8VK0V7-N001-d", - "captureName": "Pool-05257_CD-06287_AY-10151_F-Tube2_1", + "cmoSampleName": "C-PPPPP3-N001-d", + "captureName": "Pool-99992_D-99995_AY-99996_F-Tube2_1", "igoComplete": true, - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "barcodeIndex": null, "labHeadEmail": "email@internet.com", "oncotreeCode": null, @@ -223,11 +223,11 @@ "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", - "externalSampleId": "JW_MEL_007_NORM", - "investigatorName": "Jane Doe", + "externalSampleId": "SAMPLE_N_001", + "investigatorName": "Test Scientist", "investigatorEmail": "email2@internet.com", "projectManagerName": "", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorSampleId": "SAMPLE_N_001", "captureConcentrationNm": "10.377358490566039", "libraryConcentrationNgul": 10.6, "qcAccessEmails": "" diff --git a/runner/fixtures/28ca34e8-9d4c-4543-9fc7-981bf5f6a97f.files.json b/runner/fixtures/28ca34e8-9d4c-4543-9fc7-981bf5f6a97f.files.json index 0bdb67c86..d65a82db3 100644 --- a/runner/fixtures/28ca34e8-9d4c-4543-9fc7-981bf5f6a97f.files.json +++ b/runner/fixtures/28ca34e8-9d4c-4543-9fc7-981bf5f6a97f.files.json @@ -3252,7 +3252,7 @@ "tumorOrNormal": "Tumor", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", @@ -3330,7 +3330,7 @@ "tumorOrNormal": "Tumor", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", @@ -3408,7 +3408,7 @@ "tumorOrNormal": "Normal", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", @@ -3486,7 +3486,7 @@ "tumorOrNormal": "Normal", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", diff --git a/runner/fixtures/4d9c8213-df56-4a0f-8d86-ce2bd8349c59.files.json b/runner/fixtures/4d9c8213-df56-4a0f-8d86-ce2bd8349c59.files.json index 4f1e70ea3..7eb17770d 100644 --- a/runner/fixtures/4d9c8213-df56-4a0f-8d86-ce2bd8349c59.files.json +++ b/runner/fixtures/4d9c8213-df56-4a0f-8d86-ce2bd8349c59.files.json @@ -3244,7 +3244,7 @@ "tumorOrNormal": "Tumor", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", @@ -3322,7 +3322,7 @@ "tumorOrNormal": "Normal", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", @@ -3400,7 +3400,7 @@ "tumorOrNormal": "Normal", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", @@ -3478,7 +3478,7 @@ "tumorOrNormal": "Tumor", "captureInputNg": null, "collectionYear": "", - "qcAccessEmails": "email1@mskcc.org, email2@mskcc.org", + "qcAccessEmails": "user1@example.org, user2@example.org", "tissueLocation": "", "dataAnalystName": "", "dataAnalystEmail": "", diff --git a/runner/fixtures/file_system.sample.json b/runner/fixtures/file_system.sample.json index 3eb7ba7bf..5a5852adc 100644 --- a/runner/fixtures/file_system.sample.json +++ b/runner/fixtures/file_system.sample.json @@ -5,9 +5,9 @@ "fields": { "created_date": "2020-10-07T16:03:56.488Z", "modified_date": "2022-04-27T19:58:14.058Z", - "sample_id": "08944_B_4", - "sample_name": "C-4LM16H-N001-d", - "cmo_sample_name": "s_C_4LM16H_N001_d", + "sample_id": "99991_B_4", + "sample_name": "C-PPPPP1-N001-d", + "cmo_sample_name": "s_C_PPPPP1_N001_d", "latest": true, "version": 0, "redact": false @@ -19,9 +19,9 @@ "fields": { "created_date": "2020-10-07T16:03:56.493Z", "modified_date": "2022-04-27T19:24:43.595Z", - "sample_id": "08944_B_3", - "sample_name": "C-4LM16H-X001-d", - "cmo_sample_name": "s_C_4LM16H_X001_d", + "sample_id": "99991_B_3", + "sample_name": "C-PPPPP1-X001-d", + "cmo_sample_name": "s_C_PPPPP1_X001_d", "latest": true, "version": 0, "redact": false diff --git a/runner/fixtures/runner.run.json b/runner/fixtures/runner.run.json index 8b961c58c..882f2105a 100644 --- a/runner/fixtures/runner.run.json +++ b/runner/fixtures/runner.run.json @@ -177,10 +177,10 @@ "baitSet": "MSK-ACCESS-v1_0-probesAllwFP_GRCh38", "primaryId": "05500_HF_1", "barcodeId": "-", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_HF", "dnaInputNg": 0, - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "captureName": null, "barcodeIndex": "AGTTGTGC-AGTTGTGC", "sampleOrigin": "Tissue", @@ -211,10 +211,10 @@ "baitSet": "MSK-CMO-CH-v1_0-probesAllwFP_GRCh38", "sampleId": "05500_HF_1", "barcodeId": "-", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_HF", "dnaInputNg": 0, - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "captureName": null, "barcodeIndex": "AGTTGTGC-AGTTGTGC", "sampleOrigin": "Tissue", diff --git a/runner/fixtures/runner.run_test.json b/runner/fixtures/runner.run_test.json index f1db3bede..adae3df26 100644 --- a/runner/fixtures/runner.run_test.json +++ b/runner/fixtures/runner.run_test.json @@ -170,10 +170,10 @@ "baitSet": "MSK-ACCESS-v1_0-probesAllwFP_GRCh38", "primaryId": "05500_HF_1", "barcodeId": "-", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_HF", "dnaInputNg": 0, - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "captureName": null, "barcodeIndex": "AGTTGTGC-AGTTGTGC", "sampleOrigin": "Tissue", @@ -204,10 +204,10 @@ "baitSet": "MSK-CMO-CH-v1_0-probesAllwFP_GRCh38", "sampleId": "05500_HF_1", "barcodeId": "-", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_HF", "dnaInputNg": 0, - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "captureName": null, "barcodeIndex": "AGTTGTGC-AGTTGTGC", "sampleOrigin": "Tissue", diff --git a/runner/tests/operator/access/access_snps_and_indels/test_snps_and_indels_operator.py b/runner/tests/operator/access/access_snps_and_indels/test_snps_and_indels_operator.py index 465c69076..42fd94d1b 100644 --- a/runner/tests/operator/access/access_snps_and_indels/test_snps_and_indels_operator.py +++ b/runner/tests/operator/access/access_snps_and_indels/test_snps_and_indels_operator.py @@ -122,7 +122,7 @@ def test_dmp_normal(self): :return: """ # Delete the IGO test samples, so DMP normal must be used - igo_normals = File.objects.filter(path__regex="C-000884-N0") + igo_normals = File.objects.filter(path__regex="C-PPPP19-N0") [f.delete() for f in igo_normals] pipeline_slug = "AccessLegacySNVOperator" diff --git a/runner/tests/operator/access/legacy_fastq_to_bam/test_legacy_fastq_to_bam.py b/runner/tests/operator/access/legacy_fastq_to_bam/test_legacy_fastq_to_bam.py index 9b0602f96..66b575481 100644 --- a/runner/tests/operator/access/legacy_fastq_to_bam/test_legacy_fastq_to_bam.py +++ b/runner/tests/operator/access/legacy_fastq_to_bam/test_legacy_fastq_to_bam.py @@ -9,10 +9,10 @@ FIXTURES = [ - "fixtures/tests/access_fastq_to_bam/10151_F.file.json", - "fixtures/tests/access_fastq_to_bam/10151_F.filemetadata.json", - "fixtures/tests/access_fastq_to_bam/10151_F.port.json", - "fixtures/tests/access_fastq_to_bam/10151_F.run.json", + "fixtures/tests/access_fastq_to_bam/99996_F.file.json", + "fixtures/tests/access_fastq_to_bam/99996_F.filemetadata.json", + "fixtures/tests/access_fastq_to_bam/99996_F.port.json", + "fixtures/tests/access_fastq_to_bam/99996_F.run.json", ] COMMON_FIXTURES = [ diff --git a/runner/tests/operator/access/merge_fastqs/test_fastq_merge_operator.py b/runner/tests/operator/access/merge_fastqs/test_fastq_merge_operator.py index 215f93084..095dae39c 100644 --- a/runner/tests/operator/access/merge_fastqs/test_fastq_merge_operator.py +++ b/runner/tests/operator/access/merge_fastqs/test_fastq_merge_operator.py @@ -10,8 +10,8 @@ FIXTURES = [ - "fixtures/tests/merge_fastqs/10151_F_13.file.json", - "fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json", + "fixtures/tests/merge_fastqs/99996_F_13.file.json", + "fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json", ] COMMON_FIXTURES = [ @@ -38,7 +38,7 @@ def test_access_legacy_fastq_merge_operator(self): self.assertEqual(len(File.objects.all()), operator_files_count) self.assertEqual(len(FileMetadata.objects.all()), operator_files_count) - request_id = "10151_F" + request_id = "99996_F" operator_model = Operator.objects.get(id=8) operator = OperatorFactory.get_by_model(operator_model, request_id=request_id) diff --git a/runner/tests/operator/access/v2_0_0/nucleo/test_nucleo_operator.py b/runner/tests/operator/access/v2_0_0/nucleo/test_nucleo_operator.py index ceeae08ae..ab1137af8 100644 --- a/runner/tests/operator/access/v2_0_0/nucleo/test_nucleo_operator.py +++ b/runner/tests/operator/access/v2_0_0/nucleo/test_nucleo_operator.py @@ -10,8 +10,8 @@ FIXTURES = [ - "fixtures/tests/merge_fastqs/10151_F_13.file.json", - "fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json", + "fixtures/tests/merge_fastqs/99996_F_13.file.json", + "fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json", ] COMMON_FIXTURES = [ @@ -38,7 +38,7 @@ def test_access_nucleo_operator(self): self.assertEqual(len(File.objects.all()), operator_files_count) self.assertEqual(len(FileMetadata.objects.all()), operator_files_count) - request_id = "10151_F" + request_id = "99996_F" operator_model = Operator.objects.get(id=10) operator = OperatorFactory.get_by_model(operator_model, request_id=request_id) diff --git a/runner/tests/operator/access/v2_0_0/qc/files_fixture.json b/runner/tests/operator/access/v2_0_0/qc/files_fixture.json index 475f9f701..357ed6c96 100644 --- a/runner/tests/operator/access/v2_0_0/qc/files_fixture.json +++ b/runner/tests/operator/access/v2_0_0/qc/files_fixture.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -31,8 +31,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bam", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bam", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -44,8 +44,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -57,8 +57,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -70,8 +70,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -83,8 +83,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -96,8 +96,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bai", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bai", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -109,8 +109,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -122,8 +122,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/runner/tests/operator/access/v2_0_0/qc/files_metadata_fixture.json b/runner/tests/operator/access/v2_0_0/qc/files_metadata_fixture.json index b6941c631..2c9b4b11a 100644 --- a/runner/tests/operator/access/v2_0_0/qc/files_metadata_fixture.json +++ b/runner/tests/operator/access/v2_0_0/qc/files_metadata_fixture.json @@ -10,9 +10,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -41,9 +41,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -72,9 +72,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -103,9 +103,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -134,9 +134,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", diff --git a/runner/tests/operator/access/v2_0_0/qc/ports_fixture.json b/runner/tests/operator/access/v2_0_0/qc/ports_fixture.json index 4c1154bff..df3c3ba50 100644 --- a/runner/tests/operator/access/v2_0_0/qc/ports_fixture.json +++ b/runner/tests/operator/access/v2_0_0/qc/ports_fixture.json @@ -18,11 +18,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "class": "File" }] } @@ -51,11 +51,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "class": "File" }] } @@ -84,11 +84,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "class": "File" }] } @@ -117,11 +117,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "class": "File" }] } @@ -150,11 +150,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "class": "File" }] } diff --git a/runner/tests/operator/access/v2_1_0/nucleo/test_nucleo_operator.py b/runner/tests/operator/access/v2_1_0/nucleo/test_nucleo_operator.py index dcd781ce1..43f66eb23 100644 --- a/runner/tests/operator/access/v2_1_0/nucleo/test_nucleo_operator.py +++ b/runner/tests/operator/access/v2_1_0/nucleo/test_nucleo_operator.py @@ -10,8 +10,8 @@ FIXTURES = [ - "fixtures/tests/merge_fastqs/10151_F_13.file.json", - "fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json", + "fixtures/tests/merge_fastqs/99996_F_13.file.json", + "fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json", ] COMMON_FIXTURES = [ @@ -38,7 +38,7 @@ def test_access_nucleo_operator(self): self.assertEqual(len(File.objects.all()), operator_files_count) self.assertEqual(len(FileMetadata.objects.all()), operator_files_count) - request_id = "10151_F" + request_id = "99996_F" operator_model = Operator.objects.get(id=16) operator = OperatorFactory.get_by_model(operator_model, request_id=request_id) diff --git a/runner/tests/operator/access/v2_1_0/qc/input_template.json.jinja2 b/runner/tests/operator/access/v2_1_0/qc/input_template.json.jinja2 index 23512b562..ba6f84561 100644 --- a/runner/tests/operator/access/v2_1_0/qc/input_template.json.jinja2 +++ b/runner/tests/operator/access/v2_1_0/qc/input_template.json.jinja2 @@ -13,7 +13,7 @@ "multiqc_config": { "class": "File", - "location": "juno:///juno/work/access/testing/users/johnsoni/access_qc/access_qc_generation/multiqc_configs/config.yaml" + "location": "juno:///juno/work/access/testing/users/testuser/access_qc/access_qc_generation/multiqc_configs/config.yaml" }, "biometrics_bed_file": { "class": "File", diff --git a/runner/tests/operator/access/v2_2_0/nucleo/test_nucleo_operator.py b/runner/tests/operator/access/v2_2_0/nucleo/test_nucleo_operator.py index 84ea17f2e..3797a9489 100644 --- a/runner/tests/operator/access/v2_2_0/nucleo/test_nucleo_operator.py +++ b/runner/tests/operator/access/v2_2_0/nucleo/test_nucleo_operator.py @@ -9,8 +9,8 @@ FIXTURES = [ - "fixtures/tests/merge_fastqs/10151_F_13.file.json", - "fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json", + "fixtures/tests/merge_fastqs/99996_F_13.file.json", + "fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json", ] COMMON_FIXTURES = [ @@ -37,7 +37,7 @@ def test_access_nucleo_operator(self): self.assertEqual(len(File.objects.all()), operator_files_count) self.assertEqual(len(FileMetadata.objects.all()), operator_files_count) - request_id = "10151_F" + request_id = "99996_F" operator_model = Operator.objects.get(id=29) operator = OperatorFactory.get_by_model(operator_model, request_id=request_id) diff --git a/runner/tests/operator/access/v2_2_0/qc/files_fixture.json b/runner/tests/operator/access/v2_2_0/qc/files_fixture.json index 475f9f701..357ed6c96 100644 --- a/runner/tests/operator/access/v2_2_0/qc/files_fixture.json +++ b/runner/tests/operator/access/v2_2_0/qc/files_fixture.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -31,8 +31,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bam", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bam", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -44,8 +44,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -57,8 +57,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -70,8 +70,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -83,8 +83,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -96,8 +96,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bai", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bai", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -109,8 +109,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -122,8 +122,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/runner/tests/operator/access/v2_2_0/qc/files_metadata_fixture.json b/runner/tests/operator/access/v2_2_0/qc/files_metadata_fixture.json index b6941c631..2c9b4b11a 100644 --- a/runner/tests/operator/access/v2_2_0/qc/files_metadata_fixture.json +++ b/runner/tests/operator/access/v2_2_0/qc/files_metadata_fixture.json @@ -10,9 +10,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -41,9 +41,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -72,9 +72,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -103,9 +103,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -134,9 +134,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", diff --git a/runner/tests/operator/access/v2_2_0/qc/ports_fixture.json b/runner/tests/operator/access/v2_2_0/qc/ports_fixture.json index 4c1154bff..df3c3ba50 100644 --- a/runner/tests/operator/access/v2_2_0/qc/ports_fixture.json +++ b/runner/tests/operator/access/v2_2_0/qc/ports_fixture.json @@ -18,11 +18,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "class": "File" }] } @@ -51,11 +51,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "class": "File" }] } @@ -84,11 +84,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "class": "File" }] } @@ -117,11 +117,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "class": "File" }] } @@ -150,11 +150,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "class": "File" }] } diff --git a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_alignment_pair_operator.py b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_alignment_pair_operator.py index c4e15d1f0..723be54c1 100644 --- a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_alignment_pair_operator.py +++ b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_alignment_pair_operator.py @@ -42,9 +42,9 @@ def test_operator_factory_alignment_pair2(self): This test loads some Alignment Pair fixtures and checks the number of Files available to the Operator """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id = "bar" @@ -61,9 +61,9 @@ def test_operator_factory_alignment_pair3(self): Test that a Alignment Pair operator has access to all files in the database, even non-Argos files """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) self.assertEqual(len(File.objects.all()), 4) diff --git a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_construct_argos_pair.py b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_construct_argos_pair.py index 0d4b63520..bdd226f57 100644 --- a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_construct_argos_pair.py +++ b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_construct_argos_pair.py @@ -27,14 +27,14 @@ def test_construct_alignment_pair_jobs1(self): Test that alignment argos jobs are correctly created """ # Load fixtures - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) files = File.objects.filter( { - "filemetadata__metadata__{}".format(settings.REQUEST_ID_METADATA_KEY): "10075_D", + "filemetadata__metadata__{}".format(settings.REQUEST_ID_METADATA_KEY): "99990_D", "filemetadata__metadata__{}".format(settings.IGO_COMPLETE_METADATA_KEY): True, } ).all() @@ -60,7 +60,7 @@ def test_construct_alignment_pair_jobs1(self): alignment_argos_inputs, error_samples = construct_alignment_pair_jobs(samples) expected_inputs = json.load( - open(os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.argos.input.json")) + open(os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.argos.input.json")) ) print("Running test_construct_alignment_pair_jobs1") diff --git a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_make_sample.py b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_make_sample.py index d2a3989e8..3c4ec6d4a 100644 --- a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_make_sample.py +++ b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_make_sample.py @@ -15,7 +15,7 @@ def test_build_sample1(self): """ data = [ { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", "id": UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac"), "metadata": { "R": "R1", @@ -24,38 +24,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, - settings.LIBRARY_ID_METADATA_KEY: "10075_D_2_3", + settings.LIBRARY_ID_METADATA_KEY: "99990_D_2_3", "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -63,10 +63,10 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", }, { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", "id": UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7"), "metadata": { "R": "R2", @@ -75,38 +75,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, "libraryIgoId": None, "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -114,7 +114,7 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", }, ] @@ -122,32 +122,32 @@ def test_build_sample1(self): expected_sample = { "CN": "MSKCC", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2_3", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "LB": "99990_D_2_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R2_bid": [UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7")], "bam": [], "bam_bid": [], - "SM": "s_C_8VK0V7_N001_d", + "SM": "s_C_PPPPP3_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", - "patient_id": "C-8VK0V7", - "request_id": "10075_D_2", + "sample_id": "99990_D_2_3", + "patient_id": "C-PPPPP3", + "request_id": "99990_D_2", "run_date": ["2019-12-12"], - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } diff --git a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_pair_request.py b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_pair_request.py index 61eb3c91b..bbb073df0 100755 --- a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_pair_request.py +++ b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_pair_request.py @@ -80,18 +80,18 @@ def test_compile_pairs1(self): """ samples = [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "sample_id": "my_sample_id2", "SM": "my_sample_id2", }, { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id1", @@ -102,10 +102,10 @@ def test_compile_pairs1(self): expected_pairs = { "tumor": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", @@ -113,10 +113,10 @@ def test_compile_pairs1(self): ], "normal": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id2", "SM": "my_sample_id2", @@ -132,8 +132,8 @@ def test_compile_pairs2(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "SM": "my_sample_id1", @@ -141,8 +141,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "SM": "my_sample_id2", @@ -150,8 +150,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id3", @@ -159,8 +159,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id4", @@ -168,8 +168,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id5", @@ -181,27 +181,27 @@ def test_compile_pairs2(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id3", "SM": "my_sample_id3", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id4", "SM": "my_sample_id4", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id5", "SM": "my_sample_id5", @@ -210,27 +210,27 @@ def test_compile_pairs2(self): "normal": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id2", "SM": "my_sample_id2", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", @@ -251,8 +251,8 @@ def test_compile_pairs3(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", } @@ -265,23 +265,23 @@ def test_compile_pairs4(self): """ Test pairing with only a single unpaired Tumor sample Test that the appropriate Normal sample is found from the other samples in the same request - missing normal for sample 10075_D_1; querying patient C-DRKHP7 + missing normal for sample 99990_D_1; querying patient C-PPPPP7 """ # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", } ] pairs = compile_pairs(samples) @@ -289,42 +289,42 @@ def test_compile_pairs4(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("40a07e9a-2198-40b7-9f7f-7696c9d6429e")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("bb7ff922-b741-4df7-ba2a-4f3b8549e8b5")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", } @@ -343,10 +343,10 @@ def test_compile_pairs5(self): This time also load File entries from another request to make sure they do not confound the pairing """ # Load fixtures - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 14) @@ -355,12 +355,12 @@ def test_compile_pairs5(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", } ] pairs = compile_pairs(samples) @@ -368,42 +368,42 @@ def test_compile_pairs5(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("40a07e9a-2198-40b7-9f7f-7696c9d6429e")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("bb7ff922-b741-4df7-ba2a-4f3b8549e8b5")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", } @@ -422,11 +422,11 @@ def test_get_pair_from_other_request(self): """ # Load fixtures # only normals - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) # only tumors - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -435,13 +435,13 @@ def test_get_pair_from_other_request(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", } ] @@ -450,44 +450,44 @@ def test_get_pair_from_other_request(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", } ], "normal": [ { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_2_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_2_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-12"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2_bid": [UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7")], "bam": [], "bam_bid": [], - "request_id": "10075_D_2", - "run_id": ["JAX_0397"], + "request_id": "99990_D_2", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], @@ -504,10 +504,10 @@ def test_get_most_recent_normal1(self): in the event that a patient has several normals Return the Normal with the most recent run_date """ - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -516,12 +516,12 @@ def test_get_most_recent_normal1(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], } ] @@ -531,12 +531,12 @@ def test_get_most_recent_normal1(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], } ], @@ -544,31 +544,31 @@ def test_get_most_recent_normal1(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_4_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_4_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_4_3", + "sample_id": "99990_D_4_3", "run_date": ["2019-12-13"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("08072445-84ff-4b43-855d-d8d2dc87e2d5")], "R2_bid": [UUID("f0d9a1e1-9414-42df-a749-08776732ee04")], "bam": [], "bam_bid": [], - "request_id": "10075_D_4", - "run_id": ["JAX_0397"], + "request_id": "99990_D_4", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], @@ -593,33 +593,33 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): bam_filetype_instance = FileType.objects.get(name="bam") # generate tumor samples - # Sample 1 C-8VK0V7 + # Sample 1 C-PPPPP3 tumor1_R1_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7.R1.fastq", - path="/C-8VK0V7.R1.fastq", + file_name="C-PPPPP3.R1.fastq", + path="/C-PPPPP3.R1.fastq", ) FileMetadata.objects.create_or_update( file=tumor1_R1_file_instance, metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_3_5", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_3_5", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-R001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-R001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -627,8 +627,8 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): settings.SAMPLE_CLASS_METADATA_KEY: "Resection", "tumorOrNormal": "Tumor", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Local Recurrence", - "externalSampleId": "SK_MEL_1091A_T", - "investigatorSampleId": "SK_MEL_1091A_T", + "externalSampleId": "SAMPLE_T_001", + "investigatorSampleId": "SAMPLE_T_001", "labHeadEmail": "", "labHeadName": "", }, @@ -636,29 +636,29 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): tumor1_R2_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7.R2.fastq", - path="/C-8VK0V7.R2.fastq", + file_name="C-PPPPP3.R2.fastq", + path="/C-PPPPP3.R2.fastq", ) FileMetadata.objects.create_or_update( file=tumor1_R2_file_instance, metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_3_5", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_3_5", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-R001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-R001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -666,8 +666,8 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): settings.SAMPLE_CLASS_METADATA_KEY: "Resection", "tumorOrNormal": "Tumor", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Local Recurrence", - "externalSampleId": "SK_MEL_1091A_T", - "investigatorSampleId": "SK_MEL_1091A_T", + "externalSampleId": "SAMPLE_T_001", + "investigatorSampleId": "SAMPLE_T_001", "labHeadEmail": "", "labHeadName": "", }, @@ -685,18 +685,18 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", settings.SAMPLE_ID_METADATA_KEY: "Sample12345", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", settings.PATIENT_ID_METADATA_KEY: "C-ABCDEF", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-ABCDEF-R001-d", @@ -724,18 +724,18 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", settings.SAMPLE_ID_METADATA_KEY: "Sample12345", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", settings.PATIENT_ID_METADATA_KEY: "C-ABCDEF", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-ABCDEF-R001-d", @@ -756,12 +756,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ] @@ -780,7 +780,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "bait_set": "IMPACT468_BAITS", "sequencingCenter": "MSKCC", @@ -797,7 +797,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "bait_set": "IMPACT468_BAITS", "sequencingCenter": "MSKCC", @@ -816,12 +816,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -830,14 +830,14 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -847,7 +847,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "bam": [], "bam_bid": [], "specimen_type": "Pooled Normal", - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", "run_id": [""], @@ -869,21 +869,21 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): dmp_bam_file_instance = File.objects.create( file_type=bam_filetype_instance, file_group=dmp_bam_filegroup_instance, - file_name="C-8VK0V7.bam", - path="/C-8VK0V7.bam", + file_name="C-PPPPP3.bam", + path="/C-PPPPP3.bam", ) FileMetadata.objects.create_or_update( file=dmp_bam_file_instance, version=1, metadata={ - "bai": "/C-8VK0V7.bai", - "bam": "/C-8VK0V7.bam", + "bai": "/C-PPPPP3.bai", + "bam": "/C-PPPPP3.bam", "type": "N", "assay": "IM6", "sample": "P-1234567-N01-IM6", "anon_id": "ABCDEF-N", "patient": { - "cmo": "8VK0V7", + "cmo": "PPPPP3", "dmp": "P-1234567", "updated": "2020-03-19T23:57:51.941963Z", "imported": "2020-03-19T23:57:51.941945Z", @@ -896,7 +896,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "imported": "2020-03-25T19:45:16.421137Z", "cmo_assay": "IMPACT468", "tumor_type": "MBC", - "external_id": "C-8VK0V7-N901-dZ-IM6", + "external_id": "C-PPPPP3-N901-dZ-IM6", "sample_type": "0", "tissue_type": "Breast", "primary_site": "Breast", @@ -917,12 +917,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -931,23 +931,23 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["DMP_FCID_DMP_BARCODEIDX"], - "LB": "C-8VK0V7-N901-dZ-IM6_1", + "LB": "C-PPPPP3-N901-dZ-IM6_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], - "SM": "s_C_8VK0V7_N901_dZ_IM6", + "ID": ["s_C_PPPPP3_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], + "SM": "s_C_PPPPP3_N901_dZ_IM6", "species": "", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "C-8VK0V7-N901-dZ-IM6", + "sample_id": "C-PPPPP3-N901-dZ-IM6", "run_date": [""], "specimen_type": "DMP Normal", "R1": [], "R2": [], "R1_bid": [], "R2_bid": [], - "bam": ["/C-8VK0V7.bam"], + "bam": ["/C-PPPPP3.bam"], "bam_bid": [], # UUID('77b9a78f-1bed-475c-9799-c18a6f57b347') - "request_id": "C-8VK0V7-N901-dZ-IM6", + "request_id": "C-PPPPP3-N901-dZ-IM6", "pi": "", "pi_email": "", "run_id": [""], @@ -971,33 +971,33 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): self.assertDictEqual(pairs, expected_pairs) # Now add a matched normal to the original request for the sample - # Sample 1 C-8VK0V7 + # Sample 1 C-PPPPP3 normal1_R1_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7-N.R1.fastq", - path="/C-8VK0V7-N.R1.fastq", + file_name="C-PPPPP3-N.R1.fastq", + path="/C-PPPPP3-N.R1.fastq", ) FileMetadata.objects.create_or_update( file=normal1_R1_file_instance, metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -1014,29 +1014,29 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): normal1_R2_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7-N.R2.fastq", - path="/C-8VK0V7-N.R2.fastq", + file_name="C-PPPPP3-N.R2.fastq", + path="/C-PPPPP3-N.R2.fastq", ) FileMetadata.objects.create_or_update( file=normal1_R2_file_instance, metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -1062,12 +1062,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -1075,27 +1075,27 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], - "LB": "s_C_8VK0V7_N001_d_1", + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], + "LB": "s_C_PPPPP3_N001_d_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA6_GTATTGGC-PPPP14"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-17"], "specimen_type": "Resection", - "R1": ["/C-8VK0V7-N.R1.fastq"], - "R2": ["/C-8VK0V7-N.R2.fastq"], + "R1": ["/C-PPPPP3-N.R1.fastq"], + "R2": ["/C-PPPPP3-N.R2.fastq"], "R1_bid": [], # UUID('bfb94fe6-bf46-431a-8f72-6ee47ee72fc9') "R2_bid": [], # UUID('1e8b68f8-c333-499c-b22d-50fbef2d2ea7') "bam": [], "bam_bid": [], - "request_id": "10075_D_3", + "request_id": "99990_D_3", "pi": "", "pi_email": "", - "run_id": ["PITT_0439"], + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -1120,10 +1120,10 @@ def test_compile_pairs_custom1(self): samples = [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -1135,7 +1135,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_date": ["2019-12-12"], "species": "Human", @@ -1144,10 +1144,10 @@ def test_compile_pairs_custom1(self): }, { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("d2d8ed36-d8f4-4e93-b038-d38328fad021")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -1159,7 +1159,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_date": ["2019-12-17"], "species": "Human", @@ -1173,10 +1173,10 @@ def test_compile_pairs_custom1(self): "tumor": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -1190,7 +1190,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-17"], "species": "Human", "specimen_type": "Resection", @@ -1203,10 +1203,10 @@ def test_compile_pairs_custom1(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -1220,7 +1220,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", diff --git a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_retrieve_samples_by_query.py b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_retrieve_samples_by_query.py index 0305e2957..c79992d67 100644 --- a/runner/tests/operator/alignment_pair_operator/v1_0_0/test_retrieve_samples_by_query.py +++ b/runner/tests/operator/alignment_pair_operator/v1_0_0/test_retrieve_samples_by_query.py @@ -57,9 +57,9 @@ def test_get_dmp_normal1(self): # load some fixtures # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) # test lookup again with some Files loaded; should still be None since it doesnt match anything yet @@ -69,13 +69,13 @@ def test_get_dmp_normal1(self): self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures but non-matching bait set; no DMP bams loaded yet - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "bar" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures and matching bait_set; no DMP bams loaded yet - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "IMPACT468_BAITS" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) @@ -84,19 +84,19 @@ def test_get_dmp_normal1(self): file_group_instance = FileGroup.objects.get(name="DMP BAMs") filetype_instance = FileType.objects.get(name="bam") file_instance = File.objects.create( - file_type=filetype_instance, file_group=file_group_instance, file_name="C-8VK0V7.bam", path="/C-8VK0V7.bam" + file_type=filetype_instance, file_group=file_group_instance, file_name="C-PPPPP3.bam", path="/C-PPPPP3.bam" ) FileMetadata.objects.create_or_update( file=file_instance, metadata={ - "bai": "/C-8VK0V7.bai", - "bam": "/C-8VK0V7.bam", + "bai": "/C-PPPPP3.bai", + "bam": "/C-PPPPP3.bam", "type": "N", "assay": "IM6", "sample": "P-1234567-N01-IM6", "anon_id": "ABCDEF-N", "patient": { - "cmo": "8VK0V7", + "cmo": "PPPPP3", "dmp": "P-1234567", "updated": "2020-03-19T23:57:51.941963Z", "imported": "2020-03-19T23:57:51.941945Z", @@ -109,7 +109,7 @@ def test_get_dmp_normal1(self): "tumor_type": "MBC", "sequencingCenter": "MSKCC", "platform": "Illumina", - "external_id": "s_C_8VK0V7_N901_dZ_IM6", + "external_id": "s_C_PPPPP3_N901_dZ_IM6", "sample_type": "0", "tissue_type": "Breast", "primary_site": "Breast", @@ -124,7 +124,7 @@ def test_get_dmp_normal1(self): ) # test with a patient ID taken from fixtures but non-matching bait_set - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "foo" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) @@ -136,7 +136,7 @@ def test_get_dmp_normal1(self): self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures and a matching bait_set - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "IMPACT468_BAITS" dmp_normal = get_dmp_normal(patient_id, bait_set) @@ -144,26 +144,26 @@ def test_get_dmp_normal1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["DMP_FCID_DMP_BARCODEIDX"], - "LB": "s_C_8VK0V7_N901_dZ_IM6_1", + "LB": "s_C_PPPPP3_N901_dZ_IM6_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], - "SM": "s_C_8VK0V7_N901_dZ_IM6", + "ID": ["s_C_PPPPP3_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], + "SM": "s_C_PPPPP3_N901_dZ_IM6", "species": "", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "s_C_8VK0V7_N901_dZ_IM6", + "sample_id": "s_C_PPPPP3_N901_dZ_IM6", "run_date": [""], "specimen_type": "DMP Normal", "R1": [], "R2": [], "R1_bid": [], "R2_bid": [], - "bam": ["/C-8VK0V7.bam"], + "bam": ["/C-PPPPP3.bam"], "bam_bid": [ # mock the UUID for testing since it will be different every time "deletemeplease" ], - "request_id": "s_C_8VK0V7_N901_dZ_IM6", + "request_id": "s_C_PPPPP3_N901_dZ_IM6", "pi": "", "pi_email": "", "run_id": [""], @@ -384,7 +384,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -401,7 +401,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -411,7 +411,7 @@ def test_get_pooled_normals1(self): ) pooled_normals = get_pooled_normals( - run_ids=["PITT_0439"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS" + run_ids=["SEQRUN_0008"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS" ) # remove the R1_bid and R2_bid for testing because they are non-deterministic # TODO: mock this ^^ @@ -422,14 +422,14 @@ def test_get_pooled_normals1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "Pooled Normal", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -438,7 +438,7 @@ def test_get_pooled_normals1(self): "R2_bid": [], # UUID('ec9817d1-d6f5-4f1d-9c0a-c82fc22d4daa') "bam": [], "bam_bid": [], - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", "run_id": [""], diff --git a/runner/tests/operator/argos_bam_operator/v1_0_0/test_argos_bam_operator.py b/runner/tests/operator/argos_bam_operator/v1_0_0/test_argos_bam_operator.py index 267e30c1a..a2d73be03 100644 --- a/runner/tests/operator/argos_bam_operator/v1_0_0/test_argos_bam_operator.py +++ b/runner/tests/operator/argos_bam_operator/v1_0_0/test_argos_bam_operator.py @@ -42,9 +42,9 @@ def test_operator_factory_argos2(self): This test loads some Argos fixtures and checks the number of Files available to the Operator """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id = "bar" @@ -62,9 +62,9 @@ def test_operator_factory_argos3(self): Test that a Argos operator has access to all files in the database, even non-Argos files """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) self.assertEqual(len(File.objects.all()), 4) diff --git a/runner/tests/operator/argos_bam_operator/v1_0_0/test_construct_argos_pair.py b/runner/tests/operator/argos_bam_operator/v1_0_0/test_construct_argos_pair.py index 8967d6af5..928512951 100644 --- a/runner/tests/operator/argos_bam_operator/v1_0_0/test_construct_argos_pair.py +++ b/runner/tests/operator/argos_bam_operator/v1_0_0/test_construct_argos_pair.py @@ -24,9 +24,9 @@ def test_construct_argos_jobs1(self): Test that Argos jobs are correctly created """ # Load fixtures - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id_metadata_key = settings.REQUEST_ID_METADATA_KEY @@ -34,7 +34,7 @@ def test_construct_argos_jobs1(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "10075_D", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99990_D", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() @@ -60,7 +60,7 @@ def test_construct_argos_jobs1(self): argos_inputs, error_samples = construct_argos_jobs(samples) expected_inputs = json.load( - open(os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.argos_bam_1_0_0.input.json")) + open(os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.argos_bam_1_0_0.input.json")) ) print("Running test_construct_argos_jobs1") self.assertTrue(argos_inputs == expected_inputs) diff --git a/runner/tests/operator/argos_bam_operator/v1_1_0/test_construct_argos_pair.py b/runner/tests/operator/argos_bam_operator/v1_1_0/test_construct_argos_pair.py index 12ac6c6a0..487688867 100644 --- a/runner/tests/operator/argos_bam_operator/v1_1_0/test_construct_argos_pair.py +++ b/runner/tests/operator/argos_bam_operator/v1_1_0/test_construct_argos_pair.py @@ -24,9 +24,9 @@ def test_construct_argos_jobs1(self): Test that Argos jobs are correctly created """ # Load fixtures - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id_metadata_key = settings.REQUEST_ID_METADATA_KEY @@ -34,7 +34,7 @@ def test_construct_argos_jobs1(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "10075_D", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99990_D", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() @@ -60,14 +60,14 @@ def test_construct_argos_jobs1(self): argos_inputs, error_samples = construct_argos_jobs(samples) expected_inputs = json.load( - open(os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.argos_bam.input.json")) + open(os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.argos_bam.input.json")) ) files.delete() print("Running test_construct_argos_jobs1") self.assertTrue(argos_inputs == expected_inputs) def test_construct_argos_jobs_pdx(self): - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "08944_B.fixtures.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99991_B.fixtures.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id_metadata_key = settings.REQUEST_ID_METADATA_KEY @@ -75,7 +75,7 @@ def test_construct_argos_jobs_pdx(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "08944_B", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99991_B", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() @@ -100,7 +100,7 @@ def test_construct_argos_jobs_pdx(self): samples.append(build_sample(igo_id_group[igo_id])) argos_inputs, error_samples = construct_argos_jobs(samples) - expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "08944_B.argos_bam.input.json"))) + expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "99991_B.argos_bam.input.json"))) print(json.dumps(argos_inputs)) print("Running test_construct_argos_jobs_pdx") self.assertTrue(argos_inputs == expected_inputs) diff --git a/runner/tests/operator/argos_operator/v1_0_0/test_argos_operator.py b/runner/tests/operator/argos_operator/v1_0_0/test_argos_operator.py index 1b710a75d..9f777e1cb 100644 --- a/runner/tests/operator/argos_operator/v1_0_0/test_argos_operator.py +++ b/runner/tests/operator/argos_operator/v1_0_0/test_argos_operator.py @@ -41,9 +41,9 @@ def test_operator_factory_argos2(self): This test loads some Argos fixtures and checks the number of Files available to the Operator """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id = "bar" @@ -61,9 +61,9 @@ def test_operator_factory_argos3(self): Test that a Argos operator has access to all files in the database, even non-Argos files """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) self.assertEqual(len(File.objects.all()), 4) diff --git a/runner/tests/operator/argos_operator/v1_0_0/test_construct_argos_pair.py b/runner/tests/operator/argos_operator/v1_0_0/test_construct_argos_pair.py index fe256ff55..0758965f4 100644 --- a/runner/tests/operator/argos_operator/v1_0_0/test_construct_argos_pair.py +++ b/runner/tests/operator/argos_operator/v1_0_0/test_construct_argos_pair.py @@ -25,14 +25,14 @@ def test_construct_argos_jobs1(self): Test that Argos jobs are correctly created """ # Load fixtures - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(settings.REQUEST_ID_METADATA_KEY): "10075_D", + "filemetadata__metadata__{}".format(settings.REQUEST_ID_METADATA_KEY): "99990_D", "filemetadata__metadata__{}".format(settings.IGO_COMPLETE_METADATA_KEY): True, } ).all() @@ -58,7 +58,7 @@ def test_construct_argos_jobs1(self): argos_inputs, error_samples = construct_argos_jobs(samples) expected_inputs = json.load( - open(os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.argos.input.json")) + open(os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.argos.input.json")) ) print("Running test_construct_argos_jobs1") diff --git a/runner/tests/operator/argos_operator/v1_0_0/test_make_sample.py b/runner/tests/operator/argos_operator/v1_0_0/test_make_sample.py index 3f1c19a53..c372140e4 100644 --- a/runner/tests/operator/argos_operator/v1_0_0/test_make_sample.py +++ b/runner/tests/operator/argos_operator/v1_0_0/test_make_sample.py @@ -15,7 +15,7 @@ def test_build_sample1(self): """ data = [ { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", "id": UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac"), "metadata": { "R": "R1", @@ -24,38 +24,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, - settings.LIBRARY_ID_METADATA_KEY: "10075_D_2_3", + settings.LIBRARY_ID_METADATA_KEY: "99990_D_2_3", "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -63,10 +63,10 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", }, { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", "id": UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7"), "metadata": { "R": "R2", @@ -75,38 +75,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, "libraryIgoId": None, "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -114,7 +114,7 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", }, ] @@ -122,32 +122,32 @@ def test_build_sample1(self): expected_sample = { "CN": "MSKCC", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2_3", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "LB": "99990_D_2_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R2_bid": [UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7")], "bam": [], "bam_bid": [], - "SM": "s_C_8VK0V7_N001_d", + "SM": "s_C_PPPPP3_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", - "patient_id": "C-8VK0V7", - "request_id": "10075_D_2", + "sample_id": "99990_D_2_3", + "patient_id": "C-PPPPP3", + "request_id": "99990_D_2", "run_date": ["2019-12-12"], - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } diff --git a/runner/tests/operator/argos_operator/v1_0_0/test_pair_request.py b/runner/tests/operator/argos_operator/v1_0_0/test_pair_request.py index db6097842..50fa6eb30 100755 --- a/runner/tests/operator/argos_operator/v1_0_0/test_pair_request.py +++ b/runner/tests/operator/argos_operator/v1_0_0/test_pair_request.py @@ -80,18 +80,18 @@ def test_compile_pairs1(self): """ samples = [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "sample_id": "my_sample_id2", "SM": "my_sample_id2", }, { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id1", @@ -102,10 +102,10 @@ def test_compile_pairs1(self): expected_pairs = { "tumor": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", @@ -113,10 +113,10 @@ def test_compile_pairs1(self): ], "normal": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id2", "SM": "my_sample_id2", @@ -132,8 +132,8 @@ def test_compile_pairs2(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "SM": "my_sample_id1", @@ -141,8 +141,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "SM": "my_sample_id2", @@ -150,8 +150,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id3", @@ -159,8 +159,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id4", @@ -168,8 +168,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id5", @@ -181,27 +181,27 @@ def test_compile_pairs2(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id3", "SM": "my_sample_id3", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id4", "SM": "my_sample_id4", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id5", "SM": "my_sample_id5", @@ -210,27 +210,27 @@ def test_compile_pairs2(self): "normal": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id2", "SM": "my_sample_id2", }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", @@ -251,8 +251,8 @@ def test_compile_pairs3(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", } @@ -265,23 +265,23 @@ def test_compile_pairs4(self): """ Test pairing with only a single unpaired Tumor sample Test that the appropriate Normal sample is found from the other samples in the same request - missing normal for sample 10075_D_1; querying patient C-DRKHP7 + missing normal for sample 99990_D_1; querying patient C-PPPPP7 """ # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", } ] pairs = compile_pairs(samples) @@ -289,42 +289,42 @@ def test_compile_pairs4(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("40a07e9a-2198-40b7-9f7f-7696c9d6429e")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("bb7ff922-b741-4df7-ba2a-4f3b8549e8b5")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", } @@ -343,10 +343,10 @@ def test_compile_pairs5(self): This time also load File entries from another request to make sure they do not confound the pairing """ # Load fixtures - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 14) @@ -355,12 +355,12 @@ def test_compile_pairs5(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", } ] pairs = compile_pairs(samples) @@ -368,42 +368,42 @@ def test_compile_pairs5(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("40a07e9a-2198-40b7-9f7f-7696c9d6429e")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("bb7ff922-b741-4df7-ba2a-4f3b8549e8b5")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", } @@ -422,11 +422,11 @@ def test_get_pair_from_other_request(self): """ # Load fixtures # only normals - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) # only tumors - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -435,13 +435,13 @@ def test_get_pair_from_other_request(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", } ] @@ -450,44 +450,44 @@ def test_get_pair_from_other_request(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", } ], "normal": [ { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_2_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_2_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-12"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2_bid": [UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7")], "bam": [], "bam_bid": [], - "request_id": "10075_D_2", - "run_id": ["JAX_0397"], + "request_id": "99990_D_2", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], @@ -504,10 +504,10 @@ def test_get_most_recent_normal1(self): in the event that a patient has several normals Return the Normal with the most recent run_date """ - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -516,12 +516,12 @@ def test_get_most_recent_normal1(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], } ] @@ -531,12 +531,12 @@ def test_get_most_recent_normal1(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], } ], @@ -544,31 +544,31 @@ def test_get_most_recent_normal1(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_4_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_4_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_4_3", + "sample_id": "99990_D_4_3", "run_date": ["2019-12-13"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("08072445-84ff-4b43-855d-d8d2dc87e2d5")], "R2_bid": [UUID("f0d9a1e1-9414-42df-a749-08776732ee04")], "bam": [], "bam_bid": [], - "request_id": "10075_D_4", - "run_id": ["JAX_0397"], + "request_id": "99990_D_4", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], @@ -593,33 +593,33 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): bam_filetype_instance = FileType.objects.get(name="bam") # generate tumor samples - # Sample 1 C-8VK0V7 + # Sample 1 C-PPPPP3 tumor1_R1_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7.R1.fastq", - path="/C-8VK0V7.R1.fastq", + file_name="C-PPPPP3.R1.fastq", + path="/C-PPPPP3.R1.fastq", ) FileMetadata.objects.create_or_update( file=tumor1_R1_file_instance, metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_3_5", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_3_5", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-R001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-R001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -627,8 +627,8 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): settings.SAMPLE_CLASS_METADATA_KEY: "Resection", "tumorOrNormal": "Tumor", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Local Recurrence", - "externalSampleId": "SK_MEL_1091A_T", - "investigatorSampleId": "SK_MEL_1091A_T", + "externalSampleId": "SAMPLE_T_001", + "investigatorSampleId": "SAMPLE_T_001", "labHeadEmail": "", "labHeadName": "", }, @@ -636,29 +636,29 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): tumor1_R2_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7.R2.fastq", - path="/C-8VK0V7.R2.fastq", + file_name="C-PPPPP3.R2.fastq", + path="/C-PPPPP3.R2.fastq", ) FileMetadata.objects.create_or_update( file=tumor1_R2_file_instance, metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_3_5", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_3_5", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-R001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-R001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -666,8 +666,8 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): settings.SAMPLE_CLASS_METADATA_KEY: "Resection", "tumorOrNormal": "Tumor", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Local Recurrence", - "externalSampleId": "SK_MEL_1091A_T", - "investigatorSampleId": "SK_MEL_1091A_T", + "externalSampleId": "SAMPLE_T_001", + "investigatorSampleId": "SAMPLE_T_001", "labHeadEmail": "", "labHeadName": "", }, @@ -685,18 +685,18 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", settings.SAMPLE_ID_METADATA_KEY: "Sample12345", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", settings.PATIENT_ID_METADATA_KEY: "C-ABCDEF", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-ABCDEF-R001-d", @@ -724,18 +724,18 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", settings.SAMPLE_ID_METADATA_KEY: "Sample12345", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", settings.PATIENT_ID_METADATA_KEY: "C-ABCDEF", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-ABCDEF-R001-d", @@ -756,12 +756,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ] @@ -780,7 +780,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "bait_set": "IMPACT468_BAITS", "sequencingCenter": "MSKCC", @@ -797,7 +797,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "bait_set": "IMPACT468_BAITS", "sequencingCenter": "MSKCC", @@ -816,12 +816,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -830,14 +830,14 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -847,7 +847,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "bam": [], "bam_bid": [], "specimen_type": "Pooled Normal", - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", "run_id": [""], @@ -869,21 +869,21 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): dmp_bam_file_instance = File.objects.create( file_type=bam_filetype_instance, file_group=dmp_bam_filegroup_instance, - file_name="C-8VK0V7.bam", - path="/C-8VK0V7.bam", + file_name="C-PPPPP3.bam", + path="/C-PPPPP3.bam", ) FileMetadata.objects.create_or_update( file=dmp_bam_file_instance, version=1, metadata={ - "bai": "/C-8VK0V7.bai", - "bam": "/C-8VK0V7.bam", + "bai": "/C-PPPPP3.bai", + "bam": "/C-PPPPP3.bam", "type": "N", "assay": "IM6", "sample": "P-1234567-N01-IM6", "anon_id": "ABCDEF-N", "patient": { - "cmo": "8VK0V7", + "cmo": "PPPPP3", "dmp": "P-1234567", "updated": "2020-03-19T23:57:51.941963Z", "imported": "2020-03-19T23:57:51.941945Z", @@ -896,7 +896,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "imported": "2020-03-25T19:45:16.421137Z", "cmo_assay": "IMPACT468", "tumor_type": "MBC", - "external_id": "C-8VK0V7-N901-dZ-IM6", + "external_id": "C-PPPPP3-N901-dZ-IM6", "sample_type": "0", "tissue_type": "Breast", "primary_site": "Breast", @@ -917,12 +917,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -931,23 +931,23 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["DMP_FCID_DMP_BARCODEIDX"], - "LB": "C-8VK0V7-N901-dZ-IM6_1", + "LB": "C-PPPPP3-N901-dZ-IM6_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], - "SM": "s_C_8VK0V7_N901_dZ_IM6", + "ID": ["s_C_PPPPP3_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], + "SM": "s_C_PPPPP3_N901_dZ_IM6", "species": "", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "C-8VK0V7-N901-dZ-IM6", + "sample_id": "C-PPPPP3-N901-dZ-IM6", "run_date": [""], "specimen_type": "DMP Normal", "R1": [], "R2": [], "R1_bid": [], "R2_bid": [], - "bam": ["/C-8VK0V7.bam"], + "bam": ["/C-PPPPP3.bam"], "bam_bid": [], # UUID('77b9a78f-1bed-475c-9799-c18a6f57b347') - "request_id": "C-8VK0V7-N901-dZ-IM6", + "request_id": "C-PPPPP3-N901-dZ-IM6", "pi": "", "pi_email": "", "run_id": [""], @@ -971,33 +971,33 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): self.assertDictEqual(pairs, expected_pairs) # Now add a matched normal to the original request for the sample - # Sample 1 C-8VK0V7 + # Sample 1 C-PPPPP3 normal1_R1_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7-N.R1.fastq", - path="/C-8VK0V7-N.R1.fastq", + file_name="C-PPPPP3-N.R1.fastq", + path="/C-PPPPP3-N.R1.fastq", ) FileMetadata.objects.create_or_update( file=normal1_R1_file_instance, metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -1014,29 +1014,29 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): normal1_R2_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7-N.R2.fastq", - path="/C-8VK0V7-N.R2.fastq", + file_name="C-PPPPP3-N.R2.fastq", + path="/C-PPPPP3-N.R2.fastq", ) FileMetadata.objects.create_or_update( file=normal1_R2_file_instance, metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -1062,12 +1062,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -1075,27 +1075,27 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], - "LB": "s_C_8VK0V7_N001_d_1", + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], + "LB": "s_C_PPPPP3_N001_d_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA6_GTATTGGC-PPPP14"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-17"], "specimen_type": "Resection", - "R1": ["/C-8VK0V7-N.R1.fastq"], - "R2": ["/C-8VK0V7-N.R2.fastq"], + "R1": ["/C-PPPPP3-N.R1.fastq"], + "R2": ["/C-PPPPP3-N.R2.fastq"], "R1_bid": [], # UUID('bfb94fe6-bf46-431a-8f72-6ee47ee72fc9') "R2_bid": [], # UUID('1e8b68f8-c333-499c-b22d-50fbef2d2ea7') "bam": [], "bam_bid": [], - "request_id": "10075_D_3", + "request_id": "99990_D_3", "pi": "", "pi_email": "", - "run_id": ["PITT_0439"], + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], } ], @@ -1120,10 +1120,10 @@ def test_compile_pairs_custom1(self): samples = [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -1135,7 +1135,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_date": ["2019-12-12"], "species": "Human", @@ -1144,10 +1144,10 @@ def test_compile_pairs_custom1(self): }, { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("d2d8ed36-d8f4-4e93-b038-d38328fad021")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -1159,7 +1159,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_date": ["2019-12-17"], "species": "Human", @@ -1173,10 +1173,10 @@ def test_compile_pairs_custom1(self): "tumor": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -1190,7 +1190,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-17"], "species": "Human", "specimen_type": "Resection", @@ -1203,10 +1203,10 @@ def test_compile_pairs_custom1(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -1220,7 +1220,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", diff --git a/runner/tests/operator/argos_operator/v1_0_0/test_retrieve_samples_by_query.py b/runner/tests/operator/argos_operator/v1_0_0/test_retrieve_samples_by_query.py index 149e79c9f..318703f91 100644 --- a/runner/tests/operator/argos_operator/v1_0_0/test_retrieve_samples_by_query.py +++ b/runner/tests/operator/argos_operator/v1_0_0/test_retrieve_samples_by_query.py @@ -57,9 +57,9 @@ def test_get_dmp_normal1(self): # load some fixtures # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) # test lookup again with some Files loaded; should still be None since it doesnt match anything yet @@ -69,13 +69,13 @@ def test_get_dmp_normal1(self): self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures but non-matching bait set; no DMP bams loaded yet - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "bar" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures and matching bait_set; no DMP bams loaded yet - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "IMPACT468_BAITS" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) @@ -84,20 +84,20 @@ def test_get_dmp_normal1(self): file_group_instance = FileGroup.objects.get(name="DMP BAMs") filetype_instance = FileType.objects.get(name="bam") file_instance = File.objects.create( - file_type=filetype_instance, file_group=file_group_instance, file_name="C-8VK0V7.bam", path="/C-8VK0V7.bam" + file_type=filetype_instance, file_group=file_group_instance, file_name="C-PPPPP3.bam", path="/C-PPPPP3.bam" ) FileMetadata.objects.create_or_update( file=file_instance, version=1, metadata={ - "bai": "/C-8VK0V7.bai", - "bam": "/C-8VK0V7.bam", + "bai": "/C-PPPPP3.bai", + "bam": "/C-PPPPP3.bam", "type": "N", "assay": "IM6", "sample": "P-1234567-N01-IM6", "anon_id": "ABCDEF-N", "patient": { - "cmo": "8VK0V7", + "cmo": "PPPPP3", "dmp": "P-1234567", "updated": "2020-03-19T23:57:51.941963Z", "imported": "2020-03-19T23:57:51.941945Z", @@ -110,7 +110,7 @@ def test_get_dmp_normal1(self): "tumor_type": "MBC", "sequencingCenter": "MSKCC", "platform": "Illumina", - "external_id": "s_C_8VK0V7_N901_dZ_IM6", + "external_id": "s_C_PPPPP3_N901_dZ_IM6", "sample_type": "0", "tissue_type": "Breast", "primary_site": "Breast", @@ -125,7 +125,7 @@ def test_get_dmp_normal1(self): ) # test with a patient ID taken from fixtures but non-matching bait_set - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "foo" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) @@ -137,7 +137,7 @@ def test_get_dmp_normal1(self): self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures and a matching bait_set - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "IMPACT468_BAITS" dmp_normal = get_dmp_normal(patient_id, bait_set) @@ -145,26 +145,26 @@ def test_get_dmp_normal1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["DMP_FCID_DMP_BARCODEIDX"], - "LB": "s_C_8VK0V7_N901_dZ_IM6_1", + "LB": "s_C_PPPPP3_N901_dZ_IM6_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], - "SM": "s_C_8VK0V7_N901_dZ_IM6", + "ID": ["s_C_PPPPP3_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], + "SM": "s_C_PPPPP3_N901_dZ_IM6", "species": "", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "s_C_8VK0V7_N901_dZ_IM6", + "sample_id": "s_C_PPPPP3_N901_dZ_IM6", "run_date": [""], "specimen_type": "DMP Normal", "R1": [], "R2": [], "R1_bid": [], "R2_bid": [], - "bam": ["/C-8VK0V7.bam"], + "bam": ["/C-PPPPP3.bam"], "bam_bid": [ # mock the UUID for testing since it will be different every time "deletemeplease" ], - "request_id": "s_C_8VK0V7_N901_dZ_IM6", + "request_id": "s_C_PPPPP3_N901_dZ_IM6", "pi": "", "pi_email": "", "run_id": [""], @@ -385,7 +385,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -402,7 +402,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -412,7 +412,7 @@ def test_get_pooled_normals1(self): ) pooled_normals = get_pooled_normals( - run_ids=["PITT_0439"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS" + run_ids=["SEQRUN_0008"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS" ) # remove the R1_bid and R2_bid for testing because they are non-deterministic # TODO: mock this ^^ @@ -423,14 +423,14 @@ def test_get_pooled_normals1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "Pooled Normal", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -439,7 +439,7 @@ def test_get_pooled_normals1(self): "R2_bid": [], # UUID('ec9817d1-d6f5-4f1d-9c0a-c82fc22d4daa') "bam": [], "bam_bid": [], - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", "run_id": [""], diff --git a/runner/tests/operator/argos_operator/v1_2_0/test_argos_operator.py b/runner/tests/operator/argos_operator/v1_2_0/test_argos_operator.py index d9f280566..2b6e1242e 100644 --- a/runner/tests/operator/argos_operator/v1_2_0/test_argos_operator.py +++ b/runner/tests/operator/argos_operator/v1_2_0/test_argos_operator.py @@ -41,9 +41,9 @@ def test_operator_factory_argos2(self): This test loads some Argos fixtures and checks the number of Files available to the Operator """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id = "bar" @@ -61,9 +61,9 @@ def test_operator_factory_argos3(self): Test that a Argos operator has access to all files in the database, even non-Argos files """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) self.assertEqual(len(File.objects.all()), 4) diff --git a/runner/tests/operator/argos_operator/v1_2_0/test_construct_argos_pair.py b/runner/tests/operator/argos_operator/v1_2_0/test_construct_argos_pair.py index 44f53d247..9127c5570 100644 --- a/runner/tests/operator/argos_operator/v1_2_0/test_construct_argos_pair.py +++ b/runner/tests/operator/argos_operator/v1_2_0/test_construct_argos_pair.py @@ -23,9 +23,9 @@ def test_construct_argos_jobs1(self): Test that Argos jobs are correctly created """ # Load fixtures - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id_metadata_key = settings.REQUEST_ID_METADATA_KEY @@ -33,7 +33,7 @@ def test_construct_argos_jobs1(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "10075_D", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99990_D", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() @@ -59,7 +59,7 @@ def test_construct_argos_jobs1(self): argos_inputs, error_samples = construct_argos_jobs(samples) expected_inputs = json.load( - open(os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.argos.input.json")) + open(os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.argos.input.json")) ) print("Running test_construct_argos_jobs1") self.assertTrue(argos_inputs == expected_inputs) diff --git a/runner/tests/operator/argos_operator/v1_2_0/test_make_sample.py b/runner/tests/operator/argos_operator/v1_2_0/test_make_sample.py index 3f1c19a53..c372140e4 100644 --- a/runner/tests/operator/argos_operator/v1_2_0/test_make_sample.py +++ b/runner/tests/operator/argos_operator/v1_2_0/test_make_sample.py @@ -15,7 +15,7 @@ def test_build_sample1(self): """ data = [ { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", "id": UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac"), "metadata": { "R": "R1", @@ -24,38 +24,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, - settings.LIBRARY_ID_METADATA_KEY: "10075_D_2_3", + settings.LIBRARY_ID_METADATA_KEY: "99990_D_2_3", "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -63,10 +63,10 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", }, { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", "id": UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7"), "metadata": { "R": "R2", @@ -75,38 +75,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, "libraryIgoId": None, "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -114,7 +114,7 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", }, ] @@ -122,32 +122,32 @@ def test_build_sample1(self): expected_sample = { "CN": "MSKCC", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2_3", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "LB": "99990_D_2_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R2_bid": [UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7")], "bam": [], "bam_bid": [], - "SM": "s_C_8VK0V7_N001_d", + "SM": "s_C_PPPPP3_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", - "patient_id": "C-8VK0V7", - "request_id": "10075_D_2", + "sample_id": "99990_D_2_3", + "patient_id": "C-PPPPP3", + "request_id": "99990_D_2", "run_date": ["2019-12-12"], - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } diff --git a/runner/tests/operator/argos_operator/v1_2_0/test_pair_request.py b/runner/tests/operator/argos_operator/v1_2_0/test_pair_request.py index e6e651c8f..b230f016b 100755 --- a/runner/tests/operator/argos_operator/v1_2_0/test_pair_request.py +++ b/runner/tests/operator/argos_operator/v1_2_0/test_pair_request.py @@ -80,9 +80,9 @@ def test_compile_pairs1(self): """ samples = [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "sample_id": "my_sample_id2", @@ -90,9 +90,9 @@ def test_compile_pairs1(self): "run_mode": "HiSeq High Output", }, { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id1", @@ -104,10 +104,10 @@ def test_compile_pairs1(self): expected_pairs = { "tumor": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", @@ -116,10 +116,10 @@ def test_compile_pairs1(self): ], "normal": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id2", "SM": "my_sample_id2", @@ -136,8 +136,8 @@ def test_compile_pairs2(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "SM": "my_sample_id1", @@ -146,8 +146,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "SM": "my_sample_id2", @@ -156,8 +156,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id3", @@ -166,8 +166,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id4", @@ -176,8 +176,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "SM": "my_sample_id5", @@ -190,9 +190,9 @@ def test_compile_pairs2(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id3", "SM": "my_sample_id3", @@ -200,9 +200,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id4", "SM": "my_sample_id4", @@ -210,9 +210,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id5", "SM": "my_sample_id5", @@ -222,9 +222,9 @@ def test_compile_pairs2(self): "normal": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", @@ -232,9 +232,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id2", "SM": "my_sample_id2", @@ -242,9 +242,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_id": "my_sample_id1", "SM": "my_sample_id1", @@ -266,8 +266,8 @@ def test_compile_pairs3(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "run_mode": "HiSeq High Output", @@ -281,23 +281,23 @@ def test_compile_pairs4(self): """ Test pairing with only a single unpaired Tumor sample Test that the appropriate Normal sample is found from the other samples in the same request - missing normal for sample 10075_D_1; querying patient C-DRKHP7 + missing normal for sample 99990_D_1; querying patient C-PPPPP7 """ # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", "run_mode": "hiseq", } ] @@ -306,43 +306,43 @@ def test_compile_pairs4(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("aef306b4-7d85-4c9f-b9a4-a115154f73bf")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("9e47ba2f-093a-4233-8339-fed03e159b3f")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["Frozen"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "run_mode": "hiseq", @@ -360,10 +360,10 @@ def test_compile_pairs5(self): This time also load File entries from another request to make sure they do not confound the pairing """ # Load fixtures - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 14) @@ -372,12 +372,12 @@ def test_compile_pairs5(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", "run_mode": "hiseq", } ] @@ -386,43 +386,43 @@ def test_compile_pairs5(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("aef306b47d854c9fb9a4a115154f73bf")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("9e47ba2f093a42338339fed03e159b3f")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["Frozen"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Tumor", "run_mode": "hiseq", @@ -439,11 +439,11 @@ def test_get_pair_from_other_request(self): """ # Load fixtures # only normals - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) # only tumors - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -452,13 +452,13 @@ def test_get_pair_from_other_request(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", "run_mode": "hiseq", } ] @@ -468,13 +468,13 @@ def test_get_pair_from_other_request(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", "run_mode": "hiseq", } ], @@ -482,32 +482,32 @@ def test_get_pair_from_other_request(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_2_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_2_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-12"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("7a3bceb31af84d3da1583731c83aeb5a")], "R2_bid": [UUID("ecf003cdbd304e909d180d99e7fd79d3")], "bam": [], "bam_bid": [], - "request_id": "10075_D_2", - "run_id": ["JAX_0397"], + "request_id": "99990_D_2", + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], @@ -521,10 +521,10 @@ def test_get_most_recent_normal1(self): in the event that a patient has several normals Return the Normal with the most recent run_date """ - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -533,12 +533,12 @@ def test_get_most_recent_normal1(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_mode": "hiseq", } @@ -549,12 +549,12 @@ def test_get_most_recent_normal1(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_mode": "hiseq", } @@ -563,31 +563,31 @@ def test_get_most_recent_normal1(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_4_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_4_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_4_3", + "sample_id": "99990_D_4_3", "run_date": ["2019-12-13"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("404ad544428c405f967aa6920d091148")], "R2_bid": [UUID("19703ff82e144f608d57891df80b2858")], "bam": [], "bam_bid": [], - "request_id": "10075_D_4", - "run_id": ["JAX_0397"], + "request_id": "99990_D_4", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", "run_mode": "hiseq", } @@ -612,33 +612,33 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): settings.POOLED_NORMAL_FILE_GROUP = str(poolednormal_filegroup_instance.id) # generate tumor samples - # Sample 1 C-8VK0V7 + # Sample 1 C-PPPPP3 tumor1_R1_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7.R1.fastq", - path="/C-8VK0V7.R1.fastq", + file_name="C-PPPPP3.R1.fastq", + path="/C-PPPPP3.R1.fastq", ) FileMetadata.objects.create_or_update( file=tumor1_R1_file_instance, metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_3_5", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_3_5", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-R001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-R001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -646,8 +646,8 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): settings.SAMPLE_CLASS_METADATA_KEY: "Resection", "tumorOrNormal": "Tumor", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Local Recurrence", - "externalSampleId": "SK_MEL_1091A_T", - "investigatorSampleId": "SK_MEL_1091A_T", + "externalSampleId": "SAMPLE_T_001", + "investigatorSampleId": "SAMPLE_T_001", "labHeadEmail": "", "labHeadName": "", "runMode": "HiSeq High Output", @@ -656,29 +656,29 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): tumor1_R2_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7.R2.fastq", - path="/C-8VK0V7.R2.fastq", + file_name="C-PPPPP3.R2.fastq", + path="/C-PPPPP3.R2.fastq", ) FileMetadata.objects.create_or_update( file=tumor1_R2_file_instance, metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_3_5", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_3_5", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-R001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-R001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -686,8 +686,8 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): settings.SAMPLE_CLASS_METADATA_KEY: "Resection", "tumorOrNormal": "Tumor", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Local Recurrence", - "externalSampleId": "SK_MEL_1091A_T", - "investigatorSampleId": "SK_MEL_1091A_T", + "externalSampleId": "SAMPLE_T_001", + "investigatorSampleId": "SAMPLE_T_001", "labHeadEmail": "", "labHeadName": "", "runMode": "HiSeq High Output", @@ -706,18 +706,18 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", settings.SAMPLE_ID_METADATA_KEY: "Sample12345", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", settings.PATIENT_ID_METADATA_KEY: "C-ABCDEF", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-ABCDEF-R001-d", @@ -746,18 +746,18 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", settings.SAMPLE_ID_METADATA_KEY: "Sample12345", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", settings.PATIENT_ID_METADATA_KEY: "C-ABCDEF", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-ABCDEF-R001-d", @@ -779,12 +779,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], "run_mode": "hiseq", } @@ -800,7 +800,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "bait_set": "IMPACT468_BAITS", "sequencingCenter": "MSKCC", @@ -817,7 +817,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "bait_set": "IMPACT468_BAITS", "sequencingCenter": "MSKCC", @@ -836,12 +836,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], "run_mode": "hiseq", } @@ -851,14 +851,14 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -868,10 +868,10 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "bam": [], "bam_bid": [], "specimen_type": "Pooled Normal", - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", - "run_id": ["PITT_0439"], + "run_id": ["SEQRUN_0008"], "preservation_type": [["Frozen"]], "run_mode": "", } @@ -891,21 +891,21 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): dmp_bam_file_instance = File.objects.create( file_type=bam_filetype_instance, file_group=dmp_bam_filegroup_instance, - file_name="C-8VK0V7.bam", - path="/C-8VK0V7.bam", + file_name="C-PPPPP3.bam", + path="/C-PPPPP3.bam", ) FileMetadata.objects.create_or_update( file=dmp_bam_file_instance, version=1, metadata={ - "bai": "/C-8VK0V7.bai", - "bam": "/C-8VK0V7.bam", + "bai": "/C-PPPPP3.bai", + "bam": "/C-PPPPP3.bam", "type": "N", "assay": "IM6", "sample": "P-1234567-N01-IM6", "anon_id": "ABCDEF-N", "patient": { - "cmo": "8VK0V7", + "cmo": "PPPPP3", "dmp": "P-1234567", "updated": "2020-03-19T23:57:51.941963Z", "imported": "2020-03-19T23:57:51.941945Z", @@ -918,7 +918,7 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "imported": "2020-03-25T19:45:16.421137Z", "cmo_assay": "IMPACT468", "tumor_type": "MBC", - "external_id": "C-8VK0V7-N901-dZ-IM6", + "external_id": "C-PPPPP3-N901-dZ-IM6", "sample_type": "0", "tissue_type": "Breast", "primary_site": "Breast", @@ -939,12 +939,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], "run_mode": "hiseq", } @@ -954,21 +954,21 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["DMP_FCID_DMP_BARCODEIDX"], - "LB": "C-8VK0V7-N901-dZ-IM6_1", + "LB": "C-PPPPP3-N901-dZ-IM6_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], - "SM": "s_C_8VK0V7_N901_dZ_IM6", + "ID": ["s_C_PPPPP3_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], + "SM": "s_C_PPPPP3_N901_dZ_IM6", "species": "", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "s_C_8VK0V7_N901_dZ_IM6", + "sample_id": "s_C_PPPPP3_N901_dZ_IM6", "run_date": [""], "specimen_type": "DMP", "R1": [[]], "R2": [[]], "R1_bid": [[]], "R2_bid": [[]], - "bam": ["/C-8VK0V7.bam"], + "bam": ["/C-PPPPP3.bam"], "bam_bid": [], # UUID('77b9a78f-1bed-475c-9799-c18a6f57b347') "request_id": None, "pi": "", @@ -995,33 +995,33 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): self.assertDictEqual(pairs, expected_pairs) # Now add a matched normal to the original request for the sample - # Sample 1 C-8VK0V7 + # Sample 1 C-PPPPP3 normal1_R1_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7-N.R1.fastq", - path="/C-8VK0V7-N.R1.fastq", + file_name="C-PPPPP3-N.R1.fastq", + path="/C-PPPPP3-N.R1.fastq", ) FileMetadata.objects.create_or_update( file=normal1_R1_file_instance, metadata={ "R": "R1", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -1039,29 +1039,29 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): normal1_R2_file_instance = File.objects.create( file_type=fastq_filetype_instance, file_group=lims_filegroup_instance, - file_name="C-8VK0V7-N.R2.fastq", - path="/C-8VK0V7-N.R2.fastq", + file_name="C-PPPPP3-N.R2.fastq", + path="/C-PPPPP3-N.R2.fastq", ) FileMetadata.objects.create_or_update( file=normal1_R2_file_instance, metadata={ "R": "R2", "sex": "F", - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "baitSet": "IMPACT468_BAITS", "species": "Human", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", settings.LIBRARY_ID_METADATA_KEY: None, - "flowCellId": "HFTCNBBXY", + "flowCellId": "FCELLAAAA6", "barcodeId": "DUAL_IDT_LIB_267", - "barcodeIndex": "GTATTGGC-TTGTCGGT", + "barcodeIndex": "GTATTGGC-PPPP14", "runDate": "2019-12-17", - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", - settings.REQUEST_ID_METADATA_KEY: "10075_D_3", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", + settings.REQUEST_ID_METADATA_KEY: "99990_D_3", "sequencingCenter": "MSKCC", "platform": "Illumina", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", settings.IGO_COMPLETE_METADATA_KEY: True, settings.ONCOTREE_METADATA_KEY: "MEL", "preservation": "Frozen", @@ -1088,12 +1088,12 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["PITT_0439"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], "run_mode": "hiseq", } @@ -1102,27 +1102,27 @@ def test_compile_pairs_pooled_normal_and_dmp_bam(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], - "LB": "s_C_8VK0V7_N001_d_1", + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], + "LB": "s_C_PPPPP3_N001_d_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HFTCNBBXY_GTATTGGC-TTGTCGGT"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA6_GTATTGGC-PPPP14"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-17"], "specimen_type": "Resection", - "R1": ["/C-8VK0V7-N.R1.fastq"], - "R2": ["/C-8VK0V7-N.R2.fastq"], + "R1": ["/C-PPPPP3-N.R1.fastq"], + "R2": ["/C-PPPPP3-N.R2.fastq"], "R1_bid": [], # UUID('bfb94fe6-bf46-431a-8f72-6ee47ee72fc9') "R2_bid": [], # UUID('1e8b68f8-c333-499c-b22d-50fbef2d2ea7') "bam": [], "bam_bid": [], - "request_id": "10075_D_3", + "request_id": "99990_D_3", "pi": "", "pi_email": "", - "run_id": ["PITT_0439"], + "run_id": ["SEQRUN_0008"], "preservation_type": ["Frozen"], "run_mode": "hiseq", } @@ -1148,10 +1148,10 @@ def test_compile_pairs_custom1(self): samples = [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -1163,7 +1163,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_date": ["2019-12-12"], "species": "Human", @@ -1173,10 +1173,10 @@ def test_compile_pairs_custom1(self): }, { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("d2d8ed36-d8f4-4e93-b038-d38328fad021")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -1188,7 +1188,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "run_date": ["2019-12-17"], "species": "Human", @@ -1203,10 +1203,10 @@ def test_compile_pairs_custom1(self): "tumor": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -1220,7 +1220,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-17"], "species": "Human", "specimen_type": "Resection", @@ -1234,10 +1234,10 @@ def test_compile_pairs_custom1(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -1251,7 +1251,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", diff --git a/runner/tests/operator/argos_operator/v1_2_0/test_retrieve_samples_by_query.py b/runner/tests/operator/argos_operator/v1_2_0/test_retrieve_samples_by_query.py index 0645c1fc7..093fc0402 100644 --- a/runner/tests/operator/argos_operator/v1_2_0/test_retrieve_samples_by_query.py +++ b/runner/tests/operator/argos_operator/v1_2_0/test_retrieve_samples_by_query.py @@ -57,9 +57,9 @@ def test_get_dmp_normal1(self): # load some fixtures # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) # test lookup again with some Files loaded; should still be None since it doesnt match anything yet @@ -69,13 +69,13 @@ def test_get_dmp_normal1(self): self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures but non-matching bait set; no DMP bams loaded yet - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "bar" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures and matching bait_set; no DMP bams loaded yet - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "IMPACT468_BAITS" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) @@ -84,20 +84,20 @@ def test_get_dmp_normal1(self): file_group_instance = FileGroup.objects.get(name="DMP BAMs") filetype_instance = FileType.objects.get(name="bam") file_instance = File.objects.create( - file_type=filetype_instance, file_group=file_group_instance, file_name="C-8VK0V7.bam", path="/C-8VK0V7.bam" + file_type=filetype_instance, file_group=file_group_instance, file_name="C-PPPPP3.bam", path="/C-PPPPP3.bam" ) FileMetadata.objects.create_or_update( file=file_instance, version=1, metadata={ - "bai": "/C-8VK0V7.bai", - "bam": "/C-8VK0V7.bam", + "bai": "/C-PPPPP3.bai", + "bam": "/C-PPPPP3.bam", "type": "N", "assay": "IM6", "sample": "P-1234567-N01-IM6", "anon_id": "ABCDEF-N", "patient": { - "cmo": "8VK0V7", + "cmo": "PPPPP3", "dmp": "P-1234567", "updated": "2020-03-19T23:57:51.941963Z", "imported": "2020-03-19T23:57:51.941945Z", @@ -110,7 +110,7 @@ def test_get_dmp_normal1(self): "tumor_type": "MBC", "sequencingCenter": "MSKCC", "platform": "Illumina", - "external_id": "s_C_8VK0V7_N901_dZ_IM6", + "external_id": "s_C_PPPPP3_N901_dZ_IM6", "sample_type": "0", "tissue_type": "Breast", "primary_site": "Breast", @@ -125,7 +125,7 @@ def test_get_dmp_normal1(self): ) # test with a patient ID taken from fixtures but non-matching bait_set - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "foo" dmp_normal = get_dmp_normal(patient_id, bait_set) self.assertEqual(dmp_normal, None) @@ -137,7 +137,7 @@ def test_get_dmp_normal1(self): self.assertEqual(dmp_normal, None) # test with a patient ID taken from fixtures and a matching bait_set - patient_id = "C-8VK0V7" + patient_id = "C-PPPPP3" bait_set = "IMPACT468_BAITS" dmp_normal = get_dmp_normal(patient_id, bait_set) @@ -145,26 +145,26 @@ def test_get_dmp_normal1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["DMP_FCID_DMP_BARCODEIDX"], - "LB": "s_C_8VK0V7_N901_dZ_IM6_1", + "LB": "s_C_PPPPP3_N901_dZ_IM6_1", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], - "SM": "s_C_8VK0V7_N901_dZ_IM6", + "ID": ["s_C_PPPPP3_N901_dZ_IM6_DMP_FCID_DMP_BARCODEIDX"], + "SM": "s_C_PPPPP3_N901_dZ_IM6", "species": "", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "s_C_8VK0V7_N901_dZ_IM6", + "sample_id": "s_C_PPPPP3_N901_dZ_IM6", "run_date": [""], "specimen_type": "DMP Normal", "R1": [], "R2": [], "R1_bid": [], "R2_bid": [], - "bam": ["/C-8VK0V7.bam"], + "bam": ["/C-PPPPP3.bam"], "bam_bid": [ # mock the UUID for testing since it will be different every time "deletemeplease" ], - "request_id": "s_C_8VK0V7_N901_dZ_IM6", + "request_id": "s_C_PPPPP3_N901_dZ_IM6", "pi": "", "pi_email": "", "run_id": [""], @@ -385,7 +385,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -402,7 +402,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -412,7 +412,7 @@ def test_get_pooled_normals1(self): ) pooled_normals = get_pooled_normals( - run_ids=["PITT_0439"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS" + run_ids=["SEQRUN_0008"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS" ) # remove the R1_bid and R2_bid for testing because they are non-deterministic # TODO: mock this ^^ @@ -423,14 +423,14 @@ def test_get_pooled_normals1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "Pooled Normal", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -439,7 +439,7 @@ def test_get_pooled_normals1(self): "R2_bid": [], # UUID('ec9817d1-d6f5-4f1d-9c0a-c82fc22d4daa') "bam": [], "bam_bid": [], - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", "run_id": [""], diff --git a/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py b/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py index 050ca354e..289585278 100644 --- a/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py +++ b/runner/tests/operator/argos_operator/v2_1_0/test_construct_argos_pair.py @@ -23,9 +23,9 @@ def test_construct_argos_jobs1(self): Test that Argos jobs are correctly created """ # Load fixtures - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id_metadata_key = settings.REQUEST_ID_METADATA_KEY @@ -33,7 +33,7 @@ def test_construct_argos_jobs1(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "10075_D", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99990_D", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() @@ -59,14 +59,14 @@ def test_construct_argos_jobs1(self): argos_inputs, error_samples = construct_argos_jobs(samples) expected_inputs = json.load( - open(os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.argos_1_7_0.input.json")) + open(os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.argos_1_7_0.input.json")) ) print("Running test_construct_argos_jobs1") self.assertTrue(argos_inputs == expected_inputs) def test_construct_argos_jobs_pdx(self): - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "08944_B.fixtures.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99991_B.fixtures.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id_metadata_key = settings.REQUEST_ID_METADATA_KEY @@ -74,7 +74,7 @@ def test_construct_argos_jobs_pdx(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "08944_B", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99991_B", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() @@ -99,12 +99,12 @@ def test_construct_argos_jobs_pdx(self): samples.append(build_sample(igo_id_group[igo_id])) argos_inputs, error_samples = construct_argos_jobs(samples) - expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "08944_B.argos.input.json"))) + expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "99991_B.argos.input.json"))) print("Running test_construct_argos_jobs_pdx") self.assertTrue(argos_inputs == expected_inputs) def test_construct_argos_jobs_bam_pdx(self): - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "16342_B.fixtures_pdx.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99909_B.fixtures_pdx.json") bam_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "argos_pdx.json") call_command("loaddata", test_files_fixture, verbosity=0) call_command("loaddata", bam_fixture, verbosity=0) @@ -114,7 +114,7 @@ def test_construct_argos_jobs_bam_pdx(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "16342_B", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99909_B", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() @@ -144,7 +144,7 @@ def test_construct_argos_jobs_bam_pdx(self): self.assertTrue(argos_inputs == expected_inputs) def test_construct_argos_jobs_bam_non_pdx(self): - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "16342_B.fixtures_non_pdx.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99909_B.fixtures_non_pdx.json") bam_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "argos_pdx.json") call_command("loaddata", test_files_fixture, verbosity=0) call_command("loaddata", bam_fixture, verbosity=0) @@ -154,7 +154,7 @@ def test_construct_argos_jobs_bam_non_pdx(self): files = File.objects.filter( **{ - "filemetadata__metadata__{}".format(request_id_metadata_key): "16342_B", + "filemetadata__metadata__{}".format(request_id_metadata_key): "99909_B", "filemetadata__metadata__{}".format(igo_complete_metadata_key): True, } ).all() diff --git a/runner/tests/operator/argos_operator/v2_2_0/test_pair_request.py b/runner/tests/operator/argos_operator/v2_2_0/test_pair_request.py index e117cfeee..73292fe4b 100755 --- a/runner/tests/operator/argos_operator/v2_2_0/test_pair_request.py +++ b/runner/tests/operator/argos_operator/v2_2_0/test_pair_request.py @@ -82,9 +82,9 @@ def test_compile_pairs1(self): """ samples = [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Normal", @@ -93,9 +93,9 @@ def test_compile_pairs1(self): "run_mode": "HiSeq High Output", }, { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -108,10 +108,10 @@ def test_compile_pairs1(self): expected_pairs = { "tumor": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id1", @@ -121,10 +121,10 @@ def test_compile_pairs1(self): ], "normal": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id2", @@ -142,8 +142,8 @@ def test_compile_pairs2(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Normal", @@ -153,8 +153,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Normal", @@ -164,8 +164,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -175,8 +175,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -186,8 +186,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -201,9 +201,9 @@ def test_compile_pairs2(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id3", @@ -212,9 +212,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id4", @@ -223,9 +223,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id5", @@ -236,9 +236,9 @@ def test_compile_pairs2(self): "normal": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id1", @@ -247,9 +247,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id2", @@ -258,9 +258,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id1", @@ -283,8 +283,8 @@ def test_compile_pairs3(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "run_mode": "HiSeq High Output", @@ -298,24 +298,24 @@ def test_compile_pairs4(self): """ Test pairing with only a single unpaired Tumor sample Test that the appropriate Normal sample is found from the other samples in the same request - missing normal for sample 10075_D_1; querying patient C-DRKHP7 + missing normal for sample 99990_D_1; querying patient C-PPPPP7 """ # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", "run_mode": "hiseq", } ] @@ -324,26 +324,26 @@ def test_compile_pairs4(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("aef306b4-7d85-4c9f-b9a4-a115154f73bf")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("9e47ba2f-093a-4233-8339-fed03e159b3f")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["Frozen"], "sample_origin": ["Whole Blood"], @@ -351,17 +351,17 @@ def test_compile_pairs4(self): "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -380,10 +380,10 @@ def test_compile_pairs5(self): This time also load File entries from another request to make sure they do not confound the pairing """ # Load fixtures - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 14) @@ -392,13 +392,13 @@ def test_compile_pairs5(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", "run_mode": "hiseq", } ] @@ -407,26 +407,26 @@ def test_compile_pairs5(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("aef306b47d854c9fb9a4a115154f73bf")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("9e47ba2f093a42338339fed03e159b3f")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["Frozen"], "sample_origin": ["Whole Blood"], @@ -434,17 +434,17 @@ def test_compile_pairs5(self): "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -462,11 +462,11 @@ def test_get_pair_from_other_request(self): """ # Load fixtures # only normals - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) # only tumors - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -475,14 +475,14 @@ def test_get_pair_from_other_request(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", "run_mode": "hiseq", } ] @@ -492,14 +492,14 @@ def test_get_pair_from_other_request(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", "sample_origin": [""], - "request_id": "10075_D_3", + "request_id": "99990_D_3", "run_mode": "hiseq", } ], @@ -507,33 +507,33 @@ def test_get_pair_from_other_request(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_2_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_2_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-12"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("7a3bceb31af84d3da1583731c83aeb5a")], "R2_bid": [UUID("ecf003cdbd304e909d180d99e7fd79d3")], "bam": [], "bam_bid": [], - "request_id": "10075_D_2", + "request_id": "99990_D_2", "sample_origin": ["Plasma"], - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], @@ -547,10 +547,10 @@ def test_get_most_recent_normal1(self): in the event that a patient has several normals Return the Normal with the most recent run_date """ - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -559,12 +559,12 @@ def test_get_most_recent_normal1(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], "run_mode": "hiseq", @@ -576,12 +576,12 @@ def test_get_most_recent_normal1(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "sample_origin": [""], "preservation_type": ["EDTA-Streck"], "run_mode": "hiseq", @@ -591,32 +591,32 @@ def test_get_most_recent_normal1(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_4_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_4_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_4_3", + "sample_id": "99990_D_4_3", "run_date": ["2019-12-13"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("404ad544428c405f967aa6920d091148")], "R2_bid": [UUID("19703ff82e144f608d57891df80b2858")], "bam": [], "bam_bid": [], - "request_id": "10075_D_4", - "run_id": ["JAX_0397"], + "request_id": "99990_D_4", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": ["Plasma"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", "run_mode": "hiseq", } @@ -634,10 +634,10 @@ def test_compile_pairs_custom1(self): samples = [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -649,7 +649,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], "run_date": ["2019-12-12"], @@ -660,10 +660,10 @@ def test_compile_pairs_custom1(self): }, { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("d2d8ed36-d8f4-4e93-b038-d38328fad021")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -675,7 +675,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], "run_date": ["2019-12-17"], @@ -691,10 +691,10 @@ def test_compile_pairs_custom1(self): "tumor": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -708,7 +708,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-17"], "species": "Human", "specimen_type": "Resection", @@ -723,10 +723,10 @@ def test_compile_pairs_custom1(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -740,7 +740,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", diff --git a/runner/tests/operator/argos_operator/v2_2_0/test_retrieve_samples_by_query.py b/runner/tests/operator/argos_operator/v2_2_0/test_retrieve_samples_by_query.py index 2d9fd47ec..3213fbe9c 100644 --- a/runner/tests/operator/argos_operator/v2_2_0/test_retrieve_samples_by_query.py +++ b/runner/tests/operator/argos_operator/v2_2_0/test_retrieve_samples_by_query.py @@ -281,7 +281,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -298,7 +298,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -308,7 +308,7 @@ def test_get_pooled_normals1(self): ) pooled_normals = get_pooled_normals( - run_ids=["PITT_0439"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS", sample_origin=[""] + run_ids=["SEQRUN_0008"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS", sample_origin=[""] ) # remove the R1_bid and R2_bid for testing because they are non-deterministic # TODO: mock this ^^ @@ -319,14 +319,14 @@ def test_get_pooled_normals1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "Pooled Normal", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -335,11 +335,11 @@ def test_get_pooled_normals1(self): "R2_bid": [], # UUID('ec9817d1-d6f5-4f1d-9c0a-c82fc22d4daa') "bam": [], "bam_bid": [], - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", "sample_origin": [[""]], - "run_id": ["PITT_0439"], + "run_id": ["SEQRUN_0008"], "preservation_type": [["Frozen"]], "run_mode": "", } diff --git a/runner/tests/operator/argos_operator/v2_3_0/test_argos_operator.py b/runner/tests/operator/argos_operator/v2_3_0/test_argos_operator.py index 6ba73af0b..c5ad118cc 100644 --- a/runner/tests/operator/argos_operator/v2_3_0/test_argos_operator.py +++ b/runner/tests/operator/argos_operator/v2_3_0/test_argos_operator.py @@ -41,9 +41,9 @@ def test_operator_factory_argos2(self): This test loads some Argos fixtures and checks the number of Files available to the Operator """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) request_id = "bar" @@ -61,9 +61,9 @@ def test_operator_factory_argos3(self): Test that a Argos operator has access to all files in the database, even non-Argos files """ # Load fixtures; 4 fastq files for 2 patient samples - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_single_TN_pair.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_single_TN_pair.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) self.assertEqual(len(File.objects.all()), 4) diff --git a/runner/tests/operator/argos_operator/v2_3_0/test_make_sample.py b/runner/tests/operator/argos_operator/v2_3_0/test_make_sample.py index 766452bdc..8d74b1291 100644 --- a/runner/tests/operator/argos_operator/v2_3_0/test_make_sample.py +++ b/runner/tests/operator/argos_operator/v2_3_0/test_make_sample.py @@ -20,7 +20,7 @@ def test_build_sample1(self): """ data = [ { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", "id": UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac"), "metadata": { "R": "R1", @@ -29,38 +29,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, - settings.LIBRARY_ID_METADATA_KEY: "10075_D_2_3", + settings.LIBRARY_ID_METADATA_KEY: "99990_D_2_3", "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -68,10 +68,10 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz", }, { - "file_name": "JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "file_name": "SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", "id": UUID("c71c259a-ebc0-4490-9af1-bc99387a70d7"), "metadata": { "R": "R2", @@ -80,38 +80,38 @@ def test_build_sample1(self): "barcodeIndex": None, "captureConcentrationNm": "10.377358490566039", "captureInputNg": "110.0", - "captureName": "Pool-05257_CD-06287_AY-10075_D_2-Tube2_1", + "captureName": "Pool-99992_D-99995_AY-99990_D_2-Tube2_1", settings.CMO_SAMPLE_CLASS_METADATA_KEY: "Normal", "collectionYear": "", "dataAnalystEmail": "", "dataAnalystName": "", - "externalSampleId": "JW_MEL_007_NORM", - "flowCellId": "HCYYWBBXY", + "externalSampleId": "SAMPLE_N_001", + "flowCellId": "FCELLAAAA4", "flowCellLanes": [1, 2, 3], settings.IGO_COMPLETE_METADATA_KEY: True, "investigatorEmail": "email2@internet.com", - "investigatorName": "Jane Doe", - "investigatorSampleId": "JW_MEL_007_NORM", + "investigatorName": "Test Scientist", + "investigatorSampleId": "SAMPLE_N_001", "labHeadEmail": "email@internet.com", - "labHeadName": "John Smith", + "labHeadName": "Test Investigator", "libraryConcentrationNgul": 10.6, "libraryIgoId": None, "libraryVolume": None, settings.ONCOTREE_METADATA_KEY: None, - settings.PATIENT_ID_METADATA_KEY: "C-8VK0V7", + settings.PATIENT_ID_METADATA_KEY: "C-PPPPP3", "piEmail": "", "preservation": "EDTA-Streck", "projectManagerName": "", "readLength": "101/8/8/101", settings.RECIPE_METADATA_KEY: "IMPACT468", - settings.REQUEST_ID_METADATA_KEY: "10075_D_2", + settings.REQUEST_ID_METADATA_KEY: "99990_D_2", "sequencingCenter": "MSKCC", "platform": "Illumina", "runDate": "2019-12-12", - "runId": "JAX_0397", + "runId": "SEQRUN_0004", "runMode": "HiSeq High Output", - settings.SAMPLE_ID_METADATA_KEY: "10075_D_2_3", - settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-8VK0V7-N001-d", + settings.SAMPLE_ID_METADATA_KEY: "99990_D_2_3", + settings.CMO_SAMPLE_NAME_METADATA_KEY: "C-PPPPP3-N001-d", "sampleOrigin": "Plasma", "sex": "F", "species": "Human", @@ -119,7 +119,7 @@ def test_build_sample1(self): "tissueLocation": "", "tumorOrNormal": "Normal", }, - "path": "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz", + "path": "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz", }, ] @@ -144,34 +144,34 @@ def test_build_sample1(self): expected_sample = { "CN": "MSKCC", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2_3", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "LB": "99990_D_2_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R1_bid": [], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R2_bid": [], "bam": [], "bam_bid": [], - "SM": "s_C_8VK0V7_N001_d", + "SM": "s_C_PPPPP3_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "sample_origin": ["Plasma"], - "patient_id": "C-8VK0V7", - "request_id": "10075_D_2", + "patient_id": "C-PPPPP3", + "request_id": "99990_D_2", "run_date": ["2019-12-12"], - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["EDTA-Streck"], "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } diff --git a/runner/tests/operator/argos_operator/v2_3_0/test_pair_request.py b/runner/tests/operator/argos_operator/v2_3_0/test_pair_request.py index 31bec0314..aaa493cc2 100755 --- a/runner/tests/operator/argos_operator/v2_3_0/test_pair_request.py +++ b/runner/tests/operator/argos_operator/v2_3_0/test_pair_request.py @@ -82,9 +82,9 @@ def test_compile_pairs1(self): """ samples = [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Normal", @@ -93,9 +93,9 @@ def test_compile_pairs1(self): "run_mode": "HiSeq High Output", }, { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -108,10 +108,10 @@ def test_compile_pairs1(self): expected_pairs = { "tumor": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id1", @@ -121,10 +121,10 @@ def test_compile_pairs1(self): ], "normal": [ { - "patient_id": "C-W86LMR", + "patient_id": "C-PPPP21", "bait_set": "IMPACT468_BAITS", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id2", @@ -142,8 +142,8 @@ def test_compile_pairs2(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Normal", @@ -153,8 +153,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Normal", @@ -164,8 +164,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -175,8 +175,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -186,8 +186,8 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -201,9 +201,9 @@ def test_compile_pairs2(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id3", @@ -212,9 +212,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id4", @@ -223,9 +223,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id5", @@ -236,9 +236,9 @@ def test_compile_pairs2(self): "normal": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id1", @@ -247,9 +247,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id2", @@ -258,9 +258,9 @@ def test_compile_pairs2(self): }, { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Normal", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "sample_id": "my_sample_id1", @@ -283,8 +283,8 @@ def test_compile_pairs3(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "tumor_type": "Normal", "run_mode": "HiSeq High Output", @@ -298,24 +298,24 @@ def test_compile_pairs4(self): """ Test pairing with only a single unpaired Tumor sample Test that the appropriate Normal sample is found from the other samples in the same request - missing normal for sample 10075_D_1; querying patient C-DRKHP7 + missing normal for sample 99990_D_1; querying patient C-PPPPP7 """ # Load fixtures: - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", "run_mode": "hiseq", } ] @@ -324,26 +324,26 @@ def test_compile_pairs4(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("aef306b4-7d85-4c9f-b9a4-a115154f73bf")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("9e47ba2f-093a-4233-8339-fed03e159b3f")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["Frozen"], "sample_origin": ["Whole Blood"], @@ -351,17 +351,17 @@ def test_compile_pairs4(self): "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -380,10 +380,10 @@ def test_compile_pairs5(self): This time also load File entries from another request to make sure they do not confound the pairing """ # Load fixtures - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "05257_CB.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99992_C.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 14) @@ -392,13 +392,13 @@ def test_compile_pairs5(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-DRKHP7", + "patient_id": "C-PPPPP7", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], - "SM": "10075_D_1", - "sample_id": "10075_D_1", + "SM": "99990_D_1", + "sample_id": "99990_D_1", "run_mode": "hiseq", } ] @@ -407,26 +407,26 @@ def test_compile_pairs5(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_C_DRKHP7_N001_d_HCYYWBBXY"], - "LB": "10075_D_2", + "ID": ["s_C_PPPPP7_N001_d_FCELLAAAA4"], + "LB": "99990_D_2", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R1_001.fastq.gz" ], "R1_bid": [UUID("aef306b47d854c9fb9a4a115154f73bf")], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D/Sample_31-N_IGO_10075_D_2/31-N_IGO_10075_D_2_S14_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D/Sample_31-N_IGO_99990_D_2/31-N_IGO_99990_D_2_S14_R2_001.fastq.gz" ], "R2_bid": [UUID("9e47ba2f093a42338339fed03e159b3f")], "bam": [], "bam_bid": [], - "SM": "s_C_DRKHP7_N001_d", + "SM": "s_C_PPPPP7_N001_d", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2", - "patient_id": "C-DRKHP7", - "request_id": "10075_D", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_2", + "patient_id": "C-PPPPP7", + "request_id": "99990_D", + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["Frozen"], "sample_origin": ["Whole Blood"], @@ -434,17 +434,17 @@ def test_compile_pairs5(self): "species": "Human", "specimen_type": "Blood", "tumor_type": "Normal", - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], "tumor": [ { "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_1", - "SM": "10075_D_1", - "patient_id": "C-DRKHP7", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_1", + "SM": "99990_D_1", + "patient_id": "C-PPPPP7", + "run_id": ["SEQRUN_0004"], "preservation_type": ["Frozen"], "sample_origin": [""], "tumor_type": "Tumor", @@ -462,11 +462,11 @@ def test_get_pair_from_other_request(self): """ # Load fixtures # only normals - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) # only tumors - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_3.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_3.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -475,14 +475,14 @@ def test_get_pair_from_other_request(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", "run_mode": "hiseq", } ] @@ -492,14 +492,14 @@ def test_get_pair_from_other_request(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", - "run_id": ["JAX_0397"], + "patient_id": "C-PPPPP3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", "sample_origin": [""], - "request_id": "10075_D_3", + "request_id": "99990_D_3", "run_mode": "hiseq", } ], @@ -507,33 +507,33 @@ def test_get_pair_from_other_request(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_2_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_2_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_2_3", + "sample_id": "99990_D_2_3", "run_date": ["2019-12-12"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_2/Sample_JW_MEL_007_NORM_IGO_10075_D_2_3/JW_MEL_007_NORM_IGO_10075_D_2_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_2/Sample_SAMPLE_N_001_IGO_99990_D_2_3/SAMPLE_N_001_IGO_99990_D_2_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("7a3bceb31af84d3da1583731c83aeb5a")], "R2_bid": [UUID("ecf003cdbd304e909d180d99e7fd79d3")], "bam": [], "bam_bid": [], - "request_id": "10075_D_2", + "request_id": "99990_D_2", "sample_origin": ["Plasma"], - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_mode": "hiseq", "preservation_type": ["EDTA-Streck"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", } ], @@ -547,10 +547,10 @@ def test_get_most_recent_normal1(self): in the event that a patient has several normals Return the Normal with the most recent run_date """ - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_2.filemetadata.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.file.json"), verbosity=0) - call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "10075_D_4.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_2.filemetadata.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.file.json"), verbosity=0) + call_command("loaddata", os.path.join(settings.TEST_FIXTURE_DIR, "99990_D_4.filemetadata.json"), verbosity=0) # check the total number of db entries now self.assertTrue(len(File.objects.all()) == 4) @@ -559,12 +559,12 @@ def test_get_most_recent_normal1(self): samples = [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], "run_mode": "hiseq", @@ -576,12 +576,12 @@ def test_get_most_recent_normal1(self): "tumor": [ { "bait_set": "IMPACT468_BAITS", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "tumor_type": "Tumor", - "sample_id": "10075_D_3_5", - "SM": "10075_D_3_5", - "request_id": "10075_D_3", - "run_id": ["JAX_0397"], + "sample_id": "99990_D_3_5", + "SM": "99990_D_3_5", + "request_id": "99990_D_3", + "run_id": ["SEQRUN_0004"], "sample_origin": [""], "preservation_type": ["EDTA-Streck"], "run_mode": "hiseq", @@ -591,32 +591,32 @@ def test_get_most_recent_normal1(self): { "CN": "MSKCC", "PL": "Illumina", - "PU": ["HCYYWBBXY"], - "LB": "10075_D_4_3", + "PU": ["FCELLAAAA4"], + "LB": "99990_D_4_3", "tumor_type": "Normal", - "ID": ["s_C_8VK0V7_N001_d_HCYYWBBXY"], - "SM": "s_C_8VK0V7_N001_d", + "ID": ["s_C_PPPPP3_N001_d_FCELLAAAA4"], + "SM": "s_C_PPPPP3_N001_d", "species": "Human", - "patient_id": "C-8VK0V7", + "patient_id": "C-PPPPP3", "bait_set": "IMPACT468_BAITS", - "sample_id": "10075_D_4_3", + "sample_id": "99990_D_4_3", "run_date": ["2019-12-13"], "specimen_type": "Blood", "R1": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R1_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R1_001.fastq.gz" ], "R2": [ - "/ifs/archive/GCL/hiseq/FASTQ/JAX_0397_BHCYYWBBXY/Project_10075_D_4/Sample_JW_MEL_007_NORM_IGO_10075_D_4_3/JW_MEL_007_NORM_IGO_10075_D_4_3_S15_R2_001.fastq.gz" + "/ifs/archive/GCL/hiseq/FASTQ/SEQRUN_0004_BFCELLAAAA4/Project_99990_D_4/Sample_SAMPLE_N_001_IGO_99990_D_4_3/SAMPLE_N_001_IGO_99990_D_4_3_S15_R2_001.fastq.gz" ], "R1_bid": [UUID("404ad544428c405f967aa6920d091148")], "R2_bid": [UUID("19703ff82e144f608d57891df80b2858")], "bam": [], "bam_bid": [], - "request_id": "10075_D_4", - "run_id": ["JAX_0397"], + "request_id": "99990_D_4", + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": ["Plasma"], - "pi": "John Smith", + "pi": "Test Investigator", "pi_email": "email@internet.com", "run_mode": "hiseq", } @@ -634,10 +634,10 @@ def test_compile_pairs_custom1(self): samples = [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("a46c5e6b-0793-4cd2-b5dd-92b3d71cf1ac")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -649,7 +649,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], "run_date": ["2019-12-12"], @@ -660,10 +660,10 @@ def test_compile_pairs_custom1(self): }, { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz"], "R1_bid": [UUID("d2d8ed36-d8f4-4e93-b038-d38328fad021")], "R2": ["/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R2_001.fastq.gz"], @@ -675,7 +675,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "preservation_type": ["EDTA-Streck"], "sample_origin": [""], "run_date": ["2019-12-17"], @@ -691,10 +691,10 @@ def test_compile_pairs_custom1(self): "tumor": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_5_HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "ID": ["s_juno_argos_demo1_5_FCELLAAAA6_GTATTGGC-PPPP14"], "LB": "juno_argos_demo1_5_1_1_1", "PL": "Illumina", - "PU": ["HFTCNBBXY_GTATTGGC-TTGTCGGT"], + "PU": ["FCELLAAAA6_GTATTGGC-PPPP14"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-T/DU874145-T_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -708,7 +708,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_5", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-17"], "species": "Human", "specimen_type": "Resection", @@ -723,10 +723,10 @@ def test_compile_pairs_custom1(self): "normal": [ { "CN": "MSKCC", - "ID": ["s_juno_argos_demo1_3_HCYYWBBXY"], + "ID": ["s_juno_argos_demo1_3_FCELLAAAA4"], "LB": "juno_argos_demo1_3", "PL": "Illumina", - "PU": ["HCYYWBBXY"], + "PU": ["FCELLAAAA4"], "R1": [ "/juno/work/ci/argos-test/data/fastq/DU874145-N/DU874145-N_IGO_00000_TEST_L001_R1_001.fastq.gz" ], @@ -740,7 +740,7 @@ def test_compile_pairs_custom1(self): "sample_id": "s_juno_argos_demo1_3", "patient_id": "DU874145", "request_id": "juno_argos_demo1", - "run_id": ["JAX_0397"], + "run_id": ["SEQRUN_0004"], "run_date": ["2019-12-12"], "species": "Human", "specimen_type": "Blood", diff --git a/runner/tests/operator/argos_operator/v2_3_0/test_retrieve_samples_by_query.py b/runner/tests/operator/argos_operator/v2_3_0/test_retrieve_samples_by_query.py index a70e77909..11f1345a8 100644 --- a/runner/tests/operator/argos_operator/v2_3_0/test_retrieve_samples_by_query.py +++ b/runner/tests/operator/argos_operator/v2_3_0/test_retrieve_samples_by_query.py @@ -281,7 +281,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R1_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -298,7 +298,7 @@ def test_get_pooled_normals1(self): FileMetadata.objects.create_or_update( file=poolednormal_R2_file_instance, metadata={ - "runId": "PITT_0439", + "runId": "SEQRUN_0008", settings.RECIPE_METADATA_KEY: "IMPACT468", "sequencingCenter": "MSKCC", "platform": "Illumina", @@ -308,7 +308,7 @@ def test_get_pooled_normals1(self): ) pooled_normals = get_pooled_normals( - run_ids=["PITT_0439"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS", sample_origin=[""] + run_ids=["SEQRUN_0008"], preservation_types=["Frozen"], bait_set="IMPACT468_BAITS", sample_origin=[""] ) # remove the R1_bid and R2_bid for testing because they are non-deterministic # TODO: mock this ^^ @@ -319,14 +319,14 @@ def test_get_pooled_normals1(self): "CN": "MSKCC", "PL": "Illumina", "PU": ["PN_FCID_FROZENPOOLEDNORMAL"], - "LB": "FROZENPOOLEDNORMAL_PITT_0439_1", + "LB": "FROZENPOOLEDNORMAL_SEQRUN_0008_1", "tumor_type": "Normal", - "ID": ["FROZENPOOLEDNORMAL_PITT_0439_PN_FCID_FROZENPOOLEDNORMAL"], - "SM": "FROZENPOOLEDNORMAL_PITT_0439", + "ID": ["FROZENPOOLEDNORMAL_SEQRUN_0008_PN_FCID_FROZENPOOLEDNORMAL"], + "SM": "FROZENPOOLEDNORMAL_SEQRUN_0008", "species": "", "patient_id": "PN_PATIENT_ID", "bait_set": "IMPACT468", - "sample_id": "FROZENPOOLEDNORMAL_PITT_0439", + "sample_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "run_date": [""], "specimen_type": "Pooled Normal", "R1": ["/FROZENPOOLEDNORMAL.R1.fastq"], @@ -335,11 +335,11 @@ def test_get_pooled_normals1(self): "R2_bid": [], # UUID('ec9817d1-d6f5-4f1d-9c0a-c82fc22d4daa') "bam": [], "bam_bid": [], - "request_id": "FROZENPOOLEDNORMAL_PITT_0439", + "request_id": "FROZENPOOLEDNORMAL_SEQRUN_0008", "pi": "", "pi_email": "", "sample_origin": [[""]], - "run_id": ["PITT_0439"], + "run_id": ["SEQRUN_0008"], "preservation_type": [["Frozen"]], "run_mode": "", } diff --git a/runner/tests/operator/cmo_ch/v2_0_0/nucleo/test_nucleo_operator.py b/runner/tests/operator/cmo_ch/v2_0_0/nucleo/test_nucleo_operator.py index d3978f86c..af3a5734a 100644 --- a/runner/tests/operator/cmo_ch/v2_0_0/nucleo/test_nucleo_operator.py +++ b/runner/tests/operator/cmo_ch/v2_0_0/nucleo/test_nucleo_operator.py @@ -12,8 +12,8 @@ FIXTURES = [ - "fixtures/tests/merge_fastqs/10151_F_13.file.json", - "fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json", + "fixtures/tests/merge_fastqs/99996_F_13.file.json", + "fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json", ] COMMON_FIXTURES = [ @@ -40,7 +40,7 @@ def test_cmoch_nucleo_operator(self): self.assertEqual(len(File.objects.all()), operator_files_count) self.assertEqual(len(FileMetadata.objects.all()), operator_files_count) - request_id = "10151_F" + request_id = "99996_F" operator_model = Operator.objects.get(id=14) operator = OperatorFactory.get_by_model(operator_model, request_id=request_id) @@ -73,13 +73,13 @@ def test_construct_cmo_ch_jobs(self): """ Test that CMO-CH jobs are correctly created """ - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "05500_HJ.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99900_H.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "05500_HJ.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99900_H.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) files = File.objects.filter( - filemetadata__metadata__requestId="05500_HJ", filemetadata__metadata__igoComplete=True + filemetadata__metadata__requestId="99900_H", filemetadata__metadata__igoComplete=True ).all() data = list() for file in files: @@ -89,9 +89,9 @@ def test_construct_cmo_ch_jobs(self): sample["file_name"] = file.file_name sample["metadata"] = file.filemetadata_set.first().metadata data.append(sample) - cmo_ch_inputs = construct_sample_inputs(data, "05500_HJ") + cmo_ch_inputs = construct_sample_inputs(data, "99900_H") self.assertTrue(len(cmo_ch_inputs) == 18) - expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "05500_HJ.input.json"))) + expected_inputs = json.load(open(os.path.join(settings.TEST_FIXTURE_DIR, "99900_H.input.json"))) cmo_ch_inputs_str = json.dumps(cmo_ch_inputs) expected_inputs_str = json.dumps(expected_inputs) self.assertTrue(cmo_ch_inputs_str == expected_inputs_str) @@ -101,10 +101,10 @@ def test_get_cmo_ch_jobs(self): Test getting the CMO-CH jobs """ operator_model = Operator.objects.get(id=14) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "05500_HJ.file.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99900_H.file.json") call_command("loaddata", test_files_fixture, verbosity=0) - test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "05500_HJ.filemetadata.json") + test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR, "99900_H.filemetadata.json") call_command("loaddata", test_files_fixture, verbosity=0) - jobs = CMOCHNucleoOperator(operator_model, request_id="05500_HJ").get_jobs() + jobs = CMOCHNucleoOperator(operator_model, request_id="99900_H").get_jobs() self.assertTrue((len(jobs) == 18)) - self.assertTrue(jobs[0].name == "CMO-CH Nucleo: 05500_HJ, 1 of 18") + self.assertTrue(jobs[0].name == "CMO-CH Nucleo: 99900_H, 1 of 18") diff --git a/runner/tests/operator/cmo_ch/v2_1_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json b/runner/tests/operator/cmo_ch/v2_1_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json index 3f50cf7d6..74d0922d0 100644 --- a/runner/tests/operator/cmo_ch/v2_1_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json +++ b/runner/tests/operator/cmo_ch/v2_1_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json @@ -1238,14 +1238,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "A-000000", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1271,15 +1271,15 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "Not imported from SMILE", "smileRequestId": "Not imported from SMILE", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", "externalSampleId": "A-000000", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1287,8 +1287,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "investigatorSampleId": "A-000000", "captureConcentrationNm": null, @@ -1345,14 +1345,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "A-000000", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1378,15 +1378,15 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "Not imported from SMILE", "smileRequestId": "Not imported from SMILE", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", "externalSampleId": "A-000000", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1394,8 +1394,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "investigatorSampleId": "A-000000", "captureConcentrationNm": null, @@ -1452,14 +1452,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1485,13 +1485,13 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1499,8 +1499,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1561,14 +1561,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "A-000000", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1594,15 +1594,15 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "Not imported from SMILE", "smileRequestId": "Not imported from SMILE", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", "externalSampleId": "A-000000", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1610,8 +1610,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "investigatorSampleId": "A-000000", "captureConcentrationNm": null, @@ -1668,14 +1668,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1701,13 +1701,13 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1715,8 +1715,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1777,14 +1777,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1810,13 +1810,13 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1824,8 +1824,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1886,14 +1886,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1919,13 +1919,13 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1933,8 +1933,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1995,14 +1995,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -2028,13 +2028,13 @@ "value": "A-000000", "namespace": "cmoId" }], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -2042,8 +2042,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", diff --git a/runner/tests/operator/cmo_ch/v2_1_0/qc/files_fixture.json b/runner/tests/operator/cmo_ch/v2_1_0/qc/files_fixture.json index 475f9f701..357ed6c96 100644 --- a/runner/tests/operator/cmo_ch/v2_1_0/qc/files_fixture.json +++ b/runner/tests/operator/cmo_ch/v2_1_0/qc/files_fixture.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -31,8 +31,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bam", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bam", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -44,8 +44,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -57,8 +57,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -70,8 +70,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -83,8 +83,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -96,8 +96,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bai", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bai", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -109,8 +109,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -122,8 +122,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/runner/tests/operator/cmo_ch/v2_1_0/qc/files_metadata_fixture.json b/runner/tests/operator/cmo_ch/v2_1_0/qc/files_metadata_fixture.json index b6941c631..2c9b4b11a 100644 --- a/runner/tests/operator/cmo_ch/v2_1_0/qc/files_metadata_fixture.json +++ b/runner/tests/operator/cmo_ch/v2_1_0/qc/files_metadata_fixture.json @@ -10,9 +10,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -41,9 +41,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -72,9 +72,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -103,9 +103,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -134,9 +134,9 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", diff --git a/runner/tests/operator/cmo_ch/v2_1_0/qc/ports_fixture.json b/runner/tests/operator/cmo_ch/v2_1_0/qc/ports_fixture.json index 4c1154bff..df3c3ba50 100644 --- a/runner/tests/operator/cmo_ch/v2_1_0/qc/ports_fixture.json +++ b/runner/tests/operator/cmo_ch/v2_1_0/qc/ports_fixture.json @@ -18,11 +18,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "class": "File" }] } @@ -51,11 +51,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "class": "File" }] } @@ -84,11 +84,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "class": "File" }] } @@ -117,11 +117,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "class": "File" }] } @@ -150,11 +150,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "class": "File" }] } diff --git a/runner/tests/operator/cmo_ch/v2_2_0/nucleo/test_nucleo_operator.py b/runner/tests/operator/cmo_ch/v2_2_0/nucleo/test_nucleo_operator.py index b42fef17d..30171ee98 100644 --- a/runner/tests/operator/cmo_ch/v2_2_0/nucleo/test_nucleo_operator.py +++ b/runner/tests/operator/cmo_ch/v2_2_0/nucleo/test_nucleo_operator.py @@ -12,8 +12,8 @@ FIXTURES = [ - "fixtures/tests/merge_fastqs/10151_F_13.file.json", - "fixtures/tests/merge_fastqs/10151_F_13.filemetadata.json", + "fixtures/tests/merge_fastqs/99996_F_13.file.json", + "fixtures/tests/merge_fastqs/99996_F_13.filemetadata.json", ] COMMON_FIXTURES = [ @@ -40,7 +40,7 @@ def test_cmoch_nucleo_operator(self): self.assertEqual(len(File.objects.all()), operator_files_count) self.assertEqual(len(FileMetadata.objects.all()), operator_files_count) - request_id = "10151_F" + request_id = "99996_F" operator_model = Operator.objects.get(id=26) operator = OperatorFactory.get_by_model(operator_model, request_id=request_id) diff --git a/runner/tests/operator/cmo_ch/v2_2_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json b/runner/tests/operator/cmo_ch/v2_2_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json index 8f22fc2e2..ff1f23323 100644 --- a/runner/tests/operator/cmo_ch/v2_2_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json +++ b/runner/tests/operator/cmo_ch/v2_2_0/qc/0a3c70a9-cf89-466b-bd39-4f409c21fb41.files.json @@ -1351,14 +1351,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "A-000000", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1387,15 +1387,15 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "Not imported from SMILE", "smileRequestId": "Not imported from SMILE", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", "externalSampleId": "A-000000", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1403,8 +1403,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "investigatorSampleId": "A-000000", "captureConcentrationNm": null, @@ -1465,14 +1465,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "A-000000", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1501,15 +1501,15 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "Not imported from SMILE", "smileRequestId": "Not imported from SMILE", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", "externalSampleId": "A-000000", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1517,8 +1517,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "investigatorSampleId": "A-000000", "captureConcentrationNm": null, @@ -1579,14 +1579,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1615,13 +1615,13 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1629,8 +1629,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1695,14 +1695,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "A-000000", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1731,15 +1731,15 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "Not imported from SMILE", "smileRequestId": "Not imported from SMILE", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", "externalSampleId": "A-000000", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1747,8 +1747,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "investigatorSampleId": "A-000000", "captureConcentrationNm": null, @@ -1809,14 +1809,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1845,13 +1845,13 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1859,8 +1859,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -1925,14 +1925,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -1961,13 +1961,13 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -1975,8 +1975,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -2041,14 +2041,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -2077,13 +2077,13 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -2091,8 +2091,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", @@ -2157,14 +2157,14 @@ "sampleType": "Normal", "captureName": null, "igoComplete": true, - "labHeadName": "Eli Diamond", + "labHeadName": "Test LabHead", "sampleClass": "Blood", "barcodeIndex": null, "cmoInfoIgoId": "12405_B_17", "cmoPatientId": "A-000000", "igoProjectId": "12405", "igoRequestId": "12405_C", - "labHeadEmail": "diamone1@mskcc.org", + "labHeadEmail": "analyst15@example.org", "libraryIgoId": null, "oncotreeCode": "HS", "preservation": "EDTA-Streck", @@ -2193,13 +2193,13 @@ "namespace": "cmoId" } ], - "qcAccessEmails": "skicmopm@mskcc.org", + "qcAccessEmails": "pm1@example.org", "smilePatientId": "98858465-5c90-4ff0-8c23-8ef9b560d083", "tissueLocation": "", "dataAnalystName": "", - "dataAccessEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,siglera@mskcc.org", + "dataAccessEmails": "pm1@example.org,analyst16@example.org,analyst17@example.org", "dataAnalystEmail": "", - "investigatorName": "Allison Sigler", + "investigatorName": "Test Analyst", "sequencingCenter": "MSKCC", "cmoSampleIdFields": { "recipe": "CustomCapture", @@ -2207,8 +2207,8 @@ "naToExtract": "", "normalizedPatientId": "MRN_REDACTED" }, - "investigatorEmail": "siglera@mskcc.org", - "otherContactEmails": "skicmopm@mskcc.org,shahr2@mskcc.org,skicmopm@mskcc.org", + "investigatorEmail": "analyst17@example.org", + "otherContactEmails": "pm1@example.org,analyst16@example.org,pm1@example.org", "projectManagerName": "", "additionalProperties": { "isCmoSample": "true", diff --git a/runner/tests/operator/cmo_ch/v2_2_0/qc/files_fixture.json b/runner/tests/operator/cmo_ch/v2_2_0/qc/files_fixture.json index 475f9f701..357ed6c96 100644 --- a/runner/tests/operator/cmo_ch/v2_2_0/qc/files_fixture.json +++ b/runner/tests/operator/cmo_ch/v2_2_0/qc/files_fixture.json @@ -5,8 +5,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -18,8 +18,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -31,8 +31,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bam", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bam", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -44,8 +44,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -57,8 +57,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bam", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bam", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -70,8 +70,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", - "path": "/test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "file_name": "C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "path": "/test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -83,8 +83,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -96,8 +96,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.576Z", "modified_date": "2020-01-06T19:59:50.579Z", - "file_name": "C-261TDL-N001-d_collapsed_grouped.bai", - "path": "/test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "file_name": "C-PPPP20-N001-d_collapsed_grouped.bai", + "path": "/test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -109,8 +109,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" @@ -122,8 +122,8 @@ "fields": { "created_date": "2020-01-06T19:59:50.591Z", "modified_date": "2020-01-06T19:59:50.592Z", - "file_name": "C-261TDL-N001-d__aln_srt_IR_FX.bai", - "path": "/test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "file_name": "C-PPPP20-N001-d__aln_srt_IR_FX.bai", + "path": "/test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "file_type": 3, "size": 0, "file_group": "1a1b29cf-3bc2-4f6c-b376-d4c5d701166a" diff --git a/runner/tests/operator/cmo_ch/v2_2_0/qc/files_metadata_fixture.json b/runner/tests/operator/cmo_ch/v2_2_0/qc/files_metadata_fixture.json index c2bde2fdf..81e7d6f9f 100644 --- a/runner/tests/operator/cmo_ch/v2_2_0/qc/files_metadata_fixture.json +++ b/runner/tests/operator/cmo_ch/v2_2_0/qc/files_metadata_fixture.json @@ -10,10 +10,10 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", "request": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -42,10 +42,10 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", "request": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -74,10 +74,10 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", "request": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -106,10 +106,10 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", "request": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", @@ -138,10 +138,10 @@ "version": 0, "metadata": { "primaryId": "05500_FH_1", - "cmoPatientId": "C-261TDL", + "cmoPatientId": "C-PPPP20", "igoRequestId": "05500_FH", "request": "05500_FH", - "cmoSampleName": "C-261TDL-N001-d", + "cmoSampleName": "C-PPPP20-N001-d", "genePanel": "-", "dataAnalystName": "-", "dataAnalystEmail": "-", diff --git a/runner/tests/operator/cmo_ch/v2_2_0/qc/ports_fixture.json b/runner/tests/operator/cmo_ch/v2_2_0/qc/ports_fixture.json index 4c1154bff..df3c3ba50 100644 --- a/runner/tests/operator/cmo_ch/v2_2_0/qc/ports_fixture.json +++ b/runner/tests/operator/cmo_ch/v2_2_0/qc/ports_fixture.json @@ -18,11 +18,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_cl_aln_srt_MD_IR_FX_BR.bai", "class": "File" }] } @@ -51,11 +51,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-simplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-simplex.bai", "class": "File" }] } @@ -84,11 +84,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bam", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d_collapsed_grouped.bai", + "location": "juno:///test/path/C-PPPP20-N001-d_collapsed_grouped.bai", "class": "File" }] } @@ -117,11 +117,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX-duplex.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX-duplex.bai", "class": "File" }] } @@ -150,11 +150,11 @@ }], "value": { "file": { - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bam", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bam", "size": 7313069069, "class": "File", "secondaryFiles": [{ - "location": "juno:///test/path/C-261TDL-N001-d__aln_srt_IR_FX.bai", + "location": "juno:///test/path/C-PPPP20-N001-d__aln_srt_IR_FX.bai", "class": "File" }] } diff --git a/runner/tests/operator/test_access_operators.py b/runner/tests/operator/test_access_operators.py index ab78151f8..ec0549274 100644 --- a/runner/tests/operator/test_access_operators.py +++ b/runner/tests/operator/test_access_operators.py @@ -5,7 +5,7 @@ from runner.operator.access import get_unfiltered_matched_normal, DMP_IMPACT_ASSAYS, ACCESS_ASSAY -TEST_PATIENT_ID = "C-000884" +TEST_PATIENT_ID = "C-PPPP19" REQUEST_ID = "access_legacy_test_request" @@ -14,7 +14,7 @@ def test_matched_igo_normal_same_request(self): """ Test a matching unfiltered normal, same request ID """ - file_name = "C-000884-N001-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" + file_name = "C-PPPP19-N001-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" file_path = "/test/" + file_name fg = FileGroup.objects.create(name="test", slug="test") @@ -38,7 +38,7 @@ def test_matched_igo_normal_different_request(self): """ Test a matching unfiltered normal, different request ID """ - file_name = "C-000884-N001-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" + file_name = "C-PPPP19-N001-d_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX.bam" file_path = "/test/" + file_name fg = FileGroup.objects.create(name="test", slug="test") @@ -62,7 +62,7 @@ def test_matched_dmp_normal_access(self): """ Test matching unfiltered normal DMP ACCESS """ - file_name = "000884-unfilter.bam" + file_name = "PPPP19-unfilter.bam" file_path = "/test/" + file_name fg = FileGroup.objects.create(name="test", slug="test") @@ -80,7 +80,7 @@ def test_matched_dmp_normal_impact(self): """ Test matching unfiltered normal DMP IMPACT """ - file_name = "C-000884.bam" + file_name = "C-PPPP19.bam" file_path = "/test/" + file_name fg = FileGroup.objects.create(name="test", slug="test") @@ -91,13 +91,13 @@ def test_matched_dmp_normal_impact(self): metadata={"cmo_assay": DMP_IMPACT_ASSAYS[0], "type": "N", "patient": {"cmo": TEST_PATIENT_ID.lstrip("C-")}}, ) - normal, sample_id = get_unfiltered_matched_normal("C-000884", REQUEST_ID) + normal, sample_id = get_unfiltered_matched_normal("C-PPPP19", REQUEST_ID) self.assertEqual(normal.file_name, file_name) def test_empty_genotyping_result(self): """ Test no matching normal found """ - normal, sample_id = get_unfiltered_matched_normal("C-000884", REQUEST_ID) + normal, sample_id = get_unfiltered_matched_normal("C-PPPP19", REQUEST_ID) self.assertIsNone(normal) self.assertEqual(sample_id, "") diff --git a/runner/tests/run/inputs.json b/runner/tests/run/inputs.json index 9c5e72e02..de54eede3 100644 --- a/runner/tests/run/inputs.json +++ b/runner/tests/run/inputs.json @@ -109,7 +109,7 @@ "genome": "GRCh37", "facets_pcval": 500, "project_prefix": [ - "09670_D" + "99906_D" ], "facets_cval": 100, "mutect_dcov": 50000, diff --git a/runner/tests/run/pair-workflow.cwl b/runner/tests/run/pair-workflow.cwl index 3575c742f..10e8383ec 100644 --- a/runner/tests/run/pair-workflow.cwl +++ b/runner/tests/run/pair-workflow.cwl @@ -1655,11 +1655,11 @@ } ], "dct:contributor": { - "foaf:mbox": "mailto:bolipatc@mskcc.org", + "foaf:mbox": "mailto:dev1@example.org", "foaf:name": "C. Allan Bolipata" }, "dct:creator": { - "foaf:mbox": "mailto:bolipatc@mskcc.org", + "foaf:mbox": "mailto:dev1@example.org", "foaf:name": "C. Allan Bolipata" } } @@ -3312,11 +3312,11 @@ } ], "dct:contributor": { - "foaf:mbox": "mailto:bolipatc@mskcc.org", + "foaf:mbox": "mailto:dev1@example.org", "foaf:name": "C. Allan Bolipata" }, "dct:creator": { - "foaf:mbox": "mailto:bolipatc@mskcc.org", + "foaf:mbox": "mailto:dev1@example.org", "foaf:name": "C. Allan Bolipata" } } diff --git a/runner/tests/views/test_run_api_view.py b/runner/tests/views/test_run_api_view.py index cceaadbb6..e334217eb 100644 --- a/runner/tests/views/test_run_api_view.py +++ b/runner/tests/views/test_run_api_view.py @@ -233,9 +233,9 @@ def test_get_input(self): self.assertTrue("inputs" in response.json()["results"][0]) def test_get_runs_sample_id(self): - response = self.client.get(self.run_api_root + "?sample_ids=08944_B_4") + response = self.client.get(self.run_api_root + "?sample_ids=99991_B_4") self.assertEqual(response.status_code, status.HTTP_200_OK) self.assertEqual(response.json()["count"], 1) - response = self.client.get(self.run_api_root + "?sample_ids=08944_B_3,08944_B_4") + response = self.client.get(self.run_api_root + "?sample_ids=99991_B_3,99991_B_4") self.assertEqual(response.status_code, status.HTTP_200_OK) self.assertEqual(response.json()["count"], 2)