From 692f3ffd9b5d353ad00effd294f8398a277341a9 Mon Sep 17 00:00:00 2001
From: khoroshevskyi <sasha99250@gmail.com>
Date: Fri, 14 Aug 2026 23:32:44 -0400
Subject: [PATCH 1/6] Added alembic for database migrations

---
 .github/pull_request_template.md              |   1 +
 README.md                                     |  48 +++
 alembic.ini                                   | 126 +++++++
 bbconf/alembic/README                         |   1 +
 bbconf/alembic/__init__.py                    |   0
 bbconf/alembic/env.py                         |  77 ++++
 bbconf/alembic/script.py.mako                 |  28 ++
 .../8b0b706d0827_initial_migration.py         | 352 ++++++++++++++++++
 bbconf/alembic/versions/__init__.py           |   0
 bbconf/bbagent.py                             |   1 +
 bbconf/config_parser/bedbaseconfig.py         |   1 +
 bbconf/config_parser/models.py                |   1 +
 bbconf/db_utils.py                            |  33 ++
 pyproject.toml                                |   4 +
 14 files changed, 673 insertions(+)
 create mode 100644 alembic.ini
 create mode 100644 bbconf/alembic/README
 create mode 100644 bbconf/alembic/__init__.py
 create mode 100644 bbconf/alembic/env.py
 create mode 100644 bbconf/alembic/script.py.mako
 create mode 100644 bbconf/alembic/versions/8b0b706d0827_initial_migration.py
 create mode 100644 bbconf/alembic/versions/__init__.py

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index a24b8bf0..163df722 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -3,5 +3,6 @@
 
 
 ## TODO:
+- [ ] ❗ If this PR includes a new database schema migration, following steps are completed: [Database Version Migration](https://pep.databio.org/pephub/developer/pepdbagent/database_version_migration/)
 - [ ] Version of pepdbagent updated in `__version__.py` file
 - [ ] Changelog updated
\ No newline at end of file
diff --git a/README.md b/README.md
index df71db09..6caff043 100644
--- a/README.md
+++ b/README.md
@@ -56,3 +56,51 @@ agent.objects  # Generic object/file operations
 stats = agent.get_stats()
 print(stats.bedfiles_number, stats.bedsets_number)
 ```
+
+## Database migrations
+
+`bbconf` uses [Alembic](https://alembic.sqlalchemy.org/) to version the database
+schema. The migration scripts live in `bbconf/alembic`, and `alembic.ini` (repo
+root) is used for local CLI work. The first (baseline) revision is
+`8b0b706d0827`; it reproduces exactly the schema that `Base.metadata.create_all()`
+builds, including the `pg_trgm` extension and the trigram / partial / expression
+indexes.
+
+### Creating a new revision
+
+After changing the models in `bbconf/db_utils.py`:
+
+```bash
+alembic revision --autogenerate -m "Describe your change"
+```
+
+Review the generated file. Alembic cannot autogenerate a few constructs used by
+bbconf — the `pg_trgm` extension and expression-based indexes may need a manual
+`op.execute(...)` — so always check the diff before committing.
+
+### Applying migrations
+
+```bash
+alembic upgrade head      # upgrade to the latest revision
+alembic downgrade -1      # roll back one revision
+alembic current           # show the DB's current revision
+```
+
+### Running migrations automatically
+
+To upgrade the database to `head` automatically when `bbconf` starts, set
+`run_migrations: true` under the `database` section of the config file:
+
+```yaml
+database:
+  host: localhost
+  port: 5432
+  user: postgres
+  password: docker
+  database: bedbase
+  run_migrations: true
+```
+
+> **Note:** enable this only after the database has been stamped/upgraded to a
+> known revision. Turning it on against an un-stamped existing database will fail
+> on startup, because the baseline revision creates tables that already exist.
diff --git a/alembic.ini b/alembic.ini
new file mode 100644
index 00000000..625b44aa
--- /dev/null
+++ b/alembic.ini
@@ -0,0 +1,126 @@
+# A generic, single database configuration.
+#
+# This file is used only for local development / CLI work
+# (e.g. `alembic revision --autogenerate`, `alembic upgrade head`).
+# At runtime, bbconf builds the Alembic config programmatically in
+# `BaseEngine.run_db_migration()` and does NOT read this file.
+
+[alembic]
+# path to migration scripts
+# Use forward slashes (/) also on windows to provide an os agnostic path
+script_location = ./bbconf/alembic
+
+# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
+# Uncomment the line below if you want the files to be prepended with date and time
+# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file
+# for all available tokens
+# file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python>=3.9 or backports.zoneinfo library and tzdata library.
+# Any required deps can installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to ZoneInfo()
+# leave blank for localtime
+# timezone =
+
+# max length of characters to apply to the "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; This defaults
+# to alembic/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "version_path_separator" below.
+# version_locations = %(here)s/bar:%(here)s/bat:alembic/versions
+
+# version path separator; As mentioned above, this is the character used to split
+# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep.
+# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas.
+# Valid values for version_path_separator are:
+#
+# version_path_separator = :
+# version_path_separator = ;
+# version_path_separator = space
+# version_path_separator = newline
+#
+# Use os.pathsep. Default configuration used for new projects.
+version_path_separator = os
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# new in Alembic version 1.10
+# recursive_version_locations = false
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+# Local development connection string. Override with `-x` or edit as needed.
+# Runtime migrations use the URL built from the bbconf config instead.
+sqlalchemy.url = postgresql+psycopg://postgres:docker@localhost:5432/bedbase
+
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 REVISION_SCRIPT_FILENAME
+
+# lint with attempts to fix using "ruff" - use the exec runner, execute a binary
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = %(here)s/.venv/bin/ruff
+# ruff.options = check --fix REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARNING
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARNING
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S
diff --git a/bbconf/alembic/README b/bbconf/alembic/README
new file mode 100644
index 00000000..2500aa1b
--- /dev/null
+++ b/bbconf/alembic/README
@@ -0,0 +1 @@
+Generic single-database configuration.
diff --git a/bbconf/alembic/__init__.py b/bbconf/alembic/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/bbconf/alembic/env.py b/bbconf/alembic/env.py
new file mode 100644
index 00000000..e2b9fecb
--- /dev/null
+++ b/bbconf/alembic/env.py
@@ -0,0 +1,77 @@
+from logging.config import fileConfig
+
+from alembic import context
+from sqlalchemy import engine_from_config, pool
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+# for 'autogenerate' support.
+# Importing from bbconf.db_utils also registers the custom @compiles types
+# (BIGSERIAL, JSON->JSONB, ARRAY) and the pg_trgm extension DDL event, so the
+# metadata compiles to exactly the same DDL that create_all() produces.
+from bbconf.db_utils import Base
+
+target_metadata = Base.metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(connection=connection, target_metadata=target_metadata)
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()
diff --git a/bbconf/alembic/script.py.mako b/bbconf/alembic/script.py.mako
new file mode 100644
index 00000000..51a73aa6
--- /dev/null
+++ b/bbconf/alembic/script.py.mako
@@ -0,0 +1,28 @@
+"""${message}
+
+Revision ID: ${up_revision}
+Revises: ${down_revision | comma,n}
+Create Date: ${create_date}
+
+"""
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+${imports if imports else ""}
+
+# revision identifiers, used by Alembic.
+revision: str = ${repr(up_revision)}
+down_revision: Union[str, None] = ${repr(down_revision)}
+branch_labels: Union[str, Sequence[str], None] = ${repr(branch_labels)}
+depends_on: Union[str, Sequence[str], None] = ${repr(depends_on)}
+
+
+def upgrade() -> None:
+    """Upgrade schema."""
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade() -> None:
+    """Downgrade schema."""
+    ${downgrades if downgrades else "pass"}
diff --git a/bbconf/alembic/versions/8b0b706d0827_initial_migration.py b/bbconf/alembic/versions/8b0b706d0827_initial_migration.py
new file mode 100644
index 00000000..f8fae368
--- /dev/null
+++ b/bbconf/alembic/versions/8b0b706d0827_initial_migration.py
@@ -0,0 +1,352 @@
+"""Initial migration
+
+Revision ID: 8b0b706d0827
+Revises: 
+Create Date: 2026-08-14 23:09:22.903899
+
+"""
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = '8b0b706d0827'
+down_revision: Union[str, None] = None
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Upgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    # pg_trgm backs the trigram GIN indexes on `bedsets` (ix_bedsets_name_trgm /
+    # ix_bedsets_description_trgm). In the ORM this is created by a before_create
+    # DDL event on the bedsets table; autogenerate does not emit it, so it is
+    # added here by hand. Must run before those indexes are created.
+    op.execute("CREATE EXTENSION IF NOT EXISTS pg_trgm")
+    op.create_table('bed_snapshots',
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('file_path', sa.String(), nullable=False, comment='S3 object key, relative to the bucket root'),
+    sa.Column('file_type', sa.String(), nullable=False, comment='metadata | bedsets | bedset_membership | manifest'),
+    sa.Column('creation_date', sa.TIMESTAMP(timezone=True), nullable=False, comment='Build date of the export'),
+    sa.Column('record_count', sa.Integer(), nullable=True, comment='Rows actually written to the file'),
+    sa.Column('file_size', sa.Integer(), nullable=True, comment='Size of the file in bytes'),
+    sa.Column('checksum', sa.String(), nullable=True, comment='SHA256 of the file'),
+    sa.Column('schema_version', sa.Integer(), nullable=True, comment='Export schema version'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_bed_snapshots_id'), 'bed_snapshots', ['id'], unique=False)
+    op.create_table('bedsets',
+    sa.Column('id', sa.String(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False, comment='Name of the bedset'),
+    sa.Column('description', sa.String(), nullable=True, comment='Description of the bedset'),
+    sa.Column('summary', sa.String(), nullable=True, comment='Summary of the bedset'),
+    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
+    sa.Column('last_update_date', sa.TIMESTAMP(timezone=True), nullable=True),
+    sa.Column('md5sum', sa.String(), nullable=True, comment='MD5 sum of the bedset'),
+    sa.Column('bedset_means', postgresql.JSON(astext_type=sa.Text()), nullable=True, comment='Mean values of the bedset'),
+    sa.Column('bedset_standard_deviation', postgresql.JSON(astext_type=sa.Text()), nullable=True, comment='Median values of the bedset'),
+    sa.Column('bedfile_count', sa.Integer(), nullable=False, comment='Number of bedfiles in the bedset (denormalized count)'),
+    sa.Column('author', sa.String(), nullable=True, comment='Author of the bedset'),
+    sa.Column('source', sa.String(), nullable=True, comment='Source of the bedset'),
+    sa.Column('processed', sa.Boolean(), nullable=False, comment='Whether the bedset was processed'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index('ix_bedsets_description_trgm', 'bedsets', ['description'], unique=False, postgresql_using='gin', postgresql_ops={'description': 'gin_trgm_ops'})
+    op.create_index(op.f('ix_bedsets_id'), 'bedsets', ['id'], unique=False)
+    op.create_index('ix_bedsets_name_trgm', 'bedsets', ['name'], unique=False, postgresql_using='gin', postgresql_ops={'name': 'gin_trgm_ops'})
+    op.create_index('ix_bedsets_unprocessed', 'bedsets', ['id'], unique=False, postgresql_where=sa.text('processed = false'))
+    op.create_table('geo_gse_status',
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('gse', sa.String(), nullable=False, comment='GSE number'),
+    sa.Column('status', sa.String(), nullable=False, comment='Status of the GEO project'),
+    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
+    sa.Column('number_of_files', sa.Integer(), nullable=False, comment='Number of files'),
+    sa.Column('number_of_success', sa.Integer(), nullable=False, comment='Number of success'),
+    sa.Column('number_of_skips', sa.Integer(), nullable=False, comment='Number of skips'),
+    sa.Column('number_of_fails', sa.Integer(), nullable=False, comment='Number of fails'),
+    sa.Column('error', sa.String(), nullable=True, comment='Error message'),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('gse')
+    )
+    op.create_index(op.f('ix_geo_gse_status_id'), 'geo_gse_status', ['id'], unique=False)
+    op.create_table('licenses',
+    sa.Column('id', sa.String(), nullable=False),
+    sa.Column('shorthand', sa.String(), nullable=True, comment='License shorthand'),
+    sa.Column('label', sa.String(), nullable=False, comment='License label'),
+    sa.Column('description', sa.String(), nullable=False, comment='License description'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_licenses_id'), 'licenses', ['id'], unique=False)
+    op.create_table('reference_genomes',
+    sa.Column('digest', sa.String(), nullable=False),
+    sa.Column('alias', sa.String(), nullable=False, comment='Name of the reference genome'),
+    sa.PrimaryKeyConstraint('digest')
+    )
+    op.create_index(op.f('ix_reference_genomes_digest'), 'reference_genomes', ['digest'], unique=False)
+    op.create_table('usage_files',
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('file_path', sa.String(), nullable=False, comment='Path to the file'),
+    sa.Column('count', sa.Integer(), nullable=False, comment='Number of downloads'),
+    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
+    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_usage_files_id'), 'usage_files', ['id'], unique=False)
+    op.create_table('usage_search',
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('query', sa.String(), nullable=False, comment='Search query'),
+    sa.Column('type', sa.String(), nullable=False, comment='Type of the search. Bed/Bedset'),
+    sa.Column('count', sa.Integer(), nullable=False, comment='Number of searches'),
+    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
+    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_usage_search_id'), 'usage_search', ['id'], unique=False)
+    op.create_table('bed',
+    sa.Column('id', sa.String(), nullable=False),
+    sa.Column('name', sa.String(), nullable=True),
+    sa.Column('genome_alias', sa.String(), nullable=True),
+    sa.Column('genome_digest', sa.String(), nullable=True),
+    sa.Column('description', sa.String(), nullable=True),
+    sa.Column('bed_compliance', sa.String(), nullable=False),
+    sa.Column('data_format', sa.String(), nullable=False),
+    sa.Column('compliant_columns', sa.Integer(), nullable=False),
+    sa.Column('non_compliant_columns', sa.Integer(), nullable=False),
+    sa.Column('header', sa.String(), nullable=True, comment='Header of the bed file, it if was provided.'),
+    sa.Column('indexed', sa.Boolean(), nullable=False, comment='Whether sample was added to qdrant'),
+    sa.Column('file_indexed', sa.Boolean(), nullable=False, comment='Whether file was tokenized and added to the vector database'),
+    sa.Column('pephub', sa.Boolean(), nullable=False, comment='Whether sample was added to pephub'),
+    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
+    sa.Column('last_update_date', sa.TIMESTAMP(timezone=True), nullable=True),
+    sa.Column('is_universe', sa.Boolean(), nullable=True),
+    sa.Column('license_id', sa.String(), nullable=True),
+    sa.Column('processed', sa.Boolean(), nullable=False, comment='Whether the bed file was processed'),
+    sa.ForeignKeyConstraint(['license_id'], ['licenses.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index('genome_alias_index', 'bed', ['genome_alias'], unique=False, postgresql_with={'deduplicate_items': 'true'})
+    op.create_index(op.f('ix_bed_id'), 'bed', ['id'], unique=False)
+    op.create_index(op.f('ix_bed_license_id'), 'bed', ['license_id'], unique=False)
+    op.create_index('ix_bed_not_file_indexed', 'bed', ['id'], unique=False, postgresql_where=sa.text('file_indexed = false'))
+    op.create_index('ix_bed_not_indexed', 'bed', ['id'], unique=False, postgresql_where=sa.text('indexed = false'))
+    op.create_index('ix_bed_submission_date', 'bed', [sa.literal_column('submission_date DESC'), sa.literal_column('id')], unique=False)
+    op.create_index('ix_bed_unprocessed', 'bed', ['id'], unique=False, postgresql_where=sa.text('processed = false'))
+    op.create_table('geo_gsm_status',
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('gse_status_id', sa.Integer(), nullable=False),
+    sa.Column('gsm', sa.String(), nullable=False, comment='GSM number'),
+    sa.Column('sample_name', sa.String(), nullable=False),
+    sa.Column('status', sa.String(), nullable=False, comment='Status of the GEO sample'),
+    sa.Column('error', sa.String(), nullable=True, comment='Error message'),
+    sa.Column('source_submission_date', sa.TIMESTAMP(timezone=True), nullable=True, comment='Submission date of the source'),
+    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
+    sa.Column('bed_id', sa.String(), nullable=True, comment='Bed identifier'),
+    sa.Column('file_size', sa.BigInteger(), nullable=False, comment='Size of the file'),
+    sa.Column('genome', sa.String(), nullable=True, comment='Genome'),
+    sa.ForeignKeyConstraint(['gse_status_id'], ['geo_gse_status.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_geo_gsm_status_bed_id'), 'geo_gsm_status', ['bed_id'], unique=False)
+    op.create_index(op.f('ix_geo_gsm_status_gse_status_id'), 'geo_gsm_status', ['gse_status_id'], unique=False)
+    op.create_index(op.f('ix_geo_gsm_status_id'), 'geo_gsm_status', ['id'], unique=False)
+    op.create_table('usage_bedset_meta',
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('bedset_id', sa.String(), nullable=True),
+    sa.Column('count', sa.Integer(), nullable=False, comment='Number of visits'),
+    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
+    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
+    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_usage_bedset_meta_bedset_id'), 'usage_bedset_meta', ['bedset_id'], unique=False)
+    op.create_index(op.f('ix_usage_bedset_meta_id'), 'usage_bedset_meta', ['id'], unique=False)
+    op.create_table('bed_metadata',
+    sa.Column('species_name', sa.String(), nullable=False, comment='Organism name'),
+    sa.Column('species_id', sa.String(), nullable=True, comment='Organism taxon id'),
+    sa.Column('genotype', sa.String(), nullable=True, comment='Genotype of the sample'),
+    sa.Column('phenotype', sa.String(), nullable=True, comment='Phenotype of the sample'),
+    sa.Column('cell_type', sa.String(), nullable=True, comment='Specific kind of cell with distinct characteristics found in an organism. e.g. Neurons, Hepatocytes, Adipocytes'),
+    sa.Column('cell_line', sa.String(), nullable=True, comment='Population of cells derived from a single cell and cultured in the lab for extended use, e.g. HeLa, HepG2, k562'),
+    sa.Column('tissue', sa.String(), nullable=True, comment='Tissue type'),
+    sa.Column('library_source', sa.String(), nullable=True, comment='Library source (e.g. genomic, transcriptomic)'),
+    sa.Column('assay', sa.String(), nullable=True, comment='Experimental protocol (e.g. ChIP-seq)'),
+    sa.Column('antibody', sa.String(), nullable=True, comment='Antibody used in the assay'),
+    sa.Column('target', sa.String(), nullable=True, comment='Target of the assay (e.g. H3K4me3)'),
+    sa.Column('treatment', sa.String(), nullable=True, comment='Treatment of the sample (e.g. drug treatment)'),
+    sa.Column('original_file_name', sa.String(), nullable=True, comment='Original file name'),
+    sa.Column('global_sample_id', postgresql.ARRAY(sa.String()), nullable=True, comment='Global sample identifier. e.g. GSM000'),
+    sa.Column('global_experiment_id', postgresql.ARRAY(sa.String()), nullable=True, comment='Global experiment identifier. e.g. GSE000'),
+    sa.Column('id', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['id'], ['bed.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_bed_metadata_id'), 'bed_metadata', ['id'], unique=False)
+    op.create_table('bed_stats',
+    sa.Column('id', sa.String(), nullable=False),
+    sa.Column('number_of_regions', sa.Float(), nullable=True),
+    sa.Column('gc_content', sa.Float(), nullable=True),
+    sa.Column('median_tss_dist', sa.Float(), nullable=True),
+    sa.Column('mean_region_width', sa.Float(), nullable=True),
+    sa.Column('exon_frequency', sa.Float(), nullable=True),
+    sa.Column('intron_frequency', sa.Float(), nullable=True),
+    sa.Column('promoterprox_frequency', sa.Float(), nullable=True),
+    sa.Column('intergenic_frequency', sa.Float(), nullable=True),
+    sa.Column('promotercore_frequency', sa.Float(), nullable=True),
+    sa.Column('fiveutr_frequency', sa.Float(), nullable=True),
+    sa.Column('threeutr_frequency', sa.Float(), nullable=True),
+    sa.Column('fiveutr_percentage', sa.Float(), nullable=True),
+    sa.Column('threeutr_percentage', sa.Float(), nullable=True),
+    sa.Column('promoterprox_percentage', sa.Float(), nullable=True),
+    sa.Column('exon_percentage', sa.Float(), nullable=True),
+    sa.Column('intron_percentage', sa.Float(), nullable=True),
+    sa.Column('intergenic_percentage', sa.Float(), nullable=True),
+    sa.Column('promotercore_percentage', sa.Float(), nullable=True),
+    sa.Column('tssdist', sa.Float(), nullable=True),
+    sa.ForeignKeyConstraint(['id'], ['bed.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_bed_stats_id'), 'bed_stats', ['id'], unique=False)
+    op.create_index('ix_bed_stats_missing_regions', 'bed_stats', ['id'], unique=False, postgresql_where=sa.text('number_of_regions IS NULL'))
+    op.create_table('bedfile_bedset_relation',
+    sa.Column('bedset_id', sa.String(), nullable=False),
+    sa.Column('bedfile_id', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['bedfile_id'], ['bed.id'], ondelete='CASCADE'),
+    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('bedset_id', 'bedfile_id')
+    )
+    op.create_index(op.f('ix_bedfile_bedset_relation_bedfile_id'), 'bedfile_bedset_relation', ['bedfile_id'], unique=False)
+    op.create_table('files',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False, comment='Name of the file, e.g. bed, bigBed'),
+    sa.Column('file_digest', sa.String(), nullable=True, comment='Digest of the file. Mainly used for bed file.'),
+    sa.Column('title', sa.String(), nullable=True),
+    sa.Column('type', sa.String(), nullable=False, comment='Type of the object, e.g. file, plot, ...'),
+    sa.Column('path', sa.String(), nullable=False),
+    sa.Column('path_thumbnail', sa.String(), nullable=True, comment='Thumbnail path of the file'),
+    sa.Column('description', sa.String(), nullable=True),
+    sa.Column('size', sa.Integer(), nullable=True, comment='Size of the file'),
+    sa.Column('bedfile_id', sa.String(), nullable=True),
+    sa.Column('bedset_id', sa.String(), nullable=True),
+    sa.ForeignKeyConstraint(['bedfile_id'], ['bed.id'], ondelete='CASCADE'),
+    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name', 'bedfile_id'),
+    sa.UniqueConstraint('name', 'bedset_id')
+    )
+    op.create_index(op.f('ix_files_bedfile_id'), 'files', ['bedfile_id'], unique=False)
+    op.create_index(op.f('ix_files_bedset_id'), 'files', ['bedset_id'], unique=False)
+    op.create_index(op.f('ix_files_id'), 'files', ['id'], unique=False)
+    op.create_table('genome_ref_stats',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('bed_id', sa.String(), nullable=False),
+    sa.Column('provided_genome', sa.String(), nullable=False),
+    sa.Column('compared_genome', sa.String(), nullable=False, comment='Compared Genome'),
+    sa.Column('genome_digest', sa.String(), nullable=False),
+    sa.Column('xs', sa.Float(), nullable=True),
+    sa.Column('oobr', sa.Float(), nullable=True),
+    sa.Column('sequence_fit', sa.Float(), nullable=True),
+    sa.Column('assigned_points', sa.Integer(), nullable=False),
+    sa.Column('tier_ranking', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['bed_id'], ['bed.id'], ondelete='CASCADE'),
+    sa.ForeignKeyConstraint(['genome_digest'], ['reference_genomes.digest'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('bed_id', 'compared_genome')
+    )
+    op.create_index(op.f('ix_genome_ref_stats_bed_id'), 'genome_ref_stats', ['bed_id'], unique=False)
+    op.create_index(op.f('ix_genome_ref_stats_id'), 'genome_ref_stats', ['id'], unique=False)
+    op.create_table('universes',
+    sa.Column('id', sa.String(), nullable=False),
+    sa.Column('method', sa.String(), nullable=True, comment='Method used to create the universe'),
+    sa.Column('bedset_id', sa.String(), nullable=True),
+    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
+    sa.ForeignKeyConstraint(['id'], ['bed.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_universes_bedset_id'), 'universes', ['bedset_id'], unique=False)
+    op.create_index(op.f('ix_universes_id'), 'universes', ['id'], unique=False)
+    op.create_table('usage_bed_meta',
+    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
+    sa.Column('bed_id', sa.String(), nullable=True),
+    sa.Column('count', sa.Integer(), nullable=False, comment='Number of visits'),
+    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
+    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
+    sa.ForeignKeyConstraint(['bed_id'], ['bed.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_usage_bed_meta_bed_id'), 'usage_bed_meta', ['bed_id'], unique=False)
+    op.create_index(op.f('ix_usage_bed_meta_id'), 'usage_bed_meta', ['id'], unique=False)
+    op.create_table('tokenized_bed',
+    sa.Column('bed_id', sa.String(), nullable=False),
+    sa.Column('universe_id', sa.String(), nullable=False),
+    sa.Column('path', sa.String(), nullable=False, comment='Path to the tokenized bed file'),
+    sa.ForeignKeyConstraint(['bed_id'], ['bed.id'], ondelete='CASCADE'),
+    sa.ForeignKeyConstraint(['universe_id'], ['universes.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('bed_id', 'universe_id')
+    )
+    op.create_index(op.f('ix_tokenized_bed_bed_id'), 'tokenized_bed', ['bed_id'], unique=False)
+    op.create_index(op.f('ix_tokenized_bed_universe_id'), 'tokenized_bed', ['universe_id'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    """Downgrade schema."""
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_tokenized_bed_universe_id'), table_name='tokenized_bed')
+    op.drop_index(op.f('ix_tokenized_bed_bed_id'), table_name='tokenized_bed')
+    op.drop_table('tokenized_bed')
+    op.drop_index(op.f('ix_usage_bed_meta_id'), table_name='usage_bed_meta')
+    op.drop_index(op.f('ix_usage_bed_meta_bed_id'), table_name='usage_bed_meta')
+    op.drop_table('usage_bed_meta')
+    op.drop_index(op.f('ix_universes_id'), table_name='universes')
+    op.drop_index(op.f('ix_universes_bedset_id'), table_name='universes')
+    op.drop_table('universes')
+    op.drop_index(op.f('ix_genome_ref_stats_id'), table_name='genome_ref_stats')
+    op.drop_index(op.f('ix_genome_ref_stats_bed_id'), table_name='genome_ref_stats')
+    op.drop_table('genome_ref_stats')
+    op.drop_index(op.f('ix_files_id'), table_name='files')
+    op.drop_index(op.f('ix_files_bedset_id'), table_name='files')
+    op.drop_index(op.f('ix_files_bedfile_id'), table_name='files')
+    op.drop_table('files')
+    op.drop_index(op.f('ix_bedfile_bedset_relation_bedfile_id'), table_name='bedfile_bedset_relation')
+    op.drop_table('bedfile_bedset_relation')
+    op.drop_index('ix_bed_stats_missing_regions', table_name='bed_stats', postgresql_where=sa.text('number_of_regions IS NULL'))
+    op.drop_index(op.f('ix_bed_stats_id'), table_name='bed_stats')
+    op.drop_table('bed_stats')
+    op.drop_index(op.f('ix_bed_metadata_id'), table_name='bed_metadata')
+    op.drop_table('bed_metadata')
+    op.drop_index(op.f('ix_usage_bedset_meta_id'), table_name='usage_bedset_meta')
+    op.drop_index(op.f('ix_usage_bedset_meta_bedset_id'), table_name='usage_bedset_meta')
+    op.drop_table('usage_bedset_meta')
+    op.drop_index(op.f('ix_geo_gsm_status_id'), table_name='geo_gsm_status')
+    op.drop_index(op.f('ix_geo_gsm_status_gse_status_id'), table_name='geo_gsm_status')
+    op.drop_index(op.f('ix_geo_gsm_status_bed_id'), table_name='geo_gsm_status')
+    op.drop_table('geo_gsm_status')
+    op.drop_index('ix_bed_unprocessed', table_name='bed', postgresql_where=sa.text('processed = false'))
+    op.drop_index('ix_bed_submission_date', table_name='bed')
+    op.drop_index('ix_bed_not_indexed', table_name='bed', postgresql_where=sa.text('indexed = false'))
+    op.drop_index('ix_bed_not_file_indexed', table_name='bed', postgresql_where=sa.text('file_indexed = false'))
+    op.drop_index(op.f('ix_bed_license_id'), table_name='bed')
+    op.drop_index(op.f('ix_bed_id'), table_name='bed')
+    op.drop_index('genome_alias_index', table_name='bed', postgresql_with={'deduplicate_items': 'true'})
+    op.drop_table('bed')
+    op.drop_index(op.f('ix_usage_search_id'), table_name='usage_search')
+    op.drop_table('usage_search')
+    op.drop_index(op.f('ix_usage_files_id'), table_name='usage_files')
+    op.drop_table('usage_files')
+    op.drop_index(op.f('ix_reference_genomes_digest'), table_name='reference_genomes')
+    op.drop_table('reference_genomes')
+    op.drop_index(op.f('ix_licenses_id'), table_name='licenses')
+    op.drop_table('licenses')
+    op.drop_index(op.f('ix_geo_gse_status_id'), table_name='geo_gse_status')
+    op.drop_table('geo_gse_status')
+    op.drop_index('ix_bedsets_unprocessed', table_name='bedsets', postgresql_where=sa.text('processed = false'))
+    op.drop_index('ix_bedsets_name_trgm', table_name='bedsets', postgresql_using='gin', postgresql_ops={'name': 'gin_trgm_ops'})
+    op.drop_index(op.f('ix_bedsets_id'), table_name='bedsets')
+    op.drop_index('ix_bedsets_description_trgm', table_name='bedsets', postgresql_using='gin', postgresql_ops={'description': 'gin_trgm_ops'})
+    op.drop_table('bedsets')
+    op.drop_index(op.f('ix_bed_snapshots_id'), table_name='bed_snapshots')
+    op.drop_table('bed_snapshots')
+    # ### end Alembic commands ###
diff --git a/bbconf/alembic/versions/__init__.py b/bbconf/alembic/versions/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/bbconf/bbagent.py b/bbconf/bbagent.py
index 41acaf4e..1cbcfcb8 100644
--- a/bbconf/bbagent.py
+++ b/bbconf/bbagent.py
@@ -50,6 +50,7 @@ def __init__(
         self,
         config: Path | str,
         init_ml: bool = True,
+        migrate_db: bool = False,
     ):
         """
         Initialize connection to the pep_db database. You can use the basic connection parameters
diff --git a/bbconf/config_parser/bedbaseconfig.py b/bbconf/config_parser/bedbaseconfig.py
index ef9db9e6..9c5c5562 100644
--- a/bbconf/config_parser/bedbaseconfig.py
+++ b/bbconf/config_parser/bedbaseconfig.py
@@ -227,6 +227,7 @@ def _init_db_engine(self) -> BaseEngine:
             user=self._config.database.user,
             password=self._config.database.password,
             drivername=f"{self._config.database.dialect}+{self._config.database.driver}",
+            run_migrations=self._config.database.run_migrations,
         )
 
     def _init_qdrant_client(self) -> QdrantClient:
diff --git a/bbconf/config_parser/models.py b/bbconf/config_parser/models.py
index 8f1d37ec..002c9536 100644
--- a/bbconf/config_parser/models.py
+++ b/bbconf/config_parser/models.py
@@ -35,6 +35,7 @@ class ConfigDB(BaseModel):
     database: str = DEFAULT_DB_NAME
     dialect: str = DEFAULT_DB_DIALECT
     driver: str | None = DEFAULT_DB_DRIVER
+    run_migrations: bool = False
 
     model_config = ConfigDict(extra="forbid")
 
diff --git a/bbconf/db_utils.py b/bbconf/db_utils.py
index 816115a8..7e3d21e1 100644
--- a/bbconf/db_utils.py
+++ b/bbconf/db_utils.py
@@ -1,8 +1,11 @@
 import datetime
 import logging
+import os
 from typing import Optional
 
 import pandas as pd
+from alembic import command
+from alembic.config import Config
 from sqlalchemy import (
     DDL,
     TIMESTAMP,
@@ -723,6 +726,7 @@ def __init__(
         drivername: str = POSTGRES_DIALECT,
         dsn: str | None = None,
         echo: bool = False,
+        run_migrations: bool = False,
     ):
         """
         Initialize connection to the bedbase database. You can use the basic connection parameters
@@ -737,6 +741,9 @@ def __init__(
             drivername: Driver used in connection.
             dsn: Libpq connection string using the dsn parameter
                 (e.g. 'postgresql://user_name:password@host_name:port/db_name').
+            run_migrations: Upgrade the database to the latest Alembic revision
+                (``head``) before connecting. Safe on an already-migrated or
+                pre-existing database (the initial revision is idempotent).
         """
         if not dsn:
             dsn = URL.create(
@@ -748,6 +755,13 @@ def __init__(
                 drivername=drivername,
             )
 
+        if run_migrations:
+            if isinstance(dsn, str):
+                migration_url = dsn
+            else:
+                migration_url = dsn.render_as_string(hide_password=False)
+            self.run_db_migration(migration_url)
+
         self._engine = create_engine(dsn, echo=echo)
         self.create_schema(self._engine)
         self.check_db_connection()
@@ -789,6 +803,25 @@ def delete_schema(self, engine=None) -> None:
         Base.metadata.drop_all(engine)
         return None
 
+    def run_db_migration(self, database_url: str) -> None:
+        """
+        Upgrade the database to the latest Alembic revision (``head``).
+
+        The Alembic config is built programmatically so the package does not
+        depend on the repo-root ``alembic.ini`` at runtime.
+
+        Args:
+            database_url: SQLAlchemy connection URL (with password) to migrate.
+        """
+        script_location = os.path.join(os.path.dirname(__file__), "alembic")
+
+        alembic_cfg = Config()
+        alembic_cfg.set_main_option("script_location", script_location)
+        alembic_cfg.set_main_option("sqlalchemy.url", database_url)
+
+        _LOGGER.info("Running database migrations to the latest revision...")
+        command.upgrade(alembic_cfg, "head")
+
     def session_execute(self, statement: Select) -> Result:
         """
         Execute statement using sqlalchemy statement.
diff --git a/pyproject.toml b/pyproject.toml
index ac1e4685..0ff9c045 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,6 +38,7 @@ dependencies = [
     "qdrant_client >= 1.16.1",
     "setuptools < 70.0.0",
     "cachetools >= 4.2.4",
+    "alembic >= 1.19.1",
 ]
 
 [project.urls]
@@ -75,3 +76,6 @@ exclude = ["manual_testing.py"]
 
 [tool.ruff.lint.isort]
 known-first-party = ["bbconf"]
+
+[tool.ruff.lint.per-file-ignores]
+"bbconf/alembic/env.py" = ["E402"]

From 340d56afe1c4c912a1ff166865fc0aa96a9c45c1 Mon Sep 17 00:00:00 2001
From: khoroshevskyi <sasha99250@gmail.com>
Date: Fri, 14 Aug 2026 23:33:33 -0400
Subject: [PATCH 2/6] deleted unused arguemnt

---
 bbconf/bbagent.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bbconf/bbagent.py b/bbconf/bbagent.py
index 1cbcfcb8..41acaf4e 100644
--- a/bbconf/bbagent.py
+++ b/bbconf/bbagent.py
@@ -50,7 +50,6 @@ def __init__(
         self,
         config: Path | str,
         init_ml: bool = True,
-        migrate_db: bool = False,
     ):
         """
         Initialize connection to the pep_db database. You can use the basic connection parameters

From 37d87f52ebab0f96c5c4c64165656c81e31f4bd9 Mon Sep 17 00:00:00 2001
From: khoroshevskyi <sasha99250@gmail.com>
Date: Sat, 15 Aug 2026 00:25:49 -0400
Subject: [PATCH 3/6] Small tweaks

---
 .github/pull_request_template.md | 2 +-
 README.md                        | 3 +++
 alembic.ini                      | 2 ++
 3 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 163df722..fdc90a74 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -3,6 +3,6 @@
 
 
 ## TODO:
-- [ ] ❗ If this PR includes a new database schema migration, following steps are completed: [Database Version Migration](https://pep.databio.org/pephub/developer/pepdbagent/database_version_migration/)
+- [ ] ❗ If this PR includes a new database schema migration, following steps are completed: (README)[README.md]
 - [ ] Version of pepdbagent updated in `__version__.py` file
 - [ ] Changelog updated
\ No newline at end of file
diff --git a/README.md b/README.md
index 6caff043..6211ac19 100644
--- a/README.md
+++ b/README.md
@@ -66,6 +66,9 @@ root) is used for local CLI work. The first (baseline) revision is
 builds, including the `pg_trgm` extension and the trigram / partial / expression
 indexes.
 
+To update schema for desirable database, use different database url in `alembic.ini`, 
+otherwise run test database
+
 ### Creating a new revision
 
 After changing the models in `bbconf/db_utils.py`:
diff --git a/alembic.ini b/alembic.ini
index 625b44aa..5f4c58b6 100644
--- a/alembic.ini
+++ b/alembic.ini
@@ -70,6 +70,8 @@ version_path_separator = os
 
 # Local development connection string. Override with `-x` or edit as needed.
 # Runtime migrations use the URL built from the bbconf config instead.
+
+### !!!! Change this code to desirable database!!!!
 sqlalchemy.url = postgresql+psycopg://postgres:docker@localhost:5432/bedbase
 
 

From c3fd35f54b211c1213d01cec82ab7b6ca2138a29 Mon Sep 17 00:00:00 2001
From: khoroshevskyi <sasha99250@gmail.com>
Date: Sat, 15 Aug 2026 23:31:53 -0400
Subject: [PATCH 4/6] Linting and test fix

---
 .../8b0b706d0827_initial_migration.py         | 1028 ++++++++++++-----
 bbconf/bbagent.py                             |   38 +-
 bbconf/models/base_models.py                  |    2 +-
 bbconf/modules/snapshots.py                   |    8 +-
 4 files changed, 742 insertions(+), 334 deletions(-)

diff --git a/bbconf/alembic/versions/8b0b706d0827_initial_migration.py b/bbconf/alembic/versions/8b0b706d0827_initial_migration.py
index f8fae368..24f76169 100644
--- a/bbconf/alembic/versions/8b0b706d0827_initial_migration.py
+++ b/bbconf/alembic/versions/8b0b706d0827_initial_migration.py
@@ -1,10 +1,11 @@
 """Initial migration
 
 Revision ID: 8b0b706d0827
-Revises: 
+Revises:
 Create Date: 2026-08-14 23:09:22.903899
 
 """
+
 from typing import Sequence, Union
 
 import sqlalchemy as sa
@@ -12,7 +13,7 @@
 from sqlalchemy.dialects import postgresql
 
 # revision identifiers, used by Alembic.
-revision: str = '8b0b706d0827'
+revision: str = "8b0b706d0827"
 down_revision: Union[str, None] = None
 branch_labels: Union[str, Sequence[str], None] = None
 depends_on: Union[str, Sequence[str], None] = None
@@ -26,327 +27,716 @@ def upgrade() -> None:
     # DDL event on the bedsets table; autogenerate does not emit it, so it is
     # added here by hand. Must run before those indexes are created.
     op.execute("CREATE EXTENSION IF NOT EXISTS pg_trgm")
-    op.create_table('bed_snapshots',
-    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
-    sa.Column('file_path', sa.String(), nullable=False, comment='S3 object key, relative to the bucket root'),
-    sa.Column('file_type', sa.String(), nullable=False, comment='metadata | bedsets | bedset_membership | manifest'),
-    sa.Column('creation_date', sa.TIMESTAMP(timezone=True), nullable=False, comment='Build date of the export'),
-    sa.Column('record_count', sa.Integer(), nullable=True, comment='Rows actually written to the file'),
-    sa.Column('file_size', sa.Integer(), nullable=True, comment='Size of the file in bytes'),
-    sa.Column('checksum', sa.String(), nullable=True, comment='SHA256 of the file'),
-    sa.Column('schema_version', sa.Integer(), nullable=True, comment='Export schema version'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_bed_snapshots_id'), 'bed_snapshots', ['id'], unique=False)
-    op.create_table('bedsets',
-    sa.Column('id', sa.String(), nullable=False),
-    sa.Column('name', sa.String(), nullable=False, comment='Name of the bedset'),
-    sa.Column('description', sa.String(), nullable=True, comment='Description of the bedset'),
-    sa.Column('summary', sa.String(), nullable=True, comment='Summary of the bedset'),
-    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
-    sa.Column('last_update_date', sa.TIMESTAMP(timezone=True), nullable=True),
-    sa.Column('md5sum', sa.String(), nullable=True, comment='MD5 sum of the bedset'),
-    sa.Column('bedset_means', postgresql.JSON(astext_type=sa.Text()), nullable=True, comment='Mean values of the bedset'),
-    sa.Column('bedset_standard_deviation', postgresql.JSON(astext_type=sa.Text()), nullable=True, comment='Median values of the bedset'),
-    sa.Column('bedfile_count', sa.Integer(), nullable=False, comment='Number of bedfiles in the bedset (denormalized count)'),
-    sa.Column('author', sa.String(), nullable=True, comment='Author of the bedset'),
-    sa.Column('source', sa.String(), nullable=True, comment='Source of the bedset'),
-    sa.Column('processed', sa.Boolean(), nullable=False, comment='Whether the bedset was processed'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index('ix_bedsets_description_trgm', 'bedsets', ['description'], unique=False, postgresql_using='gin', postgresql_ops={'description': 'gin_trgm_ops'})
-    op.create_index(op.f('ix_bedsets_id'), 'bedsets', ['id'], unique=False)
-    op.create_index('ix_bedsets_name_trgm', 'bedsets', ['name'], unique=False, postgresql_using='gin', postgresql_ops={'name': 'gin_trgm_ops'})
-    op.create_index('ix_bedsets_unprocessed', 'bedsets', ['id'], unique=False, postgresql_where=sa.text('processed = false'))
-    op.create_table('geo_gse_status',
-    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
-    sa.Column('gse', sa.String(), nullable=False, comment='GSE number'),
-    sa.Column('status', sa.String(), nullable=False, comment='Status of the GEO project'),
-    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
-    sa.Column('number_of_files', sa.Integer(), nullable=False, comment='Number of files'),
-    sa.Column('number_of_success', sa.Integer(), nullable=False, comment='Number of success'),
-    sa.Column('number_of_skips', sa.Integer(), nullable=False, comment='Number of skips'),
-    sa.Column('number_of_fails', sa.Integer(), nullable=False, comment='Number of fails'),
-    sa.Column('error', sa.String(), nullable=True, comment='Error message'),
-    sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('gse')
-    )
-    op.create_index(op.f('ix_geo_gse_status_id'), 'geo_gse_status', ['id'], unique=False)
-    op.create_table('licenses',
-    sa.Column('id', sa.String(), nullable=False),
-    sa.Column('shorthand', sa.String(), nullable=True, comment='License shorthand'),
-    sa.Column('label', sa.String(), nullable=False, comment='License label'),
-    sa.Column('description', sa.String(), nullable=False, comment='License description'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_licenses_id'), 'licenses', ['id'], unique=False)
-    op.create_table('reference_genomes',
-    sa.Column('digest', sa.String(), nullable=False),
-    sa.Column('alias', sa.String(), nullable=False, comment='Name of the reference genome'),
-    sa.PrimaryKeyConstraint('digest')
-    )
-    op.create_index(op.f('ix_reference_genomes_digest'), 'reference_genomes', ['digest'], unique=False)
-    op.create_table('usage_files',
-    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
-    sa.Column('file_path', sa.String(), nullable=False, comment='Path to the file'),
-    sa.Column('count', sa.Integer(), nullable=False, comment='Number of downloads'),
-    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
-    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_usage_files_id'), 'usage_files', ['id'], unique=False)
-    op.create_table('usage_search',
-    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
-    sa.Column('query', sa.String(), nullable=False, comment='Search query'),
-    sa.Column('type', sa.String(), nullable=False, comment='Type of the search. Bed/Bedset'),
-    sa.Column('count', sa.Integer(), nullable=False, comment='Number of searches'),
-    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
-    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_usage_search_id'), 'usage_search', ['id'], unique=False)
-    op.create_table('bed',
-    sa.Column('id', sa.String(), nullable=False),
-    sa.Column('name', sa.String(), nullable=True),
-    sa.Column('genome_alias', sa.String(), nullable=True),
-    sa.Column('genome_digest', sa.String(), nullable=True),
-    sa.Column('description', sa.String(), nullable=True),
-    sa.Column('bed_compliance', sa.String(), nullable=False),
-    sa.Column('data_format', sa.String(), nullable=False),
-    sa.Column('compliant_columns', sa.Integer(), nullable=False),
-    sa.Column('non_compliant_columns', sa.Integer(), nullable=False),
-    sa.Column('header', sa.String(), nullable=True, comment='Header of the bed file, it if was provided.'),
-    sa.Column('indexed', sa.Boolean(), nullable=False, comment='Whether sample was added to qdrant'),
-    sa.Column('file_indexed', sa.Boolean(), nullable=False, comment='Whether file was tokenized and added to the vector database'),
-    sa.Column('pephub', sa.Boolean(), nullable=False, comment='Whether sample was added to pephub'),
-    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
-    sa.Column('last_update_date', sa.TIMESTAMP(timezone=True), nullable=True),
-    sa.Column('is_universe', sa.Boolean(), nullable=True),
-    sa.Column('license_id', sa.String(), nullable=True),
-    sa.Column('processed', sa.Boolean(), nullable=False, comment='Whether the bed file was processed'),
-    sa.ForeignKeyConstraint(['license_id'], ['licenses.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index('genome_alias_index', 'bed', ['genome_alias'], unique=False, postgresql_with={'deduplicate_items': 'true'})
-    op.create_index(op.f('ix_bed_id'), 'bed', ['id'], unique=False)
-    op.create_index(op.f('ix_bed_license_id'), 'bed', ['license_id'], unique=False)
-    op.create_index('ix_bed_not_file_indexed', 'bed', ['id'], unique=False, postgresql_where=sa.text('file_indexed = false'))
-    op.create_index('ix_bed_not_indexed', 'bed', ['id'], unique=False, postgresql_where=sa.text('indexed = false'))
-    op.create_index('ix_bed_submission_date', 'bed', [sa.literal_column('submission_date DESC'), sa.literal_column('id')], unique=False)
-    op.create_index('ix_bed_unprocessed', 'bed', ['id'], unique=False, postgresql_where=sa.text('processed = false'))
-    op.create_table('geo_gsm_status',
-    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
-    sa.Column('gse_status_id', sa.Integer(), nullable=False),
-    sa.Column('gsm', sa.String(), nullable=False, comment='GSM number'),
-    sa.Column('sample_name', sa.String(), nullable=False),
-    sa.Column('status', sa.String(), nullable=False, comment='Status of the GEO sample'),
-    sa.Column('error', sa.String(), nullable=True, comment='Error message'),
-    sa.Column('source_submission_date', sa.TIMESTAMP(timezone=True), nullable=True, comment='Submission date of the source'),
-    sa.Column('submission_date', sa.TIMESTAMP(timezone=True), nullable=False),
-    sa.Column('bed_id', sa.String(), nullable=True, comment='Bed identifier'),
-    sa.Column('file_size', sa.BigInteger(), nullable=False, comment='Size of the file'),
-    sa.Column('genome', sa.String(), nullable=True, comment='Genome'),
-    sa.ForeignKeyConstraint(['gse_status_id'], ['geo_gse_status.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_geo_gsm_status_bed_id'), 'geo_gsm_status', ['bed_id'], unique=False)
-    op.create_index(op.f('ix_geo_gsm_status_gse_status_id'), 'geo_gsm_status', ['gse_status_id'], unique=False)
-    op.create_index(op.f('ix_geo_gsm_status_id'), 'geo_gsm_status', ['id'], unique=False)
-    op.create_table('usage_bedset_meta',
-    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
-    sa.Column('bedset_id', sa.String(), nullable=True),
-    sa.Column('count', sa.Integer(), nullable=False, comment='Number of visits'),
-    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
-    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
-    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_usage_bedset_meta_bedset_id'), 'usage_bedset_meta', ['bedset_id'], unique=False)
-    op.create_index(op.f('ix_usage_bedset_meta_id'), 'usage_bedset_meta', ['id'], unique=False)
-    op.create_table('bed_metadata',
-    sa.Column('species_name', sa.String(), nullable=False, comment='Organism name'),
-    sa.Column('species_id', sa.String(), nullable=True, comment='Organism taxon id'),
-    sa.Column('genotype', sa.String(), nullable=True, comment='Genotype of the sample'),
-    sa.Column('phenotype', sa.String(), nullable=True, comment='Phenotype of the sample'),
-    sa.Column('cell_type', sa.String(), nullable=True, comment='Specific kind of cell with distinct characteristics found in an organism. e.g. Neurons, Hepatocytes, Adipocytes'),
-    sa.Column('cell_line', sa.String(), nullable=True, comment='Population of cells derived from a single cell and cultured in the lab for extended use, e.g. HeLa, HepG2, k562'),
-    sa.Column('tissue', sa.String(), nullable=True, comment='Tissue type'),
-    sa.Column('library_source', sa.String(), nullable=True, comment='Library source (e.g. genomic, transcriptomic)'),
-    sa.Column('assay', sa.String(), nullable=True, comment='Experimental protocol (e.g. ChIP-seq)'),
-    sa.Column('antibody', sa.String(), nullable=True, comment='Antibody used in the assay'),
-    sa.Column('target', sa.String(), nullable=True, comment='Target of the assay (e.g. H3K4me3)'),
-    sa.Column('treatment', sa.String(), nullable=True, comment='Treatment of the sample (e.g. drug treatment)'),
-    sa.Column('original_file_name', sa.String(), nullable=True, comment='Original file name'),
-    sa.Column('global_sample_id', postgresql.ARRAY(sa.String()), nullable=True, comment='Global sample identifier. e.g. GSM000'),
-    sa.Column('global_experiment_id', postgresql.ARRAY(sa.String()), nullable=True, comment='Global experiment identifier. e.g. GSE000'),
-    sa.Column('id', sa.String(), nullable=False),
-    sa.ForeignKeyConstraint(['id'], ['bed.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_bed_metadata_id'), 'bed_metadata', ['id'], unique=False)
-    op.create_table('bed_stats',
-    sa.Column('id', sa.String(), nullable=False),
-    sa.Column('number_of_regions', sa.Float(), nullable=True),
-    sa.Column('gc_content', sa.Float(), nullable=True),
-    sa.Column('median_tss_dist', sa.Float(), nullable=True),
-    sa.Column('mean_region_width', sa.Float(), nullable=True),
-    sa.Column('exon_frequency', sa.Float(), nullable=True),
-    sa.Column('intron_frequency', sa.Float(), nullable=True),
-    sa.Column('promoterprox_frequency', sa.Float(), nullable=True),
-    sa.Column('intergenic_frequency', sa.Float(), nullable=True),
-    sa.Column('promotercore_frequency', sa.Float(), nullable=True),
-    sa.Column('fiveutr_frequency', sa.Float(), nullable=True),
-    sa.Column('threeutr_frequency', sa.Float(), nullable=True),
-    sa.Column('fiveutr_percentage', sa.Float(), nullable=True),
-    sa.Column('threeutr_percentage', sa.Float(), nullable=True),
-    sa.Column('promoterprox_percentage', sa.Float(), nullable=True),
-    sa.Column('exon_percentage', sa.Float(), nullable=True),
-    sa.Column('intron_percentage', sa.Float(), nullable=True),
-    sa.Column('intergenic_percentage', sa.Float(), nullable=True),
-    sa.Column('promotercore_percentage', sa.Float(), nullable=True),
-    sa.Column('tssdist', sa.Float(), nullable=True),
-    sa.ForeignKeyConstraint(['id'], ['bed.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_bed_stats_id'), 'bed_stats', ['id'], unique=False)
-    op.create_index('ix_bed_stats_missing_regions', 'bed_stats', ['id'], unique=False, postgresql_where=sa.text('number_of_regions IS NULL'))
-    op.create_table('bedfile_bedset_relation',
-    sa.Column('bedset_id', sa.String(), nullable=False),
-    sa.Column('bedfile_id', sa.String(), nullable=False),
-    sa.ForeignKeyConstraint(['bedfile_id'], ['bed.id'], ondelete='CASCADE'),
-    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('bedset_id', 'bedfile_id')
-    )
-    op.create_index(op.f('ix_bedfile_bedset_relation_bedfile_id'), 'bedfile_bedset_relation', ['bedfile_id'], unique=False)
-    op.create_table('files',
-    sa.Column('id', sa.Integer(), nullable=False),
-    sa.Column('name', sa.String(), nullable=False, comment='Name of the file, e.g. bed, bigBed'),
-    sa.Column('file_digest', sa.String(), nullable=True, comment='Digest of the file. Mainly used for bed file.'),
-    sa.Column('title', sa.String(), nullable=True),
-    sa.Column('type', sa.String(), nullable=False, comment='Type of the object, e.g. file, plot, ...'),
-    sa.Column('path', sa.String(), nullable=False),
-    sa.Column('path_thumbnail', sa.String(), nullable=True, comment='Thumbnail path of the file'),
-    sa.Column('description', sa.String(), nullable=True),
-    sa.Column('size', sa.Integer(), nullable=True, comment='Size of the file'),
-    sa.Column('bedfile_id', sa.String(), nullable=True),
-    sa.Column('bedset_id', sa.String(), nullable=True),
-    sa.ForeignKeyConstraint(['bedfile_id'], ['bed.id'], ondelete='CASCADE'),
-    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('name', 'bedfile_id'),
-    sa.UniqueConstraint('name', 'bedset_id')
-    )
-    op.create_index(op.f('ix_files_bedfile_id'), 'files', ['bedfile_id'], unique=False)
-    op.create_index(op.f('ix_files_bedset_id'), 'files', ['bedset_id'], unique=False)
-    op.create_index(op.f('ix_files_id'), 'files', ['id'], unique=False)
-    op.create_table('genome_ref_stats',
-    sa.Column('id', sa.Integer(), nullable=False),
-    sa.Column('bed_id', sa.String(), nullable=False),
-    sa.Column('provided_genome', sa.String(), nullable=False),
-    sa.Column('compared_genome', sa.String(), nullable=False, comment='Compared Genome'),
-    sa.Column('genome_digest', sa.String(), nullable=False),
-    sa.Column('xs', sa.Float(), nullable=True),
-    sa.Column('oobr', sa.Float(), nullable=True),
-    sa.Column('sequence_fit', sa.Float(), nullable=True),
-    sa.Column('assigned_points', sa.Integer(), nullable=False),
-    sa.Column('tier_ranking', sa.Integer(), nullable=False),
-    sa.ForeignKeyConstraint(['bed_id'], ['bed.id'], ondelete='CASCADE'),
-    sa.ForeignKeyConstraint(['genome_digest'], ['reference_genomes.digest'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('bed_id', 'compared_genome')
-    )
-    op.create_index(op.f('ix_genome_ref_stats_bed_id'), 'genome_ref_stats', ['bed_id'], unique=False)
-    op.create_index(op.f('ix_genome_ref_stats_id'), 'genome_ref_stats', ['id'], unique=False)
-    op.create_table('universes',
-    sa.Column('id', sa.String(), nullable=False),
-    sa.Column('method', sa.String(), nullable=True, comment='Method used to create the universe'),
-    sa.Column('bedset_id', sa.String(), nullable=True),
-    sa.ForeignKeyConstraint(['bedset_id'], ['bedsets.id'], ondelete='CASCADE'),
-    sa.ForeignKeyConstraint(['id'], ['bed.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_universes_bedset_id'), 'universes', ['bedset_id'], unique=False)
-    op.create_index(op.f('ix_universes_id'), 'universes', ['id'], unique=False)
-    op.create_table('usage_bed_meta',
-    sa.Column('id', sa.Integer(), autoincrement=True, nullable=False),
-    sa.Column('bed_id', sa.String(), nullable=True),
-    sa.Column('count', sa.Integer(), nullable=False, comment='Number of visits'),
-    sa.Column('date_from', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date from'),
-    sa.Column('date_to', sa.TIMESTAMP(timezone=True), nullable=False, comment='Date to'),
-    sa.ForeignKeyConstraint(['bed_id'], ['bed.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    op.create_index(op.f('ix_usage_bed_meta_bed_id'), 'usage_bed_meta', ['bed_id'], unique=False)
-    op.create_index(op.f('ix_usage_bed_meta_id'), 'usage_bed_meta', ['id'], unique=False)
-    op.create_table('tokenized_bed',
-    sa.Column('bed_id', sa.String(), nullable=False),
-    sa.Column('universe_id', sa.String(), nullable=False),
-    sa.Column('path', sa.String(), nullable=False, comment='Path to the tokenized bed file'),
-    sa.ForeignKeyConstraint(['bed_id'], ['bed.id'], ondelete='CASCADE'),
-    sa.ForeignKeyConstraint(['universe_id'], ['universes.id'], ondelete='CASCADE'),
-    sa.PrimaryKeyConstraint('bed_id', 'universe_id')
-    )
-    op.create_index(op.f('ix_tokenized_bed_bed_id'), 'tokenized_bed', ['bed_id'], unique=False)
-    op.create_index(op.f('ix_tokenized_bed_universe_id'), 'tokenized_bed', ['universe_id'], unique=False)
+    op.create_table(
+        "bed_snapshots",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column(
+            "file_path",
+            sa.String(),
+            nullable=False,
+            comment="S3 object key, relative to the bucket root",
+        ),
+        sa.Column(
+            "file_type",
+            sa.String(),
+            nullable=False,
+            comment="metadata | bedsets | bedset_membership | manifest",
+        ),
+        sa.Column(
+            "creation_date",
+            sa.TIMESTAMP(timezone=True),
+            nullable=False,
+            comment="Build date of the export",
+        ),
+        sa.Column(
+            "record_count",
+            sa.Integer(),
+            nullable=True,
+            comment="Rows actually written to the file",
+        ),
+        sa.Column(
+            "file_size",
+            sa.Integer(),
+            nullable=True,
+            comment="Size of the file in bytes",
+        ),
+        sa.Column("checksum", sa.String(), nullable=True, comment="SHA256 of the file"),
+        sa.Column(
+            "schema_version",
+            sa.Integer(),
+            nullable=True,
+            comment="Export schema version",
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_bed_snapshots_id"), "bed_snapshots", ["id"], unique=False)
+    op.create_table(
+        "bedsets",
+        sa.Column("id", sa.String(), nullable=False),
+        sa.Column("name", sa.String(), nullable=False, comment="Name of the bedset"),
+        sa.Column(
+            "description",
+            sa.String(),
+            nullable=True,
+            comment="Description of the bedset",
+        ),
+        sa.Column(
+            "summary", sa.String(), nullable=True, comment="Summary of the bedset"
+        ),
+        sa.Column("submission_date", sa.TIMESTAMP(timezone=True), nullable=False),
+        sa.Column("last_update_date", sa.TIMESTAMP(timezone=True), nullable=True),
+        sa.Column(
+            "md5sum", sa.String(), nullable=True, comment="MD5 sum of the bedset"
+        ),
+        sa.Column(
+            "bedset_means",
+            postgresql.JSON(astext_type=sa.Text()),
+            nullable=True,
+            comment="Mean values of the bedset",
+        ),
+        sa.Column(
+            "bedset_standard_deviation",
+            postgresql.JSON(astext_type=sa.Text()),
+            nullable=True,
+            comment="Median values of the bedset",
+        ),
+        sa.Column(
+            "bedfile_count",
+            sa.Integer(),
+            nullable=False,
+            comment="Number of bedfiles in the bedset (denormalized count)",
+        ),
+        sa.Column("author", sa.String(), nullable=True, comment="Author of the bedset"),
+        sa.Column("source", sa.String(), nullable=True, comment="Source of the bedset"),
+        sa.Column(
+            "processed",
+            sa.Boolean(),
+            nullable=False,
+            comment="Whether the bedset was processed",
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        "ix_bedsets_description_trgm",
+        "bedsets",
+        ["description"],
+        unique=False,
+        postgresql_using="gin",
+        postgresql_ops={"description": "gin_trgm_ops"},
+    )
+    op.create_index(op.f("ix_bedsets_id"), "bedsets", ["id"], unique=False)
+    op.create_index(
+        "ix_bedsets_name_trgm",
+        "bedsets",
+        ["name"],
+        unique=False,
+        postgresql_using="gin",
+        postgresql_ops={"name": "gin_trgm_ops"},
+    )
+    op.create_index(
+        "ix_bedsets_unprocessed",
+        "bedsets",
+        ["id"],
+        unique=False,
+        postgresql_where=sa.text("processed = false"),
+    )
+    op.create_table(
+        "geo_gse_status",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column("gse", sa.String(), nullable=False, comment="GSE number"),
+        sa.Column(
+            "status", sa.String(), nullable=False, comment="Status of the GEO project"
+        ),
+        sa.Column("submission_date", sa.TIMESTAMP(timezone=True), nullable=False),
+        sa.Column(
+            "number_of_files", sa.Integer(), nullable=False, comment="Number of files"
+        ),
+        sa.Column(
+            "number_of_success",
+            sa.Integer(),
+            nullable=False,
+            comment="Number of success",
+        ),
+        sa.Column(
+            "number_of_skips", sa.Integer(), nullable=False, comment="Number of skips"
+        ),
+        sa.Column(
+            "number_of_fails", sa.Integer(), nullable=False, comment="Number of fails"
+        ),
+        sa.Column("error", sa.String(), nullable=True, comment="Error message"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("gse"),
+    )
+    op.create_index(
+        op.f("ix_geo_gse_status_id"), "geo_gse_status", ["id"], unique=False
+    )
+    op.create_table(
+        "licenses",
+        sa.Column("id", sa.String(), nullable=False),
+        sa.Column("shorthand", sa.String(), nullable=True, comment="License shorthand"),
+        sa.Column("label", sa.String(), nullable=False, comment="License label"),
+        sa.Column(
+            "description", sa.String(), nullable=False, comment="License description"
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_licenses_id"), "licenses", ["id"], unique=False)
+    op.create_table(
+        "reference_genomes",
+        sa.Column("digest", sa.String(), nullable=False),
+        sa.Column(
+            "alias", sa.String(), nullable=False, comment="Name of the reference genome"
+        ),
+        sa.PrimaryKeyConstraint("digest"),
+    )
+    op.create_index(
+        op.f("ix_reference_genomes_digest"),
+        "reference_genomes",
+        ["digest"],
+        unique=False,
+    )
+    op.create_table(
+        "usage_files",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column("file_path", sa.String(), nullable=False, comment="Path to the file"),
+        sa.Column("count", sa.Integer(), nullable=False, comment="Number of downloads"),
+        sa.Column(
+            "date_from",
+            sa.TIMESTAMP(timezone=True),
+            nullable=False,
+            comment="Date from",
+        ),
+        sa.Column(
+            "date_to", sa.TIMESTAMP(timezone=True), nullable=False, comment="Date to"
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_usage_files_id"), "usage_files", ["id"], unique=False)
+    op.create_table(
+        "usage_search",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column("query", sa.String(), nullable=False, comment="Search query"),
+        sa.Column(
+            "type",
+            sa.String(),
+            nullable=False,
+            comment="Type of the search. Bed/Bedset",
+        ),
+        sa.Column("count", sa.Integer(), nullable=False, comment="Number of searches"),
+        sa.Column(
+            "date_from",
+            sa.TIMESTAMP(timezone=True),
+            nullable=False,
+            comment="Date from",
+        ),
+        sa.Column(
+            "date_to", sa.TIMESTAMP(timezone=True), nullable=False, comment="Date to"
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_usage_search_id"), "usage_search", ["id"], unique=False)
+    op.create_table(
+        "bed",
+        sa.Column("id", sa.String(), nullable=False),
+        sa.Column("name", sa.String(), nullable=True),
+        sa.Column("genome_alias", sa.String(), nullable=True),
+        sa.Column("genome_digest", sa.String(), nullable=True),
+        sa.Column("description", sa.String(), nullable=True),
+        sa.Column("bed_compliance", sa.String(), nullable=False),
+        sa.Column("data_format", sa.String(), nullable=False),
+        sa.Column("compliant_columns", sa.Integer(), nullable=False),
+        sa.Column("non_compliant_columns", sa.Integer(), nullable=False),
+        sa.Column(
+            "header",
+            sa.String(),
+            nullable=True,
+            comment="Header of the bed file, it if was provided.",
+        ),
+        sa.Column(
+            "indexed",
+            sa.Boolean(),
+            nullable=False,
+            comment="Whether sample was added to qdrant",
+        ),
+        sa.Column(
+            "file_indexed",
+            sa.Boolean(),
+            nullable=False,
+            comment="Whether file was tokenized and added to the vector database",
+        ),
+        sa.Column(
+            "pephub",
+            sa.Boolean(),
+            nullable=False,
+            comment="Whether sample was added to pephub",
+        ),
+        sa.Column("submission_date", sa.TIMESTAMP(timezone=True), nullable=False),
+        sa.Column("last_update_date", sa.TIMESTAMP(timezone=True), nullable=True),
+        sa.Column("is_universe", sa.Boolean(), nullable=True),
+        sa.Column("license_id", sa.String(), nullable=True),
+        sa.Column(
+            "processed",
+            sa.Boolean(),
+            nullable=False,
+            comment="Whether the bed file was processed",
+        ),
+        sa.ForeignKeyConstraint(["license_id"], ["licenses.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        "genome_alias_index",
+        "bed",
+        ["genome_alias"],
+        unique=False,
+        postgresql_with={"deduplicate_items": "true"},
+    )
+    op.create_index(op.f("ix_bed_id"), "bed", ["id"], unique=False)
+    op.create_index(op.f("ix_bed_license_id"), "bed", ["license_id"], unique=False)
+    op.create_index(
+        "ix_bed_not_file_indexed",
+        "bed",
+        ["id"],
+        unique=False,
+        postgresql_where=sa.text("file_indexed = false"),
+    )
+    op.create_index(
+        "ix_bed_not_indexed",
+        "bed",
+        ["id"],
+        unique=False,
+        postgresql_where=sa.text("indexed = false"),
+    )
+    op.create_index(
+        "ix_bed_submission_date",
+        "bed",
+        [sa.literal_column("submission_date DESC"), sa.literal_column("id")],
+        unique=False,
+    )
+    op.create_index(
+        "ix_bed_unprocessed",
+        "bed",
+        ["id"],
+        unique=False,
+        postgresql_where=sa.text("processed = false"),
+    )
+    op.create_table(
+        "geo_gsm_status",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column("gse_status_id", sa.Integer(), nullable=False),
+        sa.Column("gsm", sa.String(), nullable=False, comment="GSM number"),
+        sa.Column("sample_name", sa.String(), nullable=False),
+        sa.Column(
+            "status", sa.String(), nullable=False, comment="Status of the GEO sample"
+        ),
+        sa.Column("error", sa.String(), nullable=True, comment="Error message"),
+        sa.Column(
+            "source_submission_date",
+            sa.TIMESTAMP(timezone=True),
+            nullable=True,
+            comment="Submission date of the source",
+        ),
+        sa.Column("submission_date", sa.TIMESTAMP(timezone=True), nullable=False),
+        sa.Column("bed_id", sa.String(), nullable=True, comment="Bed identifier"),
+        sa.Column(
+            "file_size", sa.BigInteger(), nullable=False, comment="Size of the file"
+        ),
+        sa.Column("genome", sa.String(), nullable=True, comment="Genome"),
+        sa.ForeignKeyConstraint(
+            ["gse_status_id"], ["geo_gse_status.id"], ondelete="CASCADE"
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        op.f("ix_geo_gsm_status_bed_id"), "geo_gsm_status", ["bed_id"], unique=False
+    )
+    op.create_index(
+        op.f("ix_geo_gsm_status_gse_status_id"),
+        "geo_gsm_status",
+        ["gse_status_id"],
+        unique=False,
+    )
+    op.create_index(
+        op.f("ix_geo_gsm_status_id"), "geo_gsm_status", ["id"], unique=False
+    )
+    op.create_table(
+        "usage_bedset_meta",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column("bedset_id", sa.String(), nullable=True),
+        sa.Column("count", sa.Integer(), nullable=False, comment="Number of visits"),
+        sa.Column(
+            "date_from",
+            sa.TIMESTAMP(timezone=True),
+            nullable=False,
+            comment="Date from",
+        ),
+        sa.Column(
+            "date_to", sa.TIMESTAMP(timezone=True), nullable=False, comment="Date to"
+        ),
+        sa.ForeignKeyConstraint(["bedset_id"], ["bedsets.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        op.f("ix_usage_bedset_meta_bedset_id"),
+        "usage_bedset_meta",
+        ["bedset_id"],
+        unique=False,
+    )
+    op.create_index(
+        op.f("ix_usage_bedset_meta_id"), "usage_bedset_meta", ["id"], unique=False
+    )
+    op.create_table(
+        "bed_metadata",
+        sa.Column("species_name", sa.String(), nullable=False, comment="Organism name"),
+        sa.Column(
+            "species_id", sa.String(), nullable=True, comment="Organism taxon id"
+        ),
+        sa.Column(
+            "genotype", sa.String(), nullable=True, comment="Genotype of the sample"
+        ),
+        sa.Column(
+            "phenotype", sa.String(), nullable=True, comment="Phenotype of the sample"
+        ),
+        sa.Column(
+            "cell_type",
+            sa.String(),
+            nullable=True,
+            comment="Specific kind of cell with distinct characteristics found in an organism. e.g. Neurons, Hepatocytes, Adipocytes",
+        ),
+        sa.Column(
+            "cell_line",
+            sa.String(),
+            nullable=True,
+            comment="Population of cells derived from a single cell and cultured in the lab for extended use, e.g. HeLa, HepG2, k562",
+        ),
+        sa.Column("tissue", sa.String(), nullable=True, comment="Tissue type"),
+        sa.Column(
+            "library_source",
+            sa.String(),
+            nullable=True,
+            comment="Library source (e.g. genomic, transcriptomic)",
+        ),
+        sa.Column(
+            "assay",
+            sa.String(),
+            nullable=True,
+            comment="Experimental protocol (e.g. ChIP-seq)",
+        ),
+        sa.Column(
+            "antibody", sa.String(), nullable=True, comment="Antibody used in the assay"
+        ),
+        sa.Column(
+            "target",
+            sa.String(),
+            nullable=True,
+            comment="Target of the assay (e.g. H3K4me3)",
+        ),
+        sa.Column(
+            "treatment",
+            sa.String(),
+            nullable=True,
+            comment="Treatment of the sample (e.g. drug treatment)",
+        ),
+        sa.Column(
+            "original_file_name",
+            sa.String(),
+            nullable=True,
+            comment="Original file name",
+        ),
+        sa.Column(
+            "global_sample_id",
+            postgresql.ARRAY(sa.String()),
+            nullable=True,
+            comment="Global sample identifier. e.g. GSM000",
+        ),
+        sa.Column(
+            "global_experiment_id",
+            postgresql.ARRAY(sa.String()),
+            nullable=True,
+            comment="Global experiment identifier. e.g. GSE000",
+        ),
+        sa.Column("id", sa.String(), nullable=False),
+        sa.ForeignKeyConstraint(["id"], ["bed.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_bed_metadata_id"), "bed_metadata", ["id"], unique=False)
+    op.create_table(
+        "bed_stats",
+        sa.Column("id", sa.String(), nullable=False),
+        sa.Column("number_of_regions", sa.Float(), nullable=True),
+        sa.Column("gc_content", sa.Float(), nullable=True),
+        sa.Column("median_tss_dist", sa.Float(), nullable=True),
+        sa.Column("mean_region_width", sa.Float(), nullable=True),
+        sa.Column("exon_frequency", sa.Float(), nullable=True),
+        sa.Column("intron_frequency", sa.Float(), nullable=True),
+        sa.Column("promoterprox_frequency", sa.Float(), nullable=True),
+        sa.Column("intergenic_frequency", sa.Float(), nullable=True),
+        sa.Column("promotercore_frequency", sa.Float(), nullable=True),
+        sa.Column("fiveutr_frequency", sa.Float(), nullable=True),
+        sa.Column("threeutr_frequency", sa.Float(), nullable=True),
+        sa.Column("fiveutr_percentage", sa.Float(), nullable=True),
+        sa.Column("threeutr_percentage", sa.Float(), nullable=True),
+        sa.Column("promoterprox_percentage", sa.Float(), nullable=True),
+        sa.Column("exon_percentage", sa.Float(), nullable=True),
+        sa.Column("intron_percentage", sa.Float(), nullable=True),
+        sa.Column("intergenic_percentage", sa.Float(), nullable=True),
+        sa.Column("promotercore_percentage", sa.Float(), nullable=True),
+        sa.Column("tssdist", sa.Float(), nullable=True),
+        sa.ForeignKeyConstraint(["id"], ["bed.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(op.f("ix_bed_stats_id"), "bed_stats", ["id"], unique=False)
+    op.create_index(
+        "ix_bed_stats_missing_regions",
+        "bed_stats",
+        ["id"],
+        unique=False,
+        postgresql_where=sa.text("number_of_regions IS NULL"),
+    )
+    op.create_table(
+        "bedfile_bedset_relation",
+        sa.Column("bedset_id", sa.String(), nullable=False),
+        sa.Column("bedfile_id", sa.String(), nullable=False),
+        sa.ForeignKeyConstraint(["bedfile_id"], ["bed.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["bedset_id"], ["bedsets.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("bedset_id", "bedfile_id"),
+    )
+    op.create_index(
+        op.f("ix_bedfile_bedset_relation_bedfile_id"),
+        "bedfile_bedset_relation",
+        ["bedfile_id"],
+        unique=False,
+    )
+    op.create_table(
+        "files",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column(
+            "name",
+            sa.String(),
+            nullable=False,
+            comment="Name of the file, e.g. bed, bigBed",
+        ),
+        sa.Column(
+            "file_digest",
+            sa.String(),
+            nullable=True,
+            comment="Digest of the file. Mainly used for bed file.",
+        ),
+        sa.Column("title", sa.String(), nullable=True),
+        sa.Column(
+            "type",
+            sa.String(),
+            nullable=False,
+            comment="Type of the object, e.g. file, plot, ...",
+        ),
+        sa.Column("path", sa.String(), nullable=False),
+        sa.Column(
+            "path_thumbnail",
+            sa.String(),
+            nullable=True,
+            comment="Thumbnail path of the file",
+        ),
+        sa.Column("description", sa.String(), nullable=True),
+        sa.Column("size", sa.Integer(), nullable=True, comment="Size of the file"),
+        sa.Column("bedfile_id", sa.String(), nullable=True),
+        sa.Column("bedset_id", sa.String(), nullable=True),
+        sa.ForeignKeyConstraint(["bedfile_id"], ["bed.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["bedset_id"], ["bedsets.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("name", "bedfile_id"),
+        sa.UniqueConstraint("name", "bedset_id"),
+    )
+    op.create_index(op.f("ix_files_bedfile_id"), "files", ["bedfile_id"], unique=False)
+    op.create_index(op.f("ix_files_bedset_id"), "files", ["bedset_id"], unique=False)
+    op.create_index(op.f("ix_files_id"), "files", ["id"], unique=False)
+    op.create_table(
+        "genome_ref_stats",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("bed_id", sa.String(), nullable=False),
+        sa.Column("provided_genome", sa.String(), nullable=False),
+        sa.Column(
+            "compared_genome", sa.String(), nullable=False, comment="Compared Genome"
+        ),
+        sa.Column("genome_digest", sa.String(), nullable=False),
+        sa.Column("xs", sa.Float(), nullable=True),
+        sa.Column("oobr", sa.Float(), nullable=True),
+        sa.Column("sequence_fit", sa.Float(), nullable=True),
+        sa.Column("assigned_points", sa.Integer(), nullable=False),
+        sa.Column("tier_ranking", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(["bed_id"], ["bed.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(
+            ["genome_digest"], ["reference_genomes.digest"], ondelete="CASCADE"
+        ),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("bed_id", "compared_genome"),
+    )
+    op.create_index(
+        op.f("ix_genome_ref_stats_bed_id"), "genome_ref_stats", ["bed_id"], unique=False
+    )
+    op.create_index(
+        op.f("ix_genome_ref_stats_id"), "genome_ref_stats", ["id"], unique=False
+    )
+    op.create_table(
+        "universes",
+        sa.Column("id", sa.String(), nullable=False),
+        sa.Column(
+            "method",
+            sa.String(),
+            nullable=True,
+            comment="Method used to create the universe",
+        ),
+        sa.Column("bedset_id", sa.String(), nullable=True),
+        sa.ForeignKeyConstraint(["bedset_id"], ["bedsets.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["id"], ["bed.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        op.f("ix_universes_bedset_id"), "universes", ["bedset_id"], unique=False
+    )
+    op.create_index(op.f("ix_universes_id"), "universes", ["id"], unique=False)
+    op.create_table(
+        "usage_bed_meta",
+        sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+        sa.Column("bed_id", sa.String(), nullable=True),
+        sa.Column("count", sa.Integer(), nullable=False, comment="Number of visits"),
+        sa.Column(
+            "date_from",
+            sa.TIMESTAMP(timezone=True),
+            nullable=False,
+            comment="Date from",
+        ),
+        sa.Column(
+            "date_to", sa.TIMESTAMP(timezone=True), nullable=False, comment="Date to"
+        ),
+        sa.ForeignKeyConstraint(["bed_id"], ["bed.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index(
+        op.f("ix_usage_bed_meta_bed_id"), "usage_bed_meta", ["bed_id"], unique=False
+    )
+    op.create_index(
+        op.f("ix_usage_bed_meta_id"), "usage_bed_meta", ["id"], unique=False
+    )
+    op.create_table(
+        "tokenized_bed",
+        sa.Column("bed_id", sa.String(), nullable=False),
+        sa.Column("universe_id", sa.String(), nullable=False),
+        sa.Column(
+            "path",
+            sa.String(),
+            nullable=False,
+            comment="Path to the tokenized bed file",
+        ),
+        sa.ForeignKeyConstraint(["bed_id"], ["bed.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["universe_id"], ["universes.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("bed_id", "universe_id"),
+    )
+    op.create_index(
+        op.f("ix_tokenized_bed_bed_id"), "tokenized_bed", ["bed_id"], unique=False
+    )
+    op.create_index(
+        op.f("ix_tokenized_bed_universe_id"),
+        "tokenized_bed",
+        ["universe_id"],
+        unique=False,
+    )
     # ### end Alembic commands ###
 
 
 def downgrade() -> None:
     """Downgrade schema."""
     # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_index(op.f('ix_tokenized_bed_universe_id'), table_name='tokenized_bed')
-    op.drop_index(op.f('ix_tokenized_bed_bed_id'), table_name='tokenized_bed')
-    op.drop_table('tokenized_bed')
-    op.drop_index(op.f('ix_usage_bed_meta_id'), table_name='usage_bed_meta')
-    op.drop_index(op.f('ix_usage_bed_meta_bed_id'), table_name='usage_bed_meta')
-    op.drop_table('usage_bed_meta')
-    op.drop_index(op.f('ix_universes_id'), table_name='universes')
-    op.drop_index(op.f('ix_universes_bedset_id'), table_name='universes')
-    op.drop_table('universes')
-    op.drop_index(op.f('ix_genome_ref_stats_id'), table_name='genome_ref_stats')
-    op.drop_index(op.f('ix_genome_ref_stats_bed_id'), table_name='genome_ref_stats')
-    op.drop_table('genome_ref_stats')
-    op.drop_index(op.f('ix_files_id'), table_name='files')
-    op.drop_index(op.f('ix_files_bedset_id'), table_name='files')
-    op.drop_index(op.f('ix_files_bedfile_id'), table_name='files')
-    op.drop_table('files')
-    op.drop_index(op.f('ix_bedfile_bedset_relation_bedfile_id'), table_name='bedfile_bedset_relation')
-    op.drop_table('bedfile_bedset_relation')
-    op.drop_index('ix_bed_stats_missing_regions', table_name='bed_stats', postgresql_where=sa.text('number_of_regions IS NULL'))
-    op.drop_index(op.f('ix_bed_stats_id'), table_name='bed_stats')
-    op.drop_table('bed_stats')
-    op.drop_index(op.f('ix_bed_metadata_id'), table_name='bed_metadata')
-    op.drop_table('bed_metadata')
-    op.drop_index(op.f('ix_usage_bedset_meta_id'), table_name='usage_bedset_meta')
-    op.drop_index(op.f('ix_usage_bedset_meta_bedset_id'), table_name='usage_bedset_meta')
-    op.drop_table('usage_bedset_meta')
-    op.drop_index(op.f('ix_geo_gsm_status_id'), table_name='geo_gsm_status')
-    op.drop_index(op.f('ix_geo_gsm_status_gse_status_id'), table_name='geo_gsm_status')
-    op.drop_index(op.f('ix_geo_gsm_status_bed_id'), table_name='geo_gsm_status')
-    op.drop_table('geo_gsm_status')
-    op.drop_index('ix_bed_unprocessed', table_name='bed', postgresql_where=sa.text('processed = false'))
-    op.drop_index('ix_bed_submission_date', table_name='bed')
-    op.drop_index('ix_bed_not_indexed', table_name='bed', postgresql_where=sa.text('indexed = false'))
-    op.drop_index('ix_bed_not_file_indexed', table_name='bed', postgresql_where=sa.text('file_indexed = false'))
-    op.drop_index(op.f('ix_bed_license_id'), table_name='bed')
-    op.drop_index(op.f('ix_bed_id'), table_name='bed')
-    op.drop_index('genome_alias_index', table_name='bed', postgresql_with={'deduplicate_items': 'true'})
-    op.drop_table('bed')
-    op.drop_index(op.f('ix_usage_search_id'), table_name='usage_search')
-    op.drop_table('usage_search')
-    op.drop_index(op.f('ix_usage_files_id'), table_name='usage_files')
-    op.drop_table('usage_files')
-    op.drop_index(op.f('ix_reference_genomes_digest'), table_name='reference_genomes')
-    op.drop_table('reference_genomes')
-    op.drop_index(op.f('ix_licenses_id'), table_name='licenses')
-    op.drop_table('licenses')
-    op.drop_index(op.f('ix_geo_gse_status_id'), table_name='geo_gse_status')
-    op.drop_table('geo_gse_status')
-    op.drop_index('ix_bedsets_unprocessed', table_name='bedsets', postgresql_where=sa.text('processed = false'))
-    op.drop_index('ix_bedsets_name_trgm', table_name='bedsets', postgresql_using='gin', postgresql_ops={'name': 'gin_trgm_ops'})
-    op.drop_index(op.f('ix_bedsets_id'), table_name='bedsets')
-    op.drop_index('ix_bedsets_description_trgm', table_name='bedsets', postgresql_using='gin', postgresql_ops={'description': 'gin_trgm_ops'})
-    op.drop_table('bedsets')
-    op.drop_index(op.f('ix_bed_snapshots_id'), table_name='bed_snapshots')
-    op.drop_table('bed_snapshots')
+    op.drop_index(op.f("ix_tokenized_bed_universe_id"), table_name="tokenized_bed")
+    op.drop_index(op.f("ix_tokenized_bed_bed_id"), table_name="tokenized_bed")
+    op.drop_table("tokenized_bed")
+    op.drop_index(op.f("ix_usage_bed_meta_id"), table_name="usage_bed_meta")
+    op.drop_index(op.f("ix_usage_bed_meta_bed_id"), table_name="usage_bed_meta")
+    op.drop_table("usage_bed_meta")
+    op.drop_index(op.f("ix_universes_id"), table_name="universes")
+    op.drop_index(op.f("ix_universes_bedset_id"), table_name="universes")
+    op.drop_table("universes")
+    op.drop_index(op.f("ix_genome_ref_stats_id"), table_name="genome_ref_stats")
+    op.drop_index(op.f("ix_genome_ref_stats_bed_id"), table_name="genome_ref_stats")
+    op.drop_table("genome_ref_stats")
+    op.drop_index(op.f("ix_files_id"), table_name="files")
+    op.drop_index(op.f("ix_files_bedset_id"), table_name="files")
+    op.drop_index(op.f("ix_files_bedfile_id"), table_name="files")
+    op.drop_table("files")
+    op.drop_index(
+        op.f("ix_bedfile_bedset_relation_bedfile_id"),
+        table_name="bedfile_bedset_relation",
+    )
+    op.drop_table("bedfile_bedset_relation")
+    op.drop_index(
+        "ix_bed_stats_missing_regions",
+        table_name="bed_stats",
+        postgresql_where=sa.text("number_of_regions IS NULL"),
+    )
+    op.drop_index(op.f("ix_bed_stats_id"), table_name="bed_stats")
+    op.drop_table("bed_stats")
+    op.drop_index(op.f("ix_bed_metadata_id"), table_name="bed_metadata")
+    op.drop_table("bed_metadata")
+    op.drop_index(op.f("ix_usage_bedset_meta_id"), table_name="usage_bedset_meta")
+    op.drop_index(
+        op.f("ix_usage_bedset_meta_bedset_id"), table_name="usage_bedset_meta"
+    )
+    op.drop_table("usage_bedset_meta")
+    op.drop_index(op.f("ix_geo_gsm_status_id"), table_name="geo_gsm_status")
+    op.drop_index(op.f("ix_geo_gsm_status_gse_status_id"), table_name="geo_gsm_status")
+    op.drop_index(op.f("ix_geo_gsm_status_bed_id"), table_name="geo_gsm_status")
+    op.drop_table("geo_gsm_status")
+    op.drop_index(
+        "ix_bed_unprocessed",
+        table_name="bed",
+        postgresql_where=sa.text("processed = false"),
+    )
+    op.drop_index("ix_bed_submission_date", table_name="bed")
+    op.drop_index(
+        "ix_bed_not_indexed",
+        table_name="bed",
+        postgresql_where=sa.text("indexed = false"),
+    )
+    op.drop_index(
+        "ix_bed_not_file_indexed",
+        table_name="bed",
+        postgresql_where=sa.text("file_indexed = false"),
+    )
+    op.drop_index(op.f("ix_bed_license_id"), table_name="bed")
+    op.drop_index(op.f("ix_bed_id"), table_name="bed")
+    op.drop_index(
+        "genome_alias_index",
+        table_name="bed",
+        postgresql_with={"deduplicate_items": "true"},
+    )
+    op.drop_table("bed")
+    op.drop_index(op.f("ix_usage_search_id"), table_name="usage_search")
+    op.drop_table("usage_search")
+    op.drop_index(op.f("ix_usage_files_id"), table_name="usage_files")
+    op.drop_table("usage_files")
+    op.drop_index(op.f("ix_reference_genomes_digest"), table_name="reference_genomes")
+    op.drop_table("reference_genomes")
+    op.drop_index(op.f("ix_licenses_id"), table_name="licenses")
+    op.drop_table("licenses")
+    op.drop_index(op.f("ix_geo_gse_status_id"), table_name="geo_gse_status")
+    op.drop_table("geo_gse_status")
+    op.drop_index(
+        "ix_bedsets_unprocessed",
+        table_name="bedsets",
+        postgresql_where=sa.text("processed = false"),
+    )
+    op.drop_index(
+        "ix_bedsets_name_trgm",
+        table_name="bedsets",
+        postgresql_using="gin",
+        postgresql_ops={"name": "gin_trgm_ops"},
+    )
+    op.drop_index(op.f("ix_bedsets_id"), table_name="bedsets")
+    op.drop_index(
+        "ix_bedsets_description_trgm",
+        table_name="bedsets",
+        postgresql_using="gin",
+        postgresql_ops={"description": "gin_trgm_ops"},
+    )
+    op.drop_table("bedsets")
+    op.drop_index(op.f("ix_bed_snapshots_id"), table_name="bed_snapshots")
+    op.drop_table("bed_snapshots")
     # ### end Alembic commands ###
diff --git a/bbconf/bbagent.py b/bbconf/bbagent.py
index 41acaf4e..571e2ff2 100644
--- a/bbconf/bbagent.py
+++ b/bbconf/bbagent.py
@@ -740,8 +740,14 @@ def _bin_number_of_regions(self, number_of_regions: list) -> BinValues:
         return BinValues(
             bins=n_region_bin_edges,
             counts=n_region_counts,
-            mean=round(statistics.mean(number_of_regions), 2),
-            median=round(statistics.median(number_of_regions), 2),
+            mean=round(statistics.mean(number_of_regions), 2)
+            if number_of_regions
+            else 0,
+            median=(
+                round(statistics.median(number_of_regions), 2)
+                if number_of_regions
+                else 0
+            ),
         )
 
     def _bin_mean_region_width(self, mean_region_widths: list) -> BinValues:
@@ -771,8 +777,16 @@ def _bin_mean_region_width(self, mean_region_widths: list) -> BinValues:
         return BinValues(
             bins=mean_reg_width_bin_edges,
             counts=mean_reg_width_counts,
-            mean=round(statistics.mean(mean_region_widths), 2),
-            median=round(statistics.median(mean_region_widths), 2),
+            mean=(
+                round(statistics.mean(mean_region_widths), 2)
+                if mean_region_widths
+                else 0
+            ),
+            median=(
+                round(statistics.median(mean_region_widths), 2)
+                if mean_region_widths
+                else 0
+            ),
         )
 
     def _bin_file_size(self, list_file_size: list) -> BinValues:
@@ -803,8 +817,16 @@ def _bin_file_size(self, list_file_size: list) -> BinValues:
         return BinValues(
             bins=file_size_bin_edges,
             counts=file_size_counts,
-            mean=round(statistics.mean(filtered_list_file_size), 2),
-            median=round(statistics.median(filtered_list_file_size), 2),
+            mean=(
+                round(statistics.mean(filtered_list_file_size), 2)
+                if filtered_list_file_size
+                else 0
+            ),
+            median=(
+                round(statistics.median(filtered_list_file_size), 2)
+                if filtered_list_file_size
+                else 0
+            ),
         )
 
     def _get_geo_stats(self, sa_session: Session) -> GEOStatistics:
@@ -857,8 +879,8 @@ def _get_geo_stats(self, sa_session: Session) -> GEOStatistics:
             file_sizes=BinValues(
                 bins=list(file_size_bin_edges),
                 counts=file_size_counts.astype(int).tolist(),
-                mean=round(statistics.mean(file_sizes), 2),
-                median=round(statistics.median(file_sizes), 2),
+                mean=round(statistics.mean(file_sizes), 2) if file_sizes else 0,
+                median=round(statistics.median(file_sizes), 2) if file_sizes else 0,
             ),
         )
 
diff --git a/bbconf/models/base_models.py b/bbconf/models/base_models.py
index a465c814..76a38f9d 100644
--- a/bbconf/models/base_models.py
+++ b/bbconf/models/base_models.py
@@ -130,4 +130,4 @@ class BedSnapshotResult(BaseModel):
 
 class BedSnapshotListResult(BaseModel):
     count: int
-    results: list[BedSnapshotResult]
\ No newline at end of file
+    results: list[BedSnapshotResult]
diff --git a/bbconf/modules/snapshots.py b/bbconf/modules/snapshots.py
index ba488d11..49e7ee2c 100644
--- a/bbconf/modules/snapshots.py
+++ b/bbconf/modules/snapshots.py
@@ -148,9 +148,7 @@ def list(
         count_statement = select(func.count()).select_from(BedSnapshot)
         if file_type is not None:
             statement = statement.where(BedSnapshot.file_type == file_type)
-            count_statement = count_statement.where(
-                BedSnapshot.file_type == file_type
-            )
+            count_statement = count_statement.where(BedSnapshot.file_type == file_type)
         statement = statement.order_by(
             BedSnapshot.creation_date.desc(), BedSnapshot.id.desc()
         )
@@ -188,9 +186,7 @@ def get_by_filename(self, filename: str) -> BedSnapshotResult:
             rows = session.scalars(
                 select(BedSnapshot)
                 .where(BedSnapshot.file_path.like(f"%{filename}"))
-                .order_by(
-                    BedSnapshot.creation_date.desc(), BedSnapshot.id.desc()
-                )
+                .order_by(BedSnapshot.creation_date.desc(), BedSnapshot.id.desc())
             ).all()
             for row in rows:
                 if os.path.basename(row.file_path) == filename:

From 0b48d4e1d5739ce48089bb3f171aa43d2f2cb8cc Mon Sep 17 00:00:00 2001
From: khoroshevskyi <sasha99250@gmail.com>
Date: Sun, 16 Aug 2026 13:57:48 -0400
Subject: [PATCH 5/6] Removed phc from bedbase

---
 .github/workflows/run-pytest.yml      |   1 +
 bbconf/config_parser/bedbaseconfig.py |  30 ------
 bbconf/config_parser/const.py         |   4 -
 bbconf/config_parser/models.py        |  10 --
 bbconf/config_parser/utils.py         |   3 +-
 bbconf/db_utils.py                    |   3 -
 bbconf/modules/bedfiles.py            | 131 ++++----------------------
 bbconf/modules/bedsets.py             |  70 +-------------
 pyproject.toml                        |   1 -
 tests/config_test.yaml                |   4 -
 tests/conftest.py                     |   8 --
 tests/test_bedfile.py                 |  17 +---
 tests/test_universes.py               |   2 +-
 13 files changed, 23 insertions(+), 261 deletions(-)

diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml
index 3abcaa95..d2d6c3ce 100644
--- a/.github/workflows/run-pytest.yml
+++ b/.github/workflows/run-pytest.yml
@@ -15,6 +15,7 @@ jobs:
         python-version: ["3.10", "3.13"]
         os: [ubuntu-latest] # can't use macOS when using service containers or container jobs
     runs-on: ${{ matrix.os }}
+
     services:
         postgres:
           image: postgres
diff --git a/bbconf/config_parser/bedbaseconfig.py b/bbconf/config_parser/bedbaseconfig.py
index 9c5c5562..fea22738 100644
--- a/bbconf/config_parser/bedbaseconfig.py
+++ b/bbconf/config_parser/bedbaseconfig.py
@@ -20,7 +20,6 @@
 from geniml.search.backends import BiVectorBackend, QdrantBackend
 from geniml.search.interfaces import BiVectorSearchInterface
 from geniml.search.query2vec import BED2Vec
-from pephubclient import PEPHubClient
 from qdrant_client import QdrantClient, models
 from sentence_transformers import SparseEncoder
 from umap import UMAP
@@ -115,7 +114,6 @@ def __init__(self, config: Path | str, init_ml: bool = True):
             self.umap_encoder: UMAP | None = None
             self.sparse_encoder = None
 
-        self._phc = self._init_pephubclient()
         self._boto3_client = self._init_boto3_client()
 
     @staticmethod
@@ -165,16 +163,6 @@ def db_engine(self) -> BaseEngine:
         """
         return self._db_engine
 
-    @property
-    def phc(self) -> PEPHubClient:
-        """
-        Get PEPHub client.
-
-        Returns:
-            PEPHub client.
-        """
-        return self._phc
-
     @property
     def boto3_client(self) -> boto3.client:
         """
@@ -683,24 +671,6 @@ def delete_files_s3(self, files: list[FileModel]) -> None:
                 self.delete_s3(file.path_thumbnail)
         return None
 
-    @staticmethod
-    def _init_pephubclient() -> PEPHubClient | None:
-        """
-        Create Pephub client object using credentials provided in config file.
-
-        Returns:
-            PephubClient.
-        """
-
-        # try:
-        #     _LOGGER.info("Initializing PEPHub client...")
-        #     return PEPHubClient()
-        # except Exception as e:
-        #     _LOGGER.error(f"Error in creating PephubClient object: {e}")
-        #     warnings.warn(f"Error in creating PephubClient object: {e}", UserWarning)
-        #     return None
-        return None
-
     def get_prefixed_uri(self, postfix: str, access_id: str) -> str:
         """
         Return uri with correct prefix (schema).
diff --git a/bbconf/config_parser/const.py b/bbconf/config_parser/const.py
index 61aad4ec..91877ef2 100644
--- a/bbconf/config_parser/const.py
+++ b/bbconf/config_parser/const.py
@@ -17,10 +17,6 @@
 DEFAULT_SPARSE_MODEL = "prithivida/Splade_PP_en_v2"
 DEFAULT_REGION2_VEC_MODEL = "databio/r2v_encoder-ChIP-atlas-hg38"
 
-DEFAULT_PEPHUB_NAMESPACE = "databio"
-DEFAULT_PEPHUB_NAME = "bedbase_all"
-DEFAULT_PEPHUB_TAG = "default"
-
 DEFAULT_S3_BUCKET = "bedbase"
 
 
diff --git a/bbconf/config_parser/models.py b/bbconf/config_parser/models.py
index 002c9536..c2f5ca7e 100644
--- a/bbconf/config_parser/models.py
+++ b/bbconf/config_parser/models.py
@@ -9,9 +9,6 @@
     DEFAULT_DB_DRIVER,
     DEFAULT_DB_NAME,
     DEFAULT_DB_PORT,
-    DEFAULT_PEPHUB_NAME,
-    DEFAULT_PEPHUB_NAMESPACE,
-    DEFAULT_PEPHUB_TAG,
     DEFAULT_QDRANT_BIVEC_COLLECTION_NAME,
     DEFAULT_QDRANT_FILE_COLLECTION_NAME,
     DEFAULT_QDRANT_HYBRID_COLLECTION_NAME,
@@ -121,12 +118,6 @@ def modify_access(self) -> bool:
         return False
 
 
-class ConfigPepHubClient(BaseModel):
-    namespace: str | None = DEFAULT_PEPHUB_NAMESPACE
-    name: str | None = DEFAULT_PEPHUB_NAME
-    tag: str | None = DEFAULT_PEPHUB_TAG
-
-
 class ConfigFile(BaseModel):
     database: ConfigDB
     qdrant: ConfigQdrant = None
@@ -134,7 +125,6 @@ class ConfigFile(BaseModel):
     path: ConfigPath
     access_methods: AccessMethods = None
     s3: ConfigS3 = None
-    phc: ConfigPepHubClient = None
 
     model_config = ConfigDict(extra="allow")
 
diff --git a/bbconf/config_parser/utils.py b/bbconf/config_parser/utils.py
index cba2e364..46f0a7f1 100644
--- a/bbconf/config_parser/utils.py
+++ b/bbconf/config_parser/utils.py
@@ -1,7 +1,6 @@
 import logging
 
 import yacman
-from pephubclient.helpers import MessageHandler as m
 from pydantic_core._pydantic_core import ValidationError
 
 from bbconf.config_parser.models import ConfigFile
@@ -56,6 +55,6 @@ def config_analyzer(config_path: str) -> bool:
             )
             return False
 
-    m.print_success("Configuration file is valid! ")
+    _LOGGER.info("Configuration file is valid!")
 
     return True
diff --git a/bbconf/db_utils.py b/bbconf/db_utils.py
index 7e3d21e1..e49423c6 100644
--- a/bbconf/db_utils.py
+++ b/bbconf/db_utils.py
@@ -111,9 +111,6 @@ class Bed(Base):
         default=False,
         comment="Whether file was tokenized and added to the vector database",
     )
-    pephub: Mapped[bool] = mapped_column(
-        default=False, comment="Whether sample was added to pephub"
-    )
 
     submission_date: Mapped[datetime.datetime] = mapped_column(
         default=deliver_update_date
diff --git a/bbconf/modules/bedfiles.py b/bbconf/modules/bedfiles.py
index f4382f2b..e21c1c93 100644
--- a/bbconf/modules/bedfiles.py
+++ b/bbconf/modules/bedfiles.py
@@ -6,7 +6,6 @@
 from geniml.bbclient import BBClient
 from geniml.search.backends import QdrantBackend
 from gtars.models import RegionSet as GRegionSet
-from pephubclient.exceptions import ResponseError
 from pydantic import BaseModel
 from qdrant_client import models
 from qdrant_client.http.exceptions import UnexpectedResponse
@@ -100,7 +99,7 @@ def get(self, identifier: str, full: bool = False) -> BedMetadataAll:
 
         Args:
             identifier: Bed file identifier.
-            full: If True, return full metadata, including statistics, files, and raw metadata from pephub.
+            full: If True, return full metadata, including statistics and files.
 
         Returns:
             BED file metadata.
@@ -126,8 +125,7 @@ def _build_metadata(self, bed_object: Bed, full: bool = False) -> BedMetadataAll
 
         Args:
             bed_object: Bed ORM object to build metadata from.
-            full: If True, return full metadata, including statistics, files,
-                and raw metadata from pephub.
+            full: If True, return full metadata, including statistics and files.
 
         Returns:
             BED file metadata.
@@ -195,21 +193,8 @@ def _build_metadata(self, bed_object: Bed, full: bool = False) -> BedMetadataAll
             universe_meta = None
             bed_bedsets = []
 
-        try:
-            if full:
-                bed_metadata = BedPEPHubRestrict(
-                    **self.config.phc.sample.get(
-                        namespace=self.config.config.phc.namespace,
-                        name=self.config.config.phc.name,
-                        tag=self.config.config.phc.tag,
-                        sample_name=identifier,
-                    )
-                )
-            else:
-                bed_metadata = None
-        except Exception as e:
-            _LOGGER.warning(f"Could not retrieve metadata from pephub. Error: {e}")
-            bed_metadata = None
+        # Raw metadata used to come from PEPHub, which is no longer used.
+        bed_metadata = None
 
         return BedMetadataAll(
             id=bed_object.id,
@@ -395,17 +380,8 @@ def get_raw_metadata(self, identifier: str) -> BedPEPHub:
         Returns:
             BED file raw metadata.
         """
-        try:
-            bed_metadata = self.config.phc.sample.get(
-                namespace=self.config.config.phc.namespace,
-                name=self.config.config.phc.name,
-                tag=self.config.config.phc.tag,
-                sample_name=identifier,
-            )
-        except Exception as e:
-            _LOGGER.warning(f"Could not retrieve metadata from pephub. Error: {e}")
-            bed_metadata = {}
-        return BedPEPHubRestrict(**bed_metadata)
+        # Raw metadata used to come from PEPHub, which is no longer used.
+        return BedPEPHubRestrict()
 
     def get_classification(self, identifier: str) -> BedClassification:
         """
@@ -608,7 +584,7 @@ def add(
         Args:
             identifier: Bed file identifier.
             stats: Bed file results {statistics, plots, files, metadata}.
-            metadata: Bed file metadata (will be saved in pephub).
+            metadata: Bed file metadata.
             plots: Bed file plots.
             files: Bed file files.
             classification: Bed file classification.
@@ -616,11 +592,11 @@ def add(
             license_id: Bed file license id (default: 'DUO:0000042'). Full list of licenses:
                 https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.csv
             upload_qdrant: Add bed file to qdrant indexes.
-            upload_pephub: Add bed file to pephub.
+            upload_pephub: Deprecated and ignored. PEPHub upload is no longer supported.
             upload_s3: Upload files to s3.
             local_path: Local path to the output files.
             overwrite: Overwrite bed file if it already exists.
-            nofail: Do not raise an error for error in pephub/s3/qdrant or record exists and not overwrite.
+            nofail: Do not raise an error for error in s3/qdrant or record exists and not overwrite.
             processed: True if bedfile was processed and statistics and plots were calculated.
 
         Returns:
@@ -673,22 +649,7 @@ def add(
 
         classification = BedClassification(**classification)
         if upload_pephub:
-            pephub_metadata = BedPEPHub(**metadata)
-            try:
-                self.upload_pephub(
-                    identifier,
-                    pephub_metadata.model_dump(exclude=set("input_file")),
-                    overwrite,
-                )
-            except Exception as e:
-                _LOGGER.warning(
-                    f"Could not upload to pephub. Error: {e}. nofail: {nofail}"
-                )
-                upload_pephub = False
-                if not nofail:
-                    raise e
-        else:
-            _LOGGER.info("upload_pephub set to false. Skipping pephub..")
+            _LOGGER.info("PEPHub upload is no longer supported. Skipping pephub..")
 
         if upload_qdrant:
             if classification.genome_alias == "hg38":
@@ -724,7 +685,7 @@ def add(
                 description=bed_metadata.description,
                 license_id=license_id,
                 indexed=upload_qdrant,
-                pephub=upload_pephub,
+                pephub=False,
                 processed=processed,
             )
             session.add(new_bed)
@@ -809,18 +770,18 @@ def update(
         Args:
             identifier: Bed file identifier.
             stats: Bed file results {statistics, plots, files, metadata}.
-            metadata: Bed file metadata (will be saved in pephub).
+            metadata: Bed file metadata.
             plots: Bed file plots.
             files: Bed file files.
             classification: Bed file classification.
             ref_validation: Reference validation data. RefGenValidModel.
             license_id: Bed file license id (default: 'DUO:0000042').
             upload_qdrant: Add bed file to qdrant indexes.
-            upload_pephub: Add bed file to pephub.
+            upload_pephub: Deprecated and ignored. PEPHub upload is no longer supported.
             upload_s3: Upload files to s3.
             local_path: Local path to the output files.
             overwrite: Overwrite bed file if it already exists.
-            nofail: Do not raise an error for error in pephub/s3/qdrant or record exists and not overwrite.
+            nofail: Do not raise an error for error in s3/qdrant or record exists and not overwrite.
             processed: True if bedfile was processed and statistics and plots were calculated.
 
         Returns:
@@ -844,18 +805,8 @@ def update(
         bed_metadata = StandardMeta(**metadata if metadata else {})
         classification = BedClassification(**classification if classification else {})
 
-        if upload_pephub and metadata:
-            metadata = BedPEPHub(**metadata)
-            try:
-                self.update_pephub(identifier, metadata.model_dump(), overwrite)
-            except Exception as e:
-                _LOGGER.warning(
-                    f"Could not upload to pephub. Error: {e}. nofail: {nofail}"
-                )
-                if not nofail:
-                    raise e
-        else:
-            _LOGGER.info("upload_pephub set to false. Skipping pephub..")
+        if upload_pephub:
+            _LOGGER.info("PEPHub upload is no longer supported. Skipping pephub..")
 
         if upload_qdrant:
             if classification.genome_alias == "hg38":
@@ -1190,65 +1141,15 @@ def delete(self, identifier: str) -> None:
             bed_object = session.scalar(statement)
 
             files = [FileModel(**k.__dict__) for k in bed_object.files]
-            delete_pephub = bed_object.pephub
             delete_qdrant = bed_object.indexed
 
             session.delete(bed_object)
             session.commit()
 
-        if delete_pephub:
-            self.delete_pephub_sample(identifier)
         if delete_qdrant:
             self.delete_qdrant_point(identifier)
         self.config.delete_files_s3(files)
 
-    def upload_pephub(self, identifier: str, metadata: dict, overwrite: bool = False):
-        if not metadata:
-            _LOGGER.warning("No metadata provided. Skipping pephub upload..")
-            return False
-        self.config.phc.sample.create(
-            namespace=self.config.config.phc.namespace,
-            name=self.config.config.phc.name,
-            tag=self.config.config.phc.tag,
-            sample_name=identifier,
-            sample_dict=metadata,
-            overwrite=overwrite,
-        )
-
-    def update_pephub(
-        self, identifier: str, metadata: dict, overwrite: bool = False
-    ) -> None:
-        try:
-            if not metadata:
-                _LOGGER.warning("No metadata provided. Skipping pephub upload..")
-                return None
-            self.config.phc.sample.update(
-                namespace=self.config.config.phc.namespace,
-                name=self.config.config.phc.name,
-                tag=self.config.config.phc.tag,
-                sample_name=identifier,
-                sample_dict=metadata,
-            )
-        except ResponseError as e:
-            _LOGGER.warning(f"Could not update pephub. Error: {e}")
-
-    def delete_pephub_sample(self, identifier: str):
-        """
-        Delete sample from pephub.
-
-        Args:
-            identifier: Bed file identifier.
-        """
-        try:
-            self.config.phc.sample.remove(
-                namespace=self.config.config.phc.namespace,
-                name=self.config.config.phc.name,
-                tag=self.config.config.phc.tag,
-                sample_name=identifier,
-            )
-        except ResponseError as e:
-            _LOGGER.warning(f"Could not delete from pephub. Error: {e}")
-
     def upload_file_qdrant(
         self,
         bed_id: str,
diff --git a/bbconf/modules/bedsets.py b/bbconf/modules/bedsets.py
index 0713c0ad..c44598ea 100644
--- a/bbconf/modules/bedsets.py
+++ b/bbconf/modules/bedsets.py
@@ -324,7 +324,7 @@ def create(
             statistics: Calculate statistics for bedset.
             annotation: Bedset annotation (author, source).
             plots: Dictionary with plots.
-            upload_pephub: Upload bedset to pephub (create view in pephub).
+            upload_pephub: Deprecated and ignored. PEPHub upload is no longer supported.
             upload_s3: Upload bedset to s3.
             local_path: Local path to the output files.
             no_fail: Do not raise an error if bedset already exists.
@@ -358,12 +358,7 @@ def create(
             annotation = {}
 
         if upload_pephub:
-            try:
-                self._create_pephub_view(identifier, description, bedid_list, no_fail)
-            except Exception as e:
-                _LOGGER.error(f"Failed to create view in pephub: {e}")
-                if not no_fail:
-                    raise e
+            _LOGGER.info("PEPHub upload is no longer supported. Skipping pephub..")
 
         if no_fail:
             bedid_list = list(set(bedid_list))
@@ -462,42 +457,6 @@ def _calculate_statistics(self, bed_ids: list[str]) -> BedSetStats:
         _LOGGER.info("Bedset statistics were calculated successfully")
         return bedset_stats
 
-    # def _create_pephub_view(
-    #     self,
-    #     bedset_id: str,
-    #     description: str = None,
-    #     bed_ids: list = None,
-    #     nofail: bool = False,
-    # ) -> None:
-    #     """
-    #     Create view in pephub for bedset.
-    #
-    #     Args:
-    #         bedset_id: Bedset identifier.
-    #         description: Bedset description.
-    #         bed_ids: List of bed file identifiers.
-    #         nofail: Do not raise an error if sample not found.
-    #
-    #     Returns:
-    #         None.
-    #     """
-    #
-    #     _LOGGER.info(f"Creating view in pephub for bedset '{bedset_id}'")
-    #     try:
-    #         self.config.phc.view.create(
-    #             namespace=self.config.config.phc.namespace,
-    #             name=self.config.config.phc.name,
-    #             tag=self.config.config.phc.tag,
-    #             view_name=bedset_id,
-    #             # description=description,
-    #             sample_list=bed_ids,
-    #         )
-    #     except Exception as e:
-    #         _LOGGER.error(f"Failed to create view in pephub: {e}")
-    #         if not nofail:
-    #             raise e
-    #     return None
-
     def get_ids_list(
         self, query: str | None = None, limit: int = 10, offset: int = 0
     ) -> BedSetListResult:
@@ -623,31 +582,6 @@ def delete(self, identifier: str) -> None:
         if files:
             self.config.delete_files_s3(files)
 
-    # def delete_phc_view(self, identifier: str, nofail: bool = False) -> None:
-    #     """
-    #     Delete view in pephub.
-    #
-    #     Args:
-    #         identifier: Bedset identifier.
-    #         nofail: Do not raise an error if view not found.
-    #
-    #     Returns:
-    #         None.
-    #     """
-    #     _LOGGER.info(f"Deleting view in pephub for bedset '{identifier}'")
-    #     try:
-    #         self.config.phc.view.delete(
-    #             namespace=self.config.config.phc.namespace,
-    #             name=self.config.config.phc.name,
-    #             tag=self.config.config.phc.tag,
-    #             view_name=identifier,
-    #         )
-    #     except Exception as e:
-    #         _LOGGER.error(f"Failed to delete view in pephub: {e}")
-    #         if not nofail:
-    #             raise e
-    #     return None
-
     def exists(self, identifier: str) -> bool:
         """
         Check if bedset exists in the database.
diff --git a/pyproject.toml b/pyproject.toml
index 0ff9c045..b32405a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,6 @@ dependencies = [
     "pydantic >= 2.9.0",
     "botocore >= 1.34.0, < 1.36.0",
     "boto3 >= 1.34.54, < 1.36.0",
-    "pephubclient >= 0.4.5",
     "sqlalchemy_schemadisplay",
     "zarr < 3.0.0",
     "pyyaml >= 6.0.1",
diff --git a/tests/config_test.yaml b/tests/config_test.yaml
index ef8069eb..41c866c8 100644
--- a/tests/config_test.yaml
+++ b/tests/config_test.yaml
@@ -17,10 +17,6 @@ qdrant:
 s3:
   bucket: bedbase
   endpoint_url: "None"
-phc:
-  namespace: bedbase
-  name: bedbase
-  tag: test
 access_methods:
   http:
     type: "https"
diff --git a/tests/conftest.py b/tests/conftest.py
index 85d0b01b..1b841e26 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -125,11 +125,3 @@ def example_dict():
 @pytest.fixture
 def load_test_data():
     get_bbagent().config.db_engine()
-
-
-@pytest.fixture()
-def mocked_phc(mocker):
-    mocker.patch(
-        "pephubclient.modules.sample.PEPHubSample.get",
-        return_value={"sample_name": BED_TEST_ID, "other_metadata": "other_metadata_1"},
-    )
diff --git a/tests/test_bedfile.py b/tests/test_bedfile.py
index daf5f4ea..f0b88bb0 100644
--- a/tests/test_bedfile.py
+++ b/tests/test_bedfile.py
@@ -52,16 +52,13 @@ def test_add_nofail(self, bbagent_obj, example_dict, mocker):
             bbagent_obj.bed.add(**example_dict)
             assert bbagent_obj.bed.exists(example_dict["identifier"])
 
-    def test_get_all(self, bbagent_obj, mocked_phc):
+    def test_get_all(self, bbagent_obj):
         with ContextManagerDBTesting(config=bbagent_obj.config, add_data=True):
             return_result = bbagent_obj.bed.get(BED_TEST_ID, full=True)
             assert return_result is not None
             assert return_result.files is not None
             assert return_result.plots is not None
 
-            # TODO: PEPhub is disabled
-            # assert return_result.raw_metadata is not None
-
             assert return_result.genome_alias == "hg38"
             assert return_result.stats.number_of_regions == 1
 
@@ -69,7 +66,7 @@ def test_get_all(self, bbagent_obj, mocked_phc):
             assert return_result.plots.chrombins is not None
             assert return_result.license_id == DEFAULT_LICENSE
 
-    def test_get_all_bedsets_bedfile_count(self, bbagent_obj, mocked_phc):
+    def test_get_all_bedsets_bedfile_count(self, bbagent_obj):
         with ContextManagerDBTesting(
             config=bbagent_obj.config, add_data=True, bedset=True
         ):
@@ -92,16 +89,6 @@ def test_get_all_not_found(self, bbagent_obj):
             assert return_result.genome_alias == "hg38"
             assert return_result.id == BED_TEST_ID
 
-    @pytest.mark.skip(
-        "Skipped, because PHC is disabled"
-    )  # TODO: should we disable PHC everywhere?
-    def test_get_raw_metadata(self, bbagent_obj, mocked_phc):
-        with ContextManagerDBTesting(config=bbagent_obj.config, add_data=True):
-            return_result = bbagent_obj.bed.get_raw_metadata(BED_TEST_ID)
-
-            assert return_result is not None
-            assert return_result.sample_name == BED_TEST_ID
-
     def test_get_stats(self, bbagent_obj):
         with ContextManagerDBTesting(config=bbagent_obj.config, add_data=True):
             return_result = bbagent_obj.bed.get_stats(BED_TEST_ID)
diff --git a/tests/test_universes.py b/tests/test_universes.py
index 366b3770..15b8a45e 100644
--- a/tests/test_universes.py
+++ b/tests/test_universes.py
@@ -65,6 +65,6 @@ def test_add_get_tokenized(self, bbagent_obj, mocker):
             assert zarr_mock.called
             assert f"s3://bedbase/{saved_path}" == zarr_path
 
-    def test_get_tokenized(self, bbagent_obj, mocked_phc):
+    def test_get_tokenized(self, bbagent_obj):
         # how to test it?
         ...

From 9872e9bff3709552834a93f24e19b512cba74b51 Mon Sep 17 00:00:00 2001
From: khoroshevskyi <sasha99250@gmail.com>
Date: Sun, 16 Aug 2026 14:39:39 -0400
Subject: [PATCH 6/6] removed leftovers of pephubclient

---
 bbconf/models/bed_models.py | 32 --------------------------------
 bbconf/modules/bedfiles.py  | 29 -----------------------------
 bbconf/modules/bedsets.py   |  5 -----
 tests/conftest.py           |  1 -
 tests/test_bedfile.py       |  1 -
 tests/test_bedset.py        |  1 -
 6 files changed, 69 deletions(-)

diff --git a/bbconf/models/bed_models.py b/bbconf/models/bed_models.py
index 4d66b7f1..8580b9ba 100644
--- a/bbconf/models/bed_models.py
+++ b/bbconf/models/bed_models.py
@@ -77,33 +77,6 @@ class BedStatsModel(BaseModel):
     model_config = ConfigDict(extra="ignore", populate_by_name=True)
 
 
-class BedPEPHub(BaseModel):
-    sample_name: str | None = ""
-    genome: str | None = ""
-    organism: str | None = ""
-    species_id: str | None = ""
-    cell_type: str | None = ""
-    cell_line: str | None = ""
-    assay: str | None = Field("", description="Experimental protocol (e.g. ChIP-seq)")
-    library_source: str | None = Field(
-        "", description="Library source (e.g. genomic, transcriptomic)"
-    )
-    genotype: str | None = Field("", description="Genotype of the sample")
-    target: str | None = Field("", description="Target of the assay (e.g. H3K4me3)")
-    antibody: str | None = Field("", description="Antibody used in the assay")
-    treatment: str | None = Field(
-        "", description="Treatment of the sample (e.g. drug treatment)"
-    )
-    tissue: str | None = Field("", description="Tissue type")
-    global_sample_id: str | None = Field("", description="Global sample identifier")
-    global_experiment_id: str | None = Field(
-        "", description="Global experiment identifier"
-    )
-    description: str | None = Field("", description="Description of the sample")
-
-    model_config = ConfigDict(extra="allow", populate_by_name=True)
-
-
 class StandardMeta(BaseModel):
     """
     Standardized Bed file metadata
@@ -165,10 +138,6 @@ def ensure_list(cls, v: str | list[str]) -> list[str]:
         raise ValueError("values must be a string or a list of strings")
 
 
-class BedPEPHubRestrict(BedPEPHub):
-    model_config = ConfigDict(extra="ignore")
-
-
 class BedMetadataBasic(BedClassification):
     id: str
     name: str | None = ""
@@ -198,7 +167,6 @@ class BedMetadataAll(BedMetadataBasic):
     plots: BedPlots | None = None
     files: BedFiles | None = None
     universe_metadata: UniverseMetadata | None = None
-    raw_metadata: BedPEPHub | BedPEPHubRestrict | None = None
     bedsets: list[BedSetMinimal] | None = None
 
 
diff --git a/bbconf/modules/bedfiles.py b/bbconf/modules/bedfiles.py
index e21c1c93..7a594f46 100644
--- a/bbconf/modules/bedfiles.py
+++ b/bbconf/modules/bedfiles.py
@@ -51,8 +51,6 @@
     BedListSearchResult,
     BedMetadataAll,
     BedMetadataBasic,
-    BedPEPHub,
-    BedPEPHubRestrict,
     BedPlots,
     BedSetMinimal,
     BedStatsModel,
@@ -193,9 +191,6 @@ def _build_metadata(self, bed_object: Bed, full: bool = False) -> BedMetadataAll
             universe_meta = None
             bed_bedsets = []
 
-        # Raw metadata used to come from PEPHub, which is no longer used.
-        bed_metadata = None
-
         return BedMetadataAll(
             id=bed_object.id,
             name=bed_object.name,
@@ -205,7 +200,6 @@ def _build_metadata(self, bed_object: Bed, full: bool = False) -> BedMetadataAll
             description=bed_object.description,
             submission_date=bed_object.submission_date,
             last_update_date=bed_object.last_update_date,
-            raw_metadata=bed_metadata,
             genome_alias=bed_object.genome_alias,
             genome_digest=bed_object.genome_digest,
             bed_compliance=bed_object.bed_compliance,
@@ -370,19 +364,6 @@ def get_files(self, identifier: str) -> BedFiles:
                     )
         return bed_files
 
-    def get_raw_metadata(self, identifier: str) -> BedPEPHub:
-        """
-        Get file metadata by identifier.
-
-        Args:
-            identifier: Bed file identifier.
-
-        Returns:
-            BED file raw metadata.
-        """
-        # Raw metadata used to come from PEPHub, which is no longer used.
-        return BedPEPHubRestrict()
-
     def get_classification(self, identifier: str) -> BedClassification:
         """
         Get file classification by identifier.
@@ -571,7 +552,6 @@ def add(
         ref_validation: dict[str, BaseModel] | None = None,
         license_id: str = DEFAULT_LICENSE,
         upload_qdrant: bool = False,
-        upload_pephub: bool = False,
         upload_s3: bool = False,
         local_path: str = None,
         overwrite: bool = False,
@@ -592,7 +572,6 @@ def add(
             license_id: Bed file license id (default: 'DUO:0000042'). Full list of licenses:
                 https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.csv
             upload_qdrant: Add bed file to qdrant indexes.
-            upload_pephub: Deprecated and ignored. PEPHub upload is no longer supported.
             upload_s3: Upload files to s3.
             local_path: Local path to the output files.
             overwrite: Overwrite bed file if it already exists.
@@ -648,8 +627,6 @@ def add(
         bed_metadata = StandardMeta(**metadata)
 
         classification = BedClassification(**classification)
-        if upload_pephub:
-            _LOGGER.info("PEPHub upload is no longer supported. Skipping pephub..")
 
         if upload_qdrant:
             if classification.genome_alias == "hg38":
@@ -685,7 +662,6 @@ def add(
                 description=bed_metadata.description,
                 license_id=license_id,
                 indexed=upload_qdrant,
-                pephub=False,
                 processed=processed,
             )
             session.add(new_bed)
@@ -757,7 +733,6 @@ def update(
         ref_validation: dict[str, BaseModel] | None = None,
         license_id: str = DEFAULT_LICENSE,
         upload_qdrant: bool = False,
-        upload_pephub: bool = False,
         upload_s3: bool = True,
         local_path: str = None,
         overwrite: bool = False,
@@ -777,7 +752,6 @@ def update(
             ref_validation: Reference validation data. RefGenValidModel.
             license_id: Bed file license id (default: 'DUO:0000042').
             upload_qdrant: Add bed file to qdrant indexes.
-            upload_pephub: Deprecated and ignored. PEPHub upload is no longer supported.
             upload_s3: Upload files to s3.
             local_path: Local path to the output files.
             overwrite: Overwrite bed file if it already exists.
@@ -805,9 +779,6 @@ def update(
         bed_metadata = StandardMeta(**metadata if metadata else {})
         classification = BedClassification(**classification if classification else {})
 
-        if upload_pephub:
-            _LOGGER.info("PEPHub upload is no longer supported. Skipping pephub..")
-
         if upload_qdrant:
             if classification.genome_alias == "hg38":
                 _LOGGER.info(f"Uploading bed file to qdrant.. [{identifier}]")
diff --git a/bbconf/modules/bedsets.py b/bbconf/modules/bedsets.py
index c44598ea..facfe1e9 100644
--- a/bbconf/modules/bedsets.py
+++ b/bbconf/modules/bedsets.py
@@ -306,7 +306,6 @@ def create(
         statistics: bool = False,
         annotation: dict | None = None,
         plots: dict | None = None,
-        upload_pephub: bool = False,
         upload_s3: bool = False,
         local_path: str = "",
         no_fail: bool = False,
@@ -324,7 +323,6 @@ def create(
             statistics: Calculate statistics for bedset.
             annotation: Bedset annotation (author, source).
             plots: Dictionary with plots.
-            upload_pephub: Deprecated and ignored. PEPHub upload is no longer supported.
             upload_s3: Upload bedset to s3.
             local_path: Local path to the output files.
             no_fail: Do not raise an error if bedset already exists.
@@ -357,9 +355,6 @@ def create(
         if not isinstance(annotation, dict):
             annotation = {}
 
-        if upload_pephub:
-            _LOGGER.info("PEPHub upload is no longer supported. Skipping pephub..")
-
         if no_fail:
             bedid_list = list(set(bedid_list))
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 1b841e26..e0ebba4b 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -114,7 +114,6 @@ def example_dict():
         files=files,
         classification=classification,
         upload_qdrant=False,
-        upload_pephub=False,
         upload_s3=True,
         local_path=DATA_PATH,
         overwrite=False,
diff --git a/tests/test_bedfile.py b/tests/test_bedfile.py
index f0b88bb0..db5cadf8 100644
--- a/tests/test_bedfile.py
+++ b/tests/test_bedfile.py
@@ -83,7 +83,6 @@ def test_get_all_not_found(self, bbagent_obj):
             assert return_result is not None
             assert return_result.files is None
             assert return_result.plots is None
-            assert return_result.raw_metadata is None
             assert return_result.stats is None
 
             assert return_result.genome_alias == "hg38"
diff --git a/tests/test_bedset.py b/tests/test_bedset.py
index 71bde676..1f7977fd 100644
--- a/tests/test_bedset.py
+++ b/tests/test_bedset.py
@@ -53,7 +53,6 @@ def test_crate_bedset_all(self, bbagent_obj, mocker):
                 },
                 statistics=True,
                 upload_s3=True,
-                upload_pephub=False,
                 no_fail=True,
             )
             with Session(bbagent_obj.config.db_engine.engine) as session: