diff --git a/.idea/cmem-plugin-reason.iml b/.idea/cmem-plugin-reason.iml index 284c839..ed728f5 100644 --- a/.idea/cmem-plugin-reason.iml +++ b/.idea/cmem-plugin-reason.iml @@ -1,7 +1,9 @@ - + + + diff --git a/CHANGELOG.md b/CHANGELOG.md index c76f04d..f75344f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,10 +7,15 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p ## [Unreleased] -TODO: add at least one Added, Changed, Deprecated, Removed, Fixed or Security section +### Fixed +- Fix robot.jar vulnerabilities CVE-2026-54515, CVE-2026-9828. -## [2.2.5] 2026-03-01 +### Changed + +- Remove dependency inflection + +## [2.2.6] 2026-06-29 ### Fixed diff --git a/cmem_plugin_reason/doc/validate_doc.md b/cmem_plugin_reason/doc/validate_doc.md index da28486..6e13739 100644 --- a/cmem_plugin_reason/doc/validate_doc.md +++ b/cmem_plugin_reason/doc/validate_doc.md @@ -22,6 +22,10 @@ The following reasoner options are supported: - [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural) - [Whelk](https://github.com/balhoff/whelk) (whelk) +⚠️ Only **HermiT** and **JFact** are recommended for consistency validation, since they are the +only reasoner options here that are complete OWL DL reasoners capable of generating explanations. +The remaining options are kept for backwards compatibility. + ### Produce output graph If enabled, an explanation graph is created. diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py index 6f8cd3c..b06db24 100644 --- a/cmem_plugin_reason/plugin_reason.py +++ b/cmem_plugin_reason/plugin_reason.py @@ -1,5 +1,6 @@ """Reasoning workflow plugin module""" +import re from collections import OrderedDict from collections.abc import Sequence from pathlib import Path @@ -25,7 +26,7 @@ MAX_RAM_PERCENTAGE_DEFAULT, MAX_RAM_PERCENTAGE_PARAMETER, ONTOLOGY_GRAPH_IRI_PARAMETER, - REASONER_PARAMETER, + REASON_REASONER_PARAMETER, REASONERS, VALIDATE_PROFILES_PARAMETER, cancel_workflow, @@ -152,7 +153,7 @@ IGNORE_MISSING_IMPORTS_PARAMETER, ONTOLOGY_GRAPH_IRI_PARAMETER, VALIDATE_PROFILES_PARAMETER, - REASONER_PARAMETER, + REASON_REASONER_PARAMETER, MAX_RAM_PERCENTAGE_PARAMETER, PluginParameter( param_type=GraphParameterType( @@ -390,6 +391,14 @@ def __init__( # noqa: PLR0913 C901 self.input_ports = FixedNumberOfInputs([]) self.output_port = None + @staticmethod + def underscore(word: str) -> str: + """Make an underscored, lowercase form from the expression in the string""" + word = re.sub(r"([A-Z]+)([A-Z][a-z])", r"\1_\2", word) + word = re.sub(r"([a-z\d])([A-Z])", r"\1_\2", word) + word = word.replace("-", "_") + return word.lower() + def get_graphs(self, graphs: dict, missing: list) -> None: """Get graphs from CMEM""" for iri, filename in graphs.items(): diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py index 3a91cae..c407f17 100644 --- a/cmem_plugin_reason/plugin_validate.py +++ b/cmem_plugin_reason/plugin_validate.py @@ -25,9 +25,9 @@ MAX_RAM_PERCENTAGE_DEFAULT, MAX_RAM_PERCENTAGE_PARAMETER, ONTOLOGY_GRAPH_IRI_PARAMETER, - REASONER_PARAMETER, REASONERS, VALIDATE_PROFILES_PARAMETER, + VALIDATE_REASONER_PARAMETER, cancel_workflow, create_xml_catalog_file, get_file_with_datetime, @@ -53,7 +53,7 @@ ONTOLOGY_GRAPH_IRI_PARAMETER, MAX_RAM_PERCENTAGE_PARAMETER, VALIDATE_PROFILES_PARAMETER, - REASONER_PARAMETER, + VALIDATE_REASONER_PARAMETER, PluginParameter( param_type=StringParameterType(), name="md_filename", diff --git a/cmem_plugin_reason/robot.jar b/cmem_plugin_reason/robot.jar index 086cd97..cd122d6 100644 Binary files a/cmem_plugin_reason/robot.jar and b/cmem_plugin_reason/robot.jar differ diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py index a24df81..3959bff 100644 --- a/cmem_plugin_reason/utils.py +++ b/cmem_plugin_reason/utils.py @@ -42,13 +42,23 @@ MAX_RAM_PERCENTAGE_DEFAULT = 20 URN_PATTERN = re.compile(r"^urn:[a-zA-Z0-9][a-zA-Z0-9-]*(:.+)?$", re.IGNORECASE) -REASONER_PARAMETER = PluginParameter( +REASON_REASONER_PARAMETER = PluginParameter( param_type=ChoiceParameterType(REASONERS), name="reasoner", label="Reasoner", description="Reasoner option.", ) +VALIDATE_REASONER_PARAMETER = PluginParameter( + param_type=ChoiceParameterType(REASONERS), + name="reasoner", + label="Reasoner", + description="""Reasoner option. Only "HermiT" and "JFact" are recommended for consistency + validation, since they are the only reasoners offered here that are complete OWL DL reasoners + capable of generating explanations. The remaining options are kept for backwards + compatibility.""", +) + ONTOLOGY_GRAPH_IRI_PARAMETER = PluginParameter( param_type=GraphParameterType(classes=["http://www.w3.org/2002/07/owl#Ontology"]), name="ontology_graph_iri", diff --git a/poetry.lock b/poetry.lock index 4b23592..d62ce8c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,14 +14,14 @@ files = [ [[package]] name = "anyio" -version = "4.14.1" +version = "4.14.2" description = "High-level concurrency and networking framework on top of asyncio or Trio" optional = false python-versions = ">=3.10" groups = ["dev"] files = [ - {file = "anyio-4.14.1-py3-none-any.whl", hash = "sha256:4e5533c5b8ff0a24f5d7a176cbe6877129cd183893f66b537f8f227d10527d72"}, - {file = "anyio-4.14.1.tar.gz", hash = "sha256:8d648a3544c1a700e3ff78615cd679e4c5c3f149904287e73687b2596963629e"}, + {file = "anyio-4.14.2-py3-none-any.whl", hash = "sha256:9f505dda5ac9f0c8309b5e8bd445a8c2bf7246f3ce950121e45ea15bc41d1494"}, + {file = "anyio-4.14.2.tar.gz", hash = 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ARG001 """Test Validate""" result = ValidatePlugin(