diff --git a/CHANGELOG.md b/CHANGELOG.md index bde72a0..c00726e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,25 @@ 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 +### Changed + +- Use ROBOT v1.9.11 compiled with [updated dependencies without vulnerabilities](https://github.com/eccenca/robot/tree/feature/updateDependenciesV1.9.11) +- Scan the SBOM of robot.jar (`robot.cdx.json`) with Trivy, since the jar scan cannot identify all bundled libraries +- Updated dependencies and template +- Validate plugin: the output graph is now declared a `void:Dataset` instead of an + `owl:Ontology`. +- Reason plugin: only one of "Data graph IRI" and "Ontology graph IRI" is required. With only + one, or the same graph in both, that graph is reasoned on its own, and the result is described as + "Reasoning results of graph ". + +### Fixed + +- Fix robot.jar vulnerabilities CVE-2024-7254, CVE-2026-43869, CVE-2026-43871. +- Reason plugin: selecting the same graph as data graph and ontology graph failed with + `OWLOntologyDocumentAlreadyExistsException`. +- Reason and Validate plugins: provenance data is now written with every DataIntegration + workspace provider. Before, it was only written if the workspace was stored as RDF (workspace + provider `backend` or `fileAndDataPlatform`), because it was read from the project graph. ## [2.4.1] 2026-10-07 diff --git a/Taskfile.yaml b/Taskfile.yaml index dd02bb0..008b823 100644 --- a/Taskfile.yaml +++ b/Taskfile.yaml @@ -160,7 +160,7 @@ tasks: JUNIT_FILE: ./{{.DIST_DIR}}/junit-mypy.xml check:trivy: - desc: Scan for vulnerabilities using Trivy + desc: Scan the dependencies, robot.jar and its SBOM for vulnerabilities using Trivy deps: - prepare cmds: @@ -176,6 +176,13 @@ tasks: --scanners vuln --exit-code 1 cmem_plugin_reason/robot.jar + # robot.jar is a shaded jar: libraries without Maven metadata (e.g. protobuf-java, + # libthrift) are invisible to the jar scan. robot.cdx.json is the CycloneDX SBOM + # generated by the ROBOT build of the same robot.jar and lists all bundled libraries. + - > + poetry run trivy sbom + --exit-code 1 + robot.cdx.json check:deptry: desc: Complain about unused or missing dependencies diff --git a/cmem_plugin_reason/doc/reason_doc.md b/cmem_plugin_reason/doc/reason_doc.md index a612f15..4da6c33 100644 --- a/cmem_plugin_reason/doc/reason_doc.md +++ b/cmem_plugin_reason/doc/reason_doc.md @@ -1,15 +1,19 @@ -A task performing OWL reasoning. With an OWL ontology and a data graph as input the reasoning result is written to a specified graph. +A task performing OWL reasoning. With an OWL ontology and/or a data graph as input the reasoning result is written to a +specified graph. At least one of the two input graphs must be specified. With two different input graphs, the data +graph is reasoned with the ontology imported; with only one, or the same graph in both, that graph is reasoned on its +own. ## Options ### Data graph IRI The IRI of the input data graph. The graph IRI is selected from a list of graphs of types `di:Dataset`, `void:Dataset` -and `owl:Ontology`. +and `owl:Ontology`. Optional if an ontology graph is specified. ### Ontology graph IRI -The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`. +The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type `owl:Ontology`. Optional if +a data graph is specified. ### Ignore missing imports @@ -136,7 +140,8 @@ If there are classes `Person`, `Student` and `Professor` as wells as the object ### Validate OWL2 profiles -Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph. +Validate the input ontology against OWL profiles (DL, EL, QL, RL, and Full) and annotate the result graph. +Needs an ontology graph. ### Process valid OWL profiles from input @@ -147,7 +152,7 @@ profiles validation is not done in the plugin. The valid profiles input is a com ### Output graph import Add the triple owl:imports into the output graph or add the triple - owl:imports into the ontology graph. + owl:imports into the ontology graph. Needs an ontology graph. ### Maximum RAM Percentage diff --git a/cmem_plugin_reason/doc/validate_doc.md b/cmem_plugin_reason/doc/validate_doc.md index 6e13739..23f71f6 100644 --- a/cmem_plugin_reason/doc/validate_doc.md +++ b/cmem_plugin_reason/doc/validate_doc.md @@ -36,6 +36,10 @@ The IRI of the output graph for the reasoning result. ⚠️ Existing graphs will be overwritten. +The output graph holds the explanation axioms plus the validation result and is declared a +`void:Dataset`. It is not declared an `owl:Ontology`: it does not contain an ontology of its +own, it describes the validated one. + ### Write markdown explanation file If enabled, an explanation markdown file is written to the project. diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py index a001143..cb10c3e 100644 --- a/cmem_plugin_reason/plugin_reason.py +++ b/cmem_plugin_reason/plugin_reason.py @@ -22,7 +22,6 @@ IGNORE_MISSING_IMPORTS_PARAMETER, MAX_RAM_PERCENTAGE_DEFAULT, MAX_RAM_PERCENTAGE_PARAMETER, - ONTOLOGY_GRAPH_IRI_PARAMETER, REASON_REASONER_PARAMETER, REASONERS, VALIDATE_PROFILES_PARAMETER, @@ -149,7 +148,13 @@ documentation=REASON_DOC, parameters=[ IGNORE_MISSING_IMPORTS_PARAMETER, - ONTOLOGY_GRAPH_IRI_PARAMETER, + PluginParameter( + param_type=GraphParameterType(classes=["http://www.w3.org/2002/07/owl#Ontology"]), + name="ontology_graph_iri", + label="Ontology graph IRI", + description="""The IRI of the input ontology graph. At least one of data graph and + ontology graph must be specified.""", + ), VALIDATE_PROFILES_PARAMETER, REASON_REASONER_PARAMETER, MAX_RAM_PERCENTAGE_PARAMETER, @@ -163,7 +168,8 @@ ), name="data_graph_iri", label="Data graph IRI", - description="The IRI of the input data graph.", + description="""The IRI of the input data graph. At least one of data graph and + ontology graph must be specified.""", ), PluginParameter( param_type=GraphParameterType( @@ -285,7 +291,7 @@ label="Output graph import", description="""Add the triple owl:imports to the output graph or add the triple owl:imports to - the ontology graph.""", + the ontology graph. Needs an ontology graph.""", default_value="none", ), PluginParameter( @@ -301,10 +307,10 @@ class ReasonPlugin(WorkflowPlugin): """Reason plugin""" - def __init__( # noqa: PLR0913 C901 PLR0917 + def __init__( # noqa: PLR0913, PLR0917 self, - data_graph_iri: str, - ontology_graph_iri: str, + data_graph_iri: str = "", + ontology_graph_iri: str = "", ignore_missing_imports: bool = False, output_graph_iri: str | None = None, reasoner: str | None = None, @@ -340,17 +346,9 @@ def __init__( # noqa: PLR0913 C901 PLR0917 "ObjectPropertyRange": object_property_range, "ObjectPropertyDomain": object_property_domain, } - errors = "" - if not is_valid_uri(data_graph_iri): - errors += 'Invalid IRI for parameter "Data graph IRI". ' - if not is_valid_uri(ontology_graph_iri): - errors += 'Invalid IRI for parameter "Ontology graph IRI". ' - if not is_valid_uri(output_graph_iri): - errors += 'Invalid IRI for parameter "Result graph IRI". ' - if output_graph_iri == data_graph_iri: - errors += "Result graph IRI cannot be the same as the data graph IRI. " - if output_graph_iri == ontology_graph_iri: - errors += "Result graph IRI cannot be the same as the ontology graph IRI. " + errors = self.graph_parameter_errors( + data_graph_iri, ontology_graph_iri, output_graph_iri, imports, validate_profile + ) if reasoner not in REASONERS: errors += 'Invalid value for parameter "Reasoner". ' if True not in self.axioms.values(): @@ -389,6 +387,49 @@ def __init__( # noqa: PLR0913 C901 PLR0917 self.input_ports = FixedNumberOfInputs([]) self.output_port = None + @staticmethod + def graph_parameter_errors( + data_graph_iri: str, + ontology_graph_iri: str, + output_graph_iri: str | None, + imports: str, + validate_profile: bool, + ) -> str: + """Check the graph parameters; only one of data graph and ontology graph is needed""" + errors = "" + if not data_graph_iri and not ontology_graph_iri: + errors += "At least one of data graph IRI and ontology graph IRI must be specified. " + if data_graph_iri and not is_valid_uri(data_graph_iri): + errors += 'Invalid IRI for parameter "Data graph IRI". ' + if ontology_graph_iri and not is_valid_uri(ontology_graph_iri): + errors += 'Invalid IRI for parameter "Ontology graph IRI". ' + if not is_valid_uri(output_graph_iri): + errors += 'Invalid IRI for parameter "Result graph IRI". ' + if data_graph_iri and output_graph_iri == data_graph_iri: + errors += "Result graph IRI cannot be the same as the data graph IRI. " + if ontology_graph_iri and output_graph_iri == ontology_graph_iri: + errors += "Result graph IRI cannot be the same as the ontology graph IRI. " + if imports != "none" and not ontology_graph_iri: + errors += 'Parameter "Output graph import" needs an ontology graph IRI. ' + if validate_profile and not ontology_graph_iri: + errors += 'Parameter "Validate OWL2 profiles" needs an ontology graph IRI. ' + return errors + + @property + def input_graph_iris(self) -> list[str]: + """The specified input graphs, each once: data graph and/or ontology graph""" + return list(dict.fromkeys(i for i in (self.data_graph_iri, self.ontology_graph_iri) if i)) + + @property + def main_graph_iri(self) -> str: + """The graph passed to ROBOT; with two different inputs, the data graph""" + return self.input_graph_iris[0] + + @property + def two_inputs(self) -> bool: + """Whether two different input graphs are given, so the data graph imports the ontology""" + return len(self.input_graph_iris) > 1 + @staticmethod def underscore(word: str) -> str: """Make an underscored, lowercase form from the expression in the string""" @@ -406,7 +447,7 @@ def get_graphs(self, graphs: dict, missing: list) -> None: continue self.log.info(f"Fetching graph {iri}.") fetch_graph(self.client, iri, path) - if iri == self.data_graph_iri: + if iri == self.data_graph_iri and self.two_inputs: with path.open("a", encoding="utf-8") as file: file.write( f"\n<{iri}> " @@ -418,7 +459,7 @@ def get_graphs_tree(self) -> tuple[dict, list]: # noqa: C901 """Get graph import tree. Last item in graph_iris is output_graph_iri which is excluded""" missing = [] graphs = {} - for graph_iri in [self.data_graph_iri, self.ontology_graph_iri]: + for graph_iri in self.input_graph_iris: if graph_iri not in graphs: graphs[graph_iri] = f"{uuid4().hex}.nt" tree = self.client.graph_imports.get_import_tree(graph_iri) @@ -443,8 +484,9 @@ def get_graphs_tree(self) -> tuple[dict, list]: # noqa: C901 def reason(self, graphs: dict) -> None: """Reason""" axioms = " ".join(k for k, v in self.axioms.items() if v) - data_location = f"{self.temp}/{graphs[self.data_graph_iri]}" - label = get_output_graph_label(self, self.data_graph_iri, "Reasoning Results") + data_location = f"{self.temp}/{graphs[self.main_graph_iri]}" + label = get_output_graph_label(self, self.main_graph_iri, "Reasoning Results") + sources = " ".join(f'--link-annotation dc:source "{iri}"' for iri in self.input_graph_iris) cmd = ( f'reason --input "{data_location}" ' f"--reasoner {self.reasoner} " @@ -459,11 +501,8 @@ def reason(self, graphs: dict) -> None: f'annotate --ontology-iri "{self.output_graph_iri}" ' f"--remove-annotations " f'--language-annotation rdfs:label "{label}" en ' - f"--language-annotation rdfs:comment " - f'"Reasoning results of data graph <{self.data_graph_iri}> with ontology ' - f'<{self.ontology_graph_iri}>" en ' - f'--link-annotation dc:source "{self.data_graph_iri}" ' - f'--link-annotation dc:source "{self.ontology_graph_iri}" ' + f'--language-annotation rdfs:comment "{self.result_comment()}" en ' + f"{sources} " f'--output "{self.temp}/result.ttl"' ) response = robot(cmd, self.max_ram_percentage) @@ -474,6 +513,28 @@ def reason(self, graphs: dict) -> None: raise OSError(response.stderr.decode()) raise OSError("ROBOT error") + def result_comment(self) -> str: + """Describe the input graphs of the reasoning result""" + if self.two_inputs: + return ( + f"Reasoning results of data graph <{self.data_graph_iri}> with ontology " + f"<{self.ontology_graph_iri}>" + ) + # one graph, whichever field it is in: its role is not known + return f"Reasoning results of graph <{self.main_graph_iri}>" + + def add_ontology_import(self) -> None: + """Add ontology graph import to output graph""" + query = f""" + INSERT DATA {{ + GRAPH <{self.output_graph_iri}> {{ + <{self.output_graph_iri}> + <{self.ontology_graph_iri}> + }} + }} + """ + self.client.store.sparql.update(query) + def add_result_import(self) -> None: """Add result graph import to ontology graph""" query = f""" @@ -519,7 +580,10 @@ def _execute(self) -> None: if self.imports == "import_result": self.add_result_import() - if self.imports != "import_ontology" and not self.data_imports_ontology: + if self.imports == "import_ontology" and not self.two_inputs: + # with two inputs, the import added to the data graph is carried into the output + self.add_ontology_import() + if self.two_inputs and self.imports != "import_ontology" and not self.data_imports_ontology: self.remove_ontology_import() self.context.report.update( @@ -534,11 +598,7 @@ def execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None """Execute plugin with temporary directory""" self.context = context self.client = get_client(context) - not_exist = [ - iri - for iri in (self.data_graph_iri, self.ontology_graph_iri) - if iri not in self.client.graphs - ] + not_exist = [iri for iri in self.input_graph_iris if iri not in self.client.graphs] if not_exist: raise ValueError(f"Graphs do not exist: {', '.join(not_exist)}") diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py index fd88070..74d1ccb 100644 --- a/cmem_plugin_reason/plugin_validate.py +++ b/cmem_plugin_reason/plugin_validate.py @@ -23,7 +23,6 @@ IGNORE_MISSING_IMPORTS_PARAMETER, MAX_RAM_PERCENTAGE_DEFAULT, MAX_RAM_PERCENTAGE_PARAMETER, - ONTOLOGY_GRAPH_IRI_PARAMETER, REASONERS, VALIDATE_PROFILES_PARAMETER, VALIDATE_REASONER_PARAMETER, @@ -41,6 +40,8 @@ ) LABEL = "Validate OWL consistency" +OWL_ONTOLOGY = "http://www.w3.org/2002/07/owl#Ontology" +VOID_DATASET = "http://rdfs.org/ns/void#Dataset" @Plugin( @@ -50,7 +51,12 @@ icon=Icon(file_name="file-icons--owl.svg", package=__package__), parameters=[ IGNORE_MISSING_IMPORTS_PARAMETER, - ONTOLOGY_GRAPH_IRI_PARAMETER, + PluginParameter( + param_type=GraphParameterType(classes=["http://www.w3.org/2002/07/owl#Ontology"]), + name="ontology_graph_iri", + label="Ontology graph IRI", + description="The IRI of the input ontology graph.", + ), MAX_RAM_PERCENTAGE_PARAMETER, VALIDATE_PROFILES_PARAMETER, VALIDATE_REASONER_PARAMETER, @@ -239,6 +245,25 @@ def explain(self, graphs: dict) -> None: raise OSError(response.stderr.decode()) raise OSError("ROBOT error") + def declare_dataset(self) -> None: + """Declare the output graph a void:Dataset instead of the owl:Ontology ROBOT declares it + + The output graph describes the validated ontology, it is not an ontology of its own. + """ + query = f""" + DELETE DATA {{ + GRAPH <{self.output_graph_iri}> {{ + <{self.output_graph_iri}> a <{OWL_ONTOLOGY}> . + }} + }}; + INSERT DATA {{ + GRAPH <{self.output_graph_iri}> {{ + <{self.output_graph_iri}> a <{VOID_DATASET}> . + }} + }} + """ + self.client.store.sparql.update(query) + def make_resource(self, context: ExecutionContext) -> None: """Make MD resource in project""" self.client.files.import_item( @@ -283,6 +308,7 @@ def _execute(self) -> Entities | None: return None if self.output_graph_iri: send_result(self.client, self.output_graph_iri, get_file_with_datetime(self)) + self.declare_dataset() post_provenance(self) if cancel_workflow(self): return None diff --git a/cmem_plugin_reason/robot.jar b/cmem_plugin_reason/robot.jar index bbffbca..128e387 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 1d8faf9..cb3685b 100644 --- a/cmem_plugin_reason/utils.py +++ b/cmem_plugin_reason/utils.py @@ -1,5 +1,6 @@ """Common constants and functions""" +import inspect import re import shlex from collections import OrderedDict @@ -17,9 +18,9 @@ from cmem_plugin_base.dataintegration.context import ExecutionReport from cmem_plugin_base.dataintegration.description import PluginParameter from cmem_plugin_base.dataintegration.parameter.choice import ChoiceParameterType -from cmem_plugin_base.dataintegration.parameter.graph import GraphParameterType from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin from cmem_plugin_base.dataintegration.types import BoolParameterType, IntParameterType +from cmem_plugin_base.dataintegration.utils import generate_id from defusedxml import minidom from . import __path__ @@ -28,6 +29,9 @@ NT_EXPORT_CONFIG = GraphExportConfig(serialization=GraphsRepository.formats["n-triples"]) +DI_FUNCTIONS = "https://vocab.eccenca.com/di/functions/" +DI_TASKS = "http://dataintegration.eccenca.com/" + REASONERS = OrderedDict( { "elk": "ELK", @@ -59,13 +63,6 @@ compatibility.""", ) -ONTOLOGY_GRAPH_IRI_PARAMETER = PluginParameter( - param_type=GraphParameterType(classes=["http://www.w3.org/2002/07/owl#Ontology"]), - name="ontology_graph_iri", - label="Ontology graph IRI", - description="The IRI of the input ontology graph.", -) - MAX_RAM_PERCENTAGE_PARAMETER = PluginParameter( param_type=IntParameterType(), name="max_ram_percentage", @@ -127,7 +124,9 @@ def post_provenance(plugin: WorkflowPlugin) -> None: if prov: param_sparql = "" for name, iri in prov["parameters"].items(): - param_sparql += f'\n<{prov["plugin_iri"]}> <{iri}> "{plugin.__dict__[name]}" .' + # only record parameters that are exposed as plugin attributes + if name in plugin.__dict__: + param_sparql += f'\n<{prov["plugin_iri"]}> <{iri}> "{plugin.__dict__[name]}" .' insert_query = f""" INSERT DATA {{ GRAPH <{plugin.output_graph_iri}> {{ @@ -145,61 +144,39 @@ def post_provenance(plugin: WorkflowPlugin) -> None: def get_provenance(plugin: WorkflowPlugin) -> dict | None: - """Get provenance information""" - plugin_iri = ( - f"http://dataintegration.eccenca.com/{plugin.context.task.project_id()}/" - f"{plugin.context.task.task_id()}" - ) - project_graph = f"http://di.eccenca.com/project/{plugin.context.task.project_id()}" + """Get provenance information for the running plugin task, as a snapshot of the task. - type_query = f""" - SELECT ?type {{ - GRAPH <{project_graph}> {{ - <{plugin_iri}> a ?type . - FILTER(STRSTARTS(STR(?type), "https://vocab.eccenca.com/di/functions/")) - }} - }} + Everything is derived from the plugin class and the execution context, not read from the + project graph: that graph only exists if the workspace is stored as RDF (workspace provider + "backend" or "fileAndDataPlatform"). """ - - type_rows = list(plugin.client.store.sparql.query(type_query)) - - if not type_rows: + task = getattr(plugin.context, "task", None) + if task is None: plugin.log.warning("Could not add provenance data to output graph.") return None - plugin_type = str(type_rows[0]["type"]) - - param_split = ( - plugin_type.replace( - "https://vocab.eccenca.com/di/functions/Plugin_", - "https://vocab.eccenca.com/di/functions/param_", - ) - + "_" - ) - - parameter_query = f""" - SELECT ?parameter {{ - GRAPH <{project_graph}> {{ - <{plugin_iri}> ?parameter ?o . - FILTER(STRSTARTS(STR(?parameter), "https://vocab.eccenca.com/di/functions/param_")) - }} - }} - """ - - new_plugin_iri = f"{'_'.join(plugin_iri.split('_')[:-1])}_{token_hex(8)}" - label = f"{plugin.label} plugin" - parameters = {} - - for row in plugin.client.store.sparql.query(parameter_query): - param_iri = str(row["parameter"]) - param_name = param_iri.split(param_split)[1] - parameters[param_name] = param_iri + # The plugin ID and parameters are derived the way cmem-plugin-base does for a @Plugin without + # an explicit plugin_id - if one is ever set, use it here too. They are not looked up in + # Plugin.plugins: DataIntegration's plugin discovery empties that list for every + # cmem_plugin_* package it imports, so at execution time it only holds the last package's. + plugin_class = type(plugin) + plugin_id = generate_id(f"{plugin_class.__module__}-{plugin_class.__name__}".replace(".", "-")) + parameter_names = [ + name for name in inspect.signature(plugin_class.__init__).parameters if name != "self" + ] + # The same IRIs DataIntegration uses for the task type and its parameters in the project graph + plugin_type = f"{DI_FUNCTIONS}Plugin_{plugin_id}" + param_prefix = f"{DI_FUNCTIONS}param_{plugin_id}_" + # A snapshot of the task: replace the random suffix of the task ID, so that the provenance + # does not merge with the live task + task_name = task.task_id().rsplit("_", 1)[0] + plugin_iri = f"{DI_TASKS}{task.project_id()}/{task_name}_{token_hex(8)}" return { - "plugin_iri": new_plugin_iri, - "plugin_label": label, + "plugin_iri": plugin_iri, + "plugin_label": f"{plugin.label} plugin", "plugin_type": plugin_type, - "parameters": parameters, + "parameters": {name: f"{param_prefix}{name}" for name in parameter_names}, } diff --git a/poetry.lock b/poetry.lock index 3d4b9df..54dc876 100644 --- a/poetry.lock +++ b/poetry.lock @@ -33,69 +33,69 @@ trio = ["trio (>=0.32.0)"] [[package]] name = "ast-serialize" -version = "0.11.2" +version = "0.12.1" description = "Python bindings for mypy AST serialization" optional = false python-versions = ">=3.7" groups = ["dev"] files = [ - {file = "ast_serialize-0.11.2-cp314-cp314-pyemscripten_2026_0_wasm32.whl", hash = "sha256:f6a8dfc5ab204a706f6e5d39c6f77c18c27ef084fa2081803a64a9160ce89277"}, - {file = "ast_serialize-0.11.2-cp314-cp314t-macosx_10_12_x86_64.whl", hash = "sha256:cb073bfa15742699d408ac50f60878383b5665ae1791d1b6799ea6f08633cd77"}, - {file = "ast_serialize-0.11.2-cp314-cp314t-macosx_11_0_arm64.whl", hash = "sha256:1d6ad94edbe93bf1dabc06c9f37d55b898fdabc456aa6d7ced5e23c14f795f32"}, - 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"pkg:maven/org.liveontologies/puli@0.1.0?type=jar", + "dependsOn" : [ + "pkg:maven/com.google.guava/guava@33.5.0-jre?type=jar", + "pkg:maven/org.slf4j/slf4j-api@2.0.11?type=jar" + ] + }, + { + "ref" : "pkg:maven/org.liveontologies/owlapi-proof@0.1.0?type=jar", + "dependsOn" : [ + "pkg:maven/org.liveontologies/puli@0.1.0?type=jar" + ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-owl-model@0.6.0?type=jar", + "dependsOn" : [ + "pkg:maven/io.github.liveontologies/elk-util-hashing@0.6.0?type=jar" + ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-util-hashing@0.6.0?type=jar", + "dependsOn" : [ ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-reasoner@0.6.0?type=jar", + "dependsOn" : [ + "pkg:maven/io.github.liveontologies/elk-owl-model@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-owl-implementation@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-collections@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-concurrent@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-hashing@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-logging@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-common@0.6.0?type=jar", + "pkg:maven/com.google.guava/guava@33.5.0-jre?type=jar", + "pkg:maven/org.slf4j/slf4j-api@2.0.11?type=jar" + ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-owl-implementation@0.6.0?type=jar", + "dependsOn" : [ + "pkg:maven/io.github.liveontologies/elk-owl-model@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-common@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-hashing@0.6.0?type=jar" + ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-util-common@0.6.0?type=jar", + "dependsOn" : [ + "pkg:maven/org.slf4j/slf4j-api@2.0.11?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-io@0.6.0?type=jar" + ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-util-io@0.6.0?type=jar", + "dependsOn" : [ ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-util-collections@0.6.0?type=jar", + "dependsOn" : [ + "pkg:maven/com.google.guava/guava@33.5.0-jre?type=jar" + ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-util-concurrent@0.6.0?type=jar", + "dependsOn" : [ ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-util-logging@0.6.0?type=jar", + "dependsOn" : [ + "pkg:maven/org.slf4j/slf4j-api@2.0.11?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-hashing@0.6.0?type=jar" + ] + }, + { + "ref" : "pkg:maven/io.github.liveontologies/elk-proofs@0.6.0?type=jar", + "dependsOn" : [ + "pkg:maven/io.github.liveontologies/elk-reasoner@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-common@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-collections@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-util-hashing@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-owl-model@0.6.0?type=jar", + "pkg:maven/io.github.liveontologies/elk-owl-implementation@0.6.0?type=jar", + "pkg:maven/org.liveontologies/puli@0.1.0?type=jar", + "pkg:maven/com.google.guava/guava@33.5.0-jre?type=jar", + "pkg:maven/org.slf4j/slf4j-api@2.0.11?type=jar" + ] + }, + { + "ref" : "pkg:maven/net.sourceforge.owlapi/org.semanticweb.hermit@1.4.5.456?type=jar", + "dependsOn" : [ + "pkg:maven/org.apache.ws.commons.axiom/axiom-api@1.2.14?type=jar", + "pkg:maven/org.apache.ws.commons.axiom/axiom-c14n@1.2.14?type=jar", + "pkg:maven/org.apache.ws.commons.axiom/axiom-impl@1.2.14?type=jar", + "pkg:maven/org.apache.ws.commons.axiom/axiom-dom@1.2.14?type=jar", + "pkg:maven/dk.brics.automaton/automaton@1.11-8?type=jar", + "pkg:maven/gnu.getopt/java-getopt@1.0.13?type=jar" + ] + }, + { + "ref" : "pkg:maven/org.apache.ws.commons.axiom/axiom-api@1.2.14?type=jar", + "dependsOn" : [ + "pkg:maven/org.apache.james/apache-mime4j-core@0.8.13?type=jar" + ] + }, + { + "ref" : "pkg:maven/org.apache.ws.commons.axiom/axiom-c14n@1.2.14?type=jar", + "dependsOn" : [ + "pkg:maven/org.apache.ws.commons.axiom/axiom-api@1.2.14?type=jar", + "pkg:maven/org.apache.ws.commons.axiom/axiom-impl@1.2.14?type=jar" + ] + }, + { + "ref" : "pkg:maven/org.apache.ws.commons.axiom/axiom-impl@1.2.14?type=jar", + "dependsOn" : [ + "pkg:maven/org.apache.ws.commons.axiom/axiom-api@1.2.14?type=jar" + ] + }, + { + "ref" : "pkg:maven/org.apache.ws.commons.axiom/axiom-dom@1.2.14?type=jar", + "dependsOn" : [ + "pkg:maven/org.apache.ws.commons.axiom/axiom-api@1.2.14?type=jar" + ] + }, + { + "ref" : "pkg:maven/dk.brics.automaton/automaton@1.11-8?type=jar", + "dependsOn" : [ ] + }, + { + "ref" : "pkg:maven/gnu.getopt/java-getopt@1.0.13?type=jar", + "dependsOn" : [ ] + }, + { + "ref" : "pkg:maven/net.sourceforge.owlapi/jfact@4.0.4?type=jar", + "dependsOn" : [ + "pkg:maven/net.sf.trove4j/trove4j@3.0.3?type=jar", + "pkg:maven/joda-time/joda-time@2.3?type=jar", + "pkg:maven/org.roaringbitmap/RoaringBitmap@0.4.9?type=jar" + ] + }, + { + "ref" : "pkg:maven/net.sf.trove4j/trove4j@3.0.3?type=jar", + "dependsOn" : [ ] + }, + { + "ref" : "pkg:maven/joda-time/joda-time@2.3?type=jar", + "dependsOn" : [ ] + } + ] +} \ No newline at end of file diff --git a/tests/fixture_dir/test_validate_output_elk.ttl b/tests/fixture_dir/test_validate_output_elk.ttl index 643e0df..a963baf 100644 --- a/tests/fixture_dir/test_validate_output_elk.ttl +++ b/tests/fixture_dir/test_validate_output_elk.ttl @@ -5,7 +5,7 @@ @prefix xsd: . - a owl:Ontology ; + a ; rdfs:label "Eccenca Validate Vocabulary - Validation Result"@en ; rdfs:comment "Ontology validation of "@en ; dc:source . diff --git a/tests/fixture_dir/test_validate_output_emr.ttl b/tests/fixture_dir/test_validate_output_emr.ttl index 74cd57a..32e9e78 100644 --- a/tests/fixture_dir/test_validate_output_emr.ttl +++ b/tests/fixture_dir/test_validate_output_emr.ttl @@ -3,7 +3,7 @@ @prefix owl: . @prefix rdfs: . - a owl:Ontology ; + a ; rdfs:label "Eccenca Validate Vocabulary - Validation Result"@en ; dcterms:source ; rdfs:comment "Ontology validation of "@en . diff --git a/tests/fixture_dir/test_validate_output_hermit.ttl b/tests/fixture_dir/test_validate_output_hermit.ttl index 74cd57a..32e9e78 100644 --- a/tests/fixture_dir/test_validate_output_hermit.ttl +++ b/tests/fixture_dir/test_validate_output_hermit.ttl @@ -3,7 +3,7 @@ @prefix owl: . @prefix rdfs: . - a owl:Ontology ; + a ; rdfs:label "Eccenca Validate Vocabulary - Validation Result"@en ; dcterms:source ; rdfs:comment "Ontology validation of "@en . diff --git a/tests/fixture_dir/test_validate_output_jfact.ttl b/tests/fixture_dir/test_validate_output_jfact.ttl index 74cd57a..32e9e78 100644 --- a/tests/fixture_dir/test_validate_output_jfact.ttl +++ b/tests/fixture_dir/test_validate_output_jfact.ttl @@ -3,7 +3,7 @@ @prefix owl: . @prefix rdfs: . - a owl:Ontology ; + a ; rdfs:label "Eccenca Validate Vocabulary - Validation Result"@en ; dcterms:source ; rdfs:comment "Ontology validation of "@en . diff --git a/tests/fixture_dir/test_validate_output_structural.ttl b/tests/fixture_dir/test_validate_output_structural.ttl index 9545624..bf03757 100644 --- a/tests/fixture_dir/test_validate_output_structural.ttl +++ b/tests/fixture_dir/test_validate_output_structural.ttl @@ -3,7 +3,7 @@ @prefix owl: . @prefix rdfs: . - a owl:Ontology ; + a ; rdfs:label "Eccenca Validate Vocabulary - Validation Result"@en ; dcterms:source ; rdfs:comment "Ontology validation of "@en . diff --git a/tests/fixture_dir/test_validate_output_whelk.ttl b/tests/fixture_dir/test_validate_output_whelk.ttl index 74cd57a..32e9e78 100644 --- a/tests/fixture_dir/test_validate_output_whelk.ttl +++ b/tests/fixture_dir/test_validate_output_whelk.ttl @@ -3,7 +3,7 @@ @prefix owl: . @prefix rdfs: . - a owl:Ontology ; + a ; rdfs:label "Eccenca Validate Vocabulary - Validation Result"@en ; dcterms:source ; rdfs:comment "Ontology validation of "@en . diff --git a/tests/test_reason.py b/tests/test_reason.py index f14f020..5d46c83 100644 --- a/tests/test_reason.py +++ b/tests/test_reason.py @@ -1,22 +1,26 @@ """Plugin tests.""" +import os +import tempfile from collections.abc import Generator from typing import Any import pytest from cmem_plugin_base.testing import TestExecutionContext -from rdflib import Graph +from rdflib import DCTERMS, OWL, RDF, RDFS, Graph, Literal, URIRef from rdflib.compare import isomorphic from cmem_plugin_reason.plugin_reason import ReasonPlugin from cmem_plugin_reason.utils import REASONERS from tests.utils import ( FIXTURE_DIR, + REGISTRY_STATES, UID, get_remote_graph, get_test_client, import_graph, replace_uuid, + simulate_dataintegration_discovery, ) REASON_DATA_GRAPH_IRI = f"https://ns.eccenca.com/reasoning/{UID}/data/" @@ -92,6 +96,143 @@ def test_reason(setup: None, reasoner_parameter: str) -> None: assert isomorphic(result, test) +@REGISTRY_STATES +def test_reason_provenance( + setup: None, monkeypatch: pytest.MonkeyPatch, after_discovery: bool +) -> None: + """Test Reason writes provenance without needing the project graph or the plugin registry""" + if after_discovery: + simulate_dataintegration_discovery(monkeypatch) + ReasonPlugin( + data_graph_iri=REASON_DATA_GRAPH_IRI, + ontology_graph_iri=REASON_ONTOLOGY_GRAPH_IRI_1, + output_graph_iri=REASON_RESULT_GRAPH_IRI, + reasoner="structural", + class_assertion=True, + ).execute(inputs=(), context=TestExecutionContext()) + + result = get_remote_graph(get_test_client(), REASON_RESULT_GRAPH_IRI, provenance=True) + tasks = list(result.objects(URIRef(REASON_RESULT_GRAPH_IRI), DCTERMS.creator)) + assert len(tasks) == 1 + task = tasks[0] + # a snapshot of the task, not the task itself + assert str(task).startswith("http://dataintegration.eccenca.com/TestProject/TestTask_") + functions = "https://vocab.eccenca.com/di/functions/" + assert ( + task, + RDF.type, + URIRef(f"{functions}Plugin_cmem_plugin_reason-plugin_reason-ReasonPlugin"), + ) in result + assert (task, RDFS.label, Literal("Reason plugin")) in result + assert ( + task, + URIRef(f"{functions}param_cmem_plugin_reason-plugin_reason-ReasonPlugin_reasoner"), + Literal("structural"), + ) in result + + +def test_reason_no_input_graph() -> None: + """Test Reason needs at least one of data graph and ontology graph""" + with pytest.raises( + ValueError, + match=r"At least one of data graph IRI and ontology graph IRI must be specified\.", + ): + ReasonPlugin(output_graph_iri=REASON_RESULT_GRAPH_IRI, reasoner="hermit") + + +@pytest.mark.parametrize("imports", ["import_ontology", "import_result"]) +def test_reason_output_graph_import_needs_ontology(imports: str) -> None: + """Test the output graph import is rejected without an ontology graph""" + with pytest.raises(ValueError, match='"Output graph import" needs an ontology graph IRI'): + ReasonPlugin( + data_graph_iri=REASON_DATA_GRAPH_IRI, + output_graph_iri=REASON_RESULT_GRAPH_IRI, + reasoner="hermit", + imports=imports, + ) + + +def use_real_temp_path(monkeypatch: pytest.MonkeyPatch) -> None: + """Give the plugin a temporary directory whose path contains no symbolic link + + On macOS the default one is under /var, a link to /private/var. ROBOT then sees the input + file and the same file resolved through the catalog under two different paths, which hides + a document being loaded twice - on Linux (/tmp) it fails. + """ + monkeypatch.setattr(tempfile, "tempdir", os.path.realpath(tempfile.gettempdir())) + + +def reason_and_fetch(data_graph_iri: str, ontology_graph_iri: str, imports: str = "none") -> Graph: + """Run Reason into the result graph and fetch it""" + ReasonPlugin( + data_graph_iri=data_graph_iri, + ontology_graph_iri=ontology_graph_iri, + output_graph_iri=REASON_RESULT_GRAPH_IRI, + reasoner="hermit", + sub_class=True, + class_assertion=True, + imports=imports, + ).execute(inputs=(), context=TestExecutionContext()) + return get_remote_graph(get_test_client(), REASON_RESULT_GRAPH_IRI) + + +def test_reason_same_graph_for_data_and_ontology( + setup: None, monkeypatch: pytest.MonkeyPatch +) -> None: + """Test Reason with the same graph as data and ontology graph reasons over that graph""" + use_real_temp_path(monkeypatch) + same = reason_and_fetch(REASON_ONTOLOGY_GRAPH_IRI_1, REASON_ONTOLOGY_GRAPH_IRI_1) + ontology_only = reason_and_fetch("", REASON_ONTOLOGY_GRAPH_IRI_1) + + assert isomorphic(same, ontology_only) + output = URIRef(REASON_RESULT_GRAPH_IRI) + comment = f"Reasoning results of graph <{REASON_ONTOLOGY_GRAPH_IRI_1}>" + assert (output, RDFS.comment, Literal(comment, lang="en")) in same + assert list(same.objects(output, DCTERMS.source)) == [URIRef(REASON_ONTOLOGY_GRAPH_IRI_1)] + assert (None, RDFS.subClassOf, None) in same + # the input graph's own imports are kept, but it does not import itself + assert (output, OWL.imports, URIRef(REASON_ONTOLOGY_GRAPH_IRI_1)) not in same + + +def test_reason_data_graph_only(setup: None) -> None: + """Test Reason with only a data graph""" + result = reason_and_fetch(REASON_DATA_GRAPH_IRI, "") + + output = URIRef(REASON_RESULT_GRAPH_IRI) + comment = f"Reasoning results of graph <{REASON_DATA_GRAPH_IRI}>" + assert (output, RDFS.comment, Literal(comment, lang="en")) in result + assert list(result.objects(output, DCTERMS.source)) == [URIRef(REASON_DATA_GRAPH_IRI)] + + +def test_reason_ontology_graph_only(setup: None) -> None: + """Test Reason with only an ontology graph""" + result = reason_and_fetch("", REASON_ONTOLOGY_GRAPH_IRI_1) + + output = URIRef(REASON_RESULT_GRAPH_IRI) + comment = f"Reasoning results of graph <{REASON_ONTOLOGY_GRAPH_IRI_1}>" + assert (output, RDFS.comment, Literal(comment, lang="en")) in result + assert list(result.objects(output, DCTERMS.source)) == [URIRef(REASON_ONTOLOGY_GRAPH_IRI_1)] + assert (None, RDFS.subClassOf, None) in result + + +def test_reason_same_graph_output_graph_import( + setup: None, monkeypatch: pytest.MonkeyPatch +) -> None: + """Test both output graph imports with the same graph as data and ontology graph""" + use_real_temp_path(monkeypatch) + output = URIRef(REASON_RESULT_GRAPH_IRI) + ontology = URIRef(REASON_ONTOLOGY_GRAPH_IRI_1) + + result = reason_and_fetch( + REASON_ONTOLOGY_GRAPH_IRI_1, REASON_ONTOLOGY_GRAPH_IRI_1, "import_ontology" + ) + assert (output, OWL.imports, ontology) in result + + reason_and_fetch(REASON_ONTOLOGY_GRAPH_IRI_1, REASON_ONTOLOGY_GRAPH_IRI_1, "import_result") + ontology_graph = get_remote_graph(get_test_client(), REASON_ONTOLOGY_GRAPH_IRI_1) + assert (ontology, OWL.imports, output) in ontology_graph + + def test_reason_input_not_exist(setup: None) -> None: """Test Reason with non-existing input graph""" plugin = ReasonPlugin( diff --git a/tests/test_validate.py b/tests/test_validate.py index 596fc86..598b5c3 100644 --- a/tests/test_validate.py +++ b/tests/test_validate.py @@ -7,18 +7,20 @@ from cmem_client.models.project import Project from cmem_plugin_base.dataintegration.entity import Entities from cmem_plugin_base.testing import TestExecutionContext -from rdflib import Graph +from rdflib import DCTERMS, OWL, RDF, RDFS, VOID, Graph, Literal, URIRef from rdflib.compare import isomorphic from cmem_plugin_reason.plugin_validate import ValidatePlugin from cmem_plugin_reason.utils import REASONERS from tests.utils import ( FIXTURE_DIR, + REGISTRY_STATES, UID, get_remote_graph, get_test_client, import_graph, replace_uuid, + simulate_dataintegration_discovery, ) VALIDATE_ONTOLOGY_GRAPH_IRI_1 = f"https://ns.eccenca.com/validateontology/{UID}/vocab/" @@ -120,6 +122,44 @@ def test_validate(setup: None, reasoner_parameter: str) -> None: raise OSError(val_errors[:-1]) +@REGISTRY_STATES +def test_validate_output_graph_provenance( + setup: None, monkeypatch: pytest.MonkeyPatch, after_discovery: bool +) -> None: + """Test Validate declares the output graph a void:Dataset and writes provenance""" + if after_discovery: + simulate_dataintegration_discovery(monkeypatch) + ValidatePlugin( + ontology_graph_iri=VALIDATE_ONTOLOGY_GRAPH_IRI_1, + output_graph_iri=VALIDATE_RESULT_GRAPH_IRI, + reasoner="hermit", + md_filename=MD_FILENAME, + mode="inconsistency", + ).execute(inputs=(), context=TestExecutionContext(PROJECT_ID)) + + result = get_remote_graph(get_test_client(), VALIDATE_RESULT_GRAPH_IRI, provenance=True) + tasks = list(result.objects(URIRef(VALIDATE_RESULT_GRAPH_IRI), DCTERMS.creator)) + assert len(tasks) == 1 + task = tasks[0] + # a snapshot of the task, not the task itself + assert str(task).startswith(f"http://dataintegration.eccenca.com/{PROJECT_ID}/TestTask_") + functions = "https://vocab.eccenca.com/di/functions/" + assert ( + task, + RDF.type, + URIRef(f"{functions}Plugin_cmem_plugin_reason-plugin_validate-ValidatePlugin"), + ) in result + assert (task, RDFS.label, Literal("Validate OWL consistency plugin")) in result + assert ( + task, + URIRef(f"{functions}param_cmem_plugin_reason-plugin_validate-ValidatePlugin_reasoner"), + Literal("hermit"), + ) in result + output = URIRef(VALIDATE_RESULT_GRAPH_IRI) + assert (output, RDF.type, VOID.Dataset) in result + assert (output, RDF.type, OWL.Ontology) not in result + + def test_validate_input_not_exist(setup: None) -> None: """Test Validate with non-existing input graph""" plugin = ValidatePlugin( diff --git a/tests/utils.py b/tests/utils.py index 348e662..21cbc47 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -3,10 +3,12 @@ from pathlib import Path from tempfile import TemporaryDirectory +import pytest from cmem_client.client import Client from cmem_client.repositories.graphs import GraphExportConfig, GraphsRepository from cmem_client.repositories.protocols.import_item import ImportConflictPolicy from cmem_plugin_base.dataintegration.client import get_client +from cmem_plugin_base.dataintegration.description import Plugin from cmem_plugin_base.testing import TestPluginContext from rdflib import DCTERMS, OWL, RDF, Graph, URIRef @@ -28,17 +30,38 @@ def get_test_client() -> Client: return get_client(TestPluginContext()) -def get_remote_graph(client: Client, iri: str) -> Graph: - """Get remote graph IRI""" +def get_remote_graph(client: Client, iri: str, provenance: bool = False) -> Graph: + """Get remote graph IRI, without the provenance data unless requested""" with TemporaryDirectory() as temp: path = Path(temp) / "graph.ttl" client.graphs.export_item(key=iri, path=path, configuration=TTL_EXPORT_CONFIG) graph = Graph().parse(source=path, format="turtle") graph.remove((URIRef(iri), DCTERMS.created, None)) graph.remove((None, RDF.type, OWL.AnnotationProperty)) + if not provenance: + for task in list(graph.objects(URIRef(iri), DCTERMS.creator)): + graph.remove((task, None, None)) + graph.remove((URIRef(iri), DCTERMS.creator, None)) return graph +#: Parametrizes a test over the plugin registry as pytest leaves it and as DataIntegration does +REGISTRY_STATES = pytest.mark.parametrize( + "after_discovery", [False, True], ids=["plugin registered", "after DataIntegration discovery"] +) + + +def simulate_dataintegration_discovery(monkeypatch: pytest.MonkeyPatch) -> None: + """Leave Plugin.plugins as DataIntegration's plugin discovery does at execution time + + DataIntegration discovers every installed cmem_plugin_* package, and the import of each one + starts with emptying Plugin.plugins. So when a task runs, the list holds only the plugins of + the last package discovered - normally not this one. Within pytest only this package is + imported, so the plugins stay registered unless a test empties the list. + """ + monkeypatch.setattr(Plugin, "plugins", []) + + def import_graph(client: Client, iri: str, filepath: str) -> None: """Import graph to CMEM""" with TemporaryDirectory() as temp: