diff --git a/CHANGELOG.md b/CHANGELOG.md index 98747bb..2c13a6f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,19 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](https://semver.org/) +## [1.0.0beta2] 2024-07-04 + +### Fixed + +- `prov:wasGeneratedBy` in output graphs now refers to a plugin IRI instead of a literal + +### Changed + +- keep original output ("No explanations found.") if no inconsistencies found with Validate plugin +- provenance data in output graphs now includes plugin parameter settings +- new icons + + ## [1.0.0beta1] 2024-07-01 ### Fixed @@ -13,14 +26,15 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p ### Changed - complete validation for IRI parameters -- Remove "Annnotate inferred subclass axioms" parameter +- remove "Annnotate inferred subclass axioms" parameter in Reason plugin +- new icons ## [1.0.0alpha3] 2024-06-28 ### Added - "Annotate inferred axioms" parameter in Reason plugin -- "Maximum RAM percentage" parameter in Reason and Validate plugins +- "Maximum RAM percentage" parameter ### Changed diff --git a/README.md b/README.md index 370a27b..4aeae68 100644 --- a/README.md +++ b/README.md @@ -90,7 +90,7 @@ Maximum heap size for the Java virtual machine in the DI container running the r # Validate -In case ontology inconsistencies are found, the plugin outputs the explanation as text in Markdown format using the path "text". +The plugin outputs the explanation as text in Markdown format using the path "text". ## Options @@ -122,6 +122,10 @@ The IRI of the output graph for the reasoning result. If enabled, an explanation markdown file is written to the project. +### Output filename + +The filename of the Markdown file with the explanation of inconsistencies. + :warning: Existing files will be overwritten. ### Stop at inconsistencies diff --git a/cmem_plugin_reason/obofoundry.png b/cmem_plugin_reason/obofoundry.png deleted file mode 100644 index 0cdc0a1..0000000 Binary files a/cmem_plugin_reason/obofoundry.png and /dev/null differ diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py index ab5908c..2059cbb 100644 --- a/cmem_plugin_reason/plugin_reason.py +++ b/cmem_plugin_reason/plugin_reason.py @@ -25,6 +25,7 @@ ROBOT, create_xml_catalog_file, get_graphs_tree, + post_provenance, remove_temp, send_result, ) @@ -32,12 +33,11 @@ @Plugin( label="Reason", - icon=Icon(file_name="obofoundry.png", package=__package__), - description="Given a data and an ontology graph, this task performs reasoning using ROBOT.", - documentation="""A task performing reasoning using ROBOT (ROBOT is an OBO Tool). - It takes an OWL ontology and a data graph as inputs and writes the reasoning result - to a specified graph. The following reasoner options are supported: ELK, Expression - Materializing Reasoner, HermiT, JFact, Structural Reasoner and Whelk.""", + icon=Icon(file_name="reason.png", package=__package__), + description="Performs OWL reasoning.", + documentation="""A task performing OWL reasoning. With an OWL ontology and a data graph as input + the reasoning result is written to a specified graph. The following reasoners are supported: + ELK, Expression Materializing Reasoner, HermiT, JFact, Structural Reasoner and Whelk.""", parameters=[ REASONER_PARAMETER, ONTOLOGY_GRAPH_IRI_PARAMETER, @@ -56,7 +56,7 @@ ), PluginParameter( param_type=StringParameterType(), - name="result_graph_iri", + name="output_graph_iri", label="Result graph IRI", description="The IRI of the output graph for the reasoning result. ⚠️ Existing graphs " "will be overwritten.", @@ -168,7 +168,7 @@ def __init__( # noqa: PLR0913 self, data_graph_iri: str = "", ontology_graph_iri: str = "", - result_graph_iri: str = "", + output_graph_iri: str = "", reasoner: str = "elk", class_assertion: bool = False, data_property_characteristic: bool = False, @@ -207,11 +207,11 @@ def __init__( # noqa: PLR0913 errors += 'Invalid IRI for parameter "Data graph IRI". ' if not validators.url(ontology_graph_iri): errors += 'Invalid IRI for parameter "Ontology graph IRI". ' - if not validators.url(result_graph_iri): + if not validators.url(output_graph_iri): errors += 'Invalid IRI for parameter "Result graph IRI". ' - if result_graph_iri and result_graph_iri == data_graph_iri: + if output_graph_iri and output_graph_iri == data_graph_iri: errors += "Result graph IRI cannot be the same as the data graph IRI. " - if result_graph_iri and result_graph_iri == ontology_graph_iri: + if output_graph_iri and output_graph_iri == ontology_graph_iri: errors += "Result graph IRI cannot be the same as the ontology graph IRI. " if reasoner not in REASONERS: errors += 'Invalid value for parameter "Reasoner". ' @@ -221,9 +221,23 @@ def __init__( # noqa: PLR0913 errors += 'Invalid value for parameter "Maximum RAM Percentage". ' if errors: raise ValueError(errors[:-1]) + self.sub_class = sub_class + self.equivalent_class = equivalent_class + self.disjoint_classes = disjoint_classes + self.data_property_characteristic = data_property_characteristic + self.equivalent_data_properties = equivalent_data_properties + self.sub_data_property = sub_data_property + self.class_assertion = class_assertion + self.property_assertion = property_assertion + self.equivalent_object_property = equivalent_object_property + self.inverse_object_properties = inverse_object_properties + self.object_property_characteristic = object_property_characteristic + self.sub_object_property = sub_object_property + self.object_property_range = object_property_range + self.object_property_domain = object_property_domain self.data_graph_iri = data_graph_iri self.ontology_graph_iri = ontology_graph_iri - self.result_graph_iri = result_graph_iri + self.output_graph_iri = output_graph_iri self.reasoner = reasoner self.max_ram_percentage = max_ram_percentage self.temp = f"reason_{uuid4().hex}" @@ -260,14 +274,12 @@ def reason(self, graphs: dict) -> None: f"--exclude-external-entities " f"reduce --reasoner {self.reasoner} " f'unmerge --input "{data_location}" ' - f'annotate --ontology-iri "{self.result_graph_iri}" ' + f'annotate --ontology-iri "{self.output_graph_iri}" ' f"--remove-annotations " f'--language-annotation rdfs:label "Eccenca Reasoning Result {utctime}" en ' f"--language-annotation rdfs:comment " f'"Reasoning result set of <{self.data_graph_iri}> and ' f'<{self.ontology_graph_iri}>" en ' - f"--language-annotation prov:wasGeneratedBy " - f'"cmem-plugin-reason ({self.reasoner})" en ' f'--link-annotation prov:wasDerivedFrom "{self.data_graph_iri}" ' f"--link-annotation prov:wasDerivedFrom " f'"{self.ontology_graph_iri}" ' @@ -290,5 +302,6 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> None: # noqa: AR create_xml_catalog_file(self.temp, graphs) self.reason(graphs) setup_cmempy_user_access(context.user) - send_result(self.result_graph_iri, Path(self.temp) / "result.ttl") - remove_temp(self, ["catalog-v001.xml", "result.ttl", *graphs.values()]) + send_result(self.output_graph_iri, Path(self.temp) / "result.ttl") + post_provenance(self, context) + remove_temp(self) diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py index eea52ca..a1c548e 100644 --- a/cmem_plugin_reason/plugin_validate.py +++ b/cmem_plugin_reason/plugin_validate.py @@ -32,16 +32,21 @@ ROBOT, create_xml_catalog_file, get_graphs_tree, + post_provenance, remove_temp, send_result, ) @Plugin( - label="Validate ontology consistency", - description="", - documentation="""""", - icon=Icon(package=__package__, file_name="obofoundry.png"), + label="Validate", + description="Validates the consistency of an OWL ontology.", + documentation="""A task validating the consistency of an OWL ontology and generating an + explanation if inconsistencies are found. The explanation can be written to the project as a + Markdown file and/or to a specified graph. The Markdown string is also provided as an output + entity using the path "text". The following reasoners are supported: ELK, Expression + Materializing Reasoner, HermiT, JFact, Structural Reasoner and Whelk.""", + icon=Icon(package=__package__, file_name="validate.png"), parameters=[ REASONER_PARAMETER, ONTOLOGY_GRAPH_IRI_PARAMETER, @@ -50,8 +55,7 @@ param_type=BoolParameterType(), name="write_md", label="Write Markdown explanation file", - description="Write Markdown file with explanation to project. ⚠️ Existing files will " - "be overwritten.", + description="Write Markdown file with explanation to project.", default_value=False, ), PluginParameter( @@ -73,7 +77,7 @@ name="md_filename", label="Output filename", description="The filename of the Markdown file with the explanation of " - "inconsistencies.", + "inconsistencies.⚠️ Existing files will be overwritten.", ), PluginParameter( param_type=BoolParameterType(), @@ -151,8 +155,6 @@ def validate(self, graphs: dict) -> None: f'--language-annotation rdfs:label "Ontology Validation Result {utctime}" en ' f"--language-annotation rdfs:comment " f'"Ontology validation of <{self.ontology_graph_iri}>" en ' - f"--language-annotation prov:wasGeneratedBy " - f'"cmem-plugin-validate ({self.reasoner})" en ' f'--link-annotation prov:wasDerivedFrom "{self.ontology_graph_iri}" ' f'--typed-annotation dc:created "{utctime}" xsd:dateTime ' f'--output "{self.temp}/output.ttl"' @@ -182,26 +184,21 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None: self.get_graphs(graphs, context) create_xml_catalog_file(self.temp, graphs) self.validate(graphs) - files = ["catalog-v001.xml", self.md_filename, *graphs.values()] - if self.produce_graph: - files.append("output.ttl") - - text = (Path(self.temp) / self.md_filename).read_text() - if text == "No explanations found.": - remove_temp(self, files) - return None if self.produce_graph: setup_cmempy_user_access(context.user) send_result(self.output_graph_iri, Path(self.temp) / "output.ttl") + setup_cmempy_user_access(context.user) + post_provenance(self, context) if self.write_md: setup_cmempy_user_access(context.user) self.make_resource(context) + text = (Path(self.temp) / self.md_filename).read_text() - remove_temp(self, files) + remove_temp(self) - if self.stop_at_inconsistencies: + if self.stop_at_inconsistencies and text != "No explanations found.": raise RuntimeError("Inconsistencies found in Ontology.") entities = [ diff --git a/cmem_plugin_reason/reason.png b/cmem_plugin_reason/reason.png new file mode 100644 index 0000000..4d479cb Binary files /dev/null and b/cmem_plugin_reason/reason.png differ diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py index eea73a7..71a788a 100644 --- a/cmem_plugin_reason/utils.py +++ b/cmem_plugin_reason/utils.py @@ -1,16 +1,21 @@ """Common constants and functions""" +import json import re import unicodedata from collections import OrderedDict from pathlib import Path +from secrets import token_hex +from shutil import rmtree from xml.etree.ElementTree import Element, SubElement, tostring from cmem.cmempy.dp.proxy.graph import get_graph_import_tree, post_streamed +from cmem.cmempy.dp.proxy.sparql import post as post_select +from cmem.cmempy.dp.proxy.update import post as post_update 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.plugins import ExecutionContext, WorkflowPlugin from cmem_plugin_base.dataintegration.types import IntParameterType from defusedxml import minidom @@ -108,14 +113,75 @@ def send_result(iri: str, filepath: Path) -> None: ) -def remove_temp(plugin: WorkflowPlugin, files: list) -> None: - """Remove temproray files""" - for file in files: - try: - (Path(plugin.temp) / file).unlink() - except (OSError, FileNotFoundError) as err: - plugin.log.warning(f"Cannot remove file {file} ({err})") +def remove_temp(plugin: WorkflowPlugin) -> None: + """Remove temporary files""" try: - Path(plugin.temp).rmdir() + rmtree(plugin.temp) except (OSError, FileNotFoundError) as err: plugin.log.warning(f"Cannot remove directory {plugin.temp} ({err})") + + +def post_provenance(plugin: WorkflowPlugin, context: ExecutionContext) -> None: + """Insert provenance""" + plugin_iri = ( + f"http://dataintegration.eccenca.com/{context.task.project_id()}/{context.task.task_id()}" + ) + project_graph = f"http://di.eccenca.com/project/{context.task.project_id()}" + + type_query = f""" + SELECT ?type ?label {{ + GRAPH <{project_graph}> {{ + <{plugin_iri}> a ?type . + <{plugin_iri}> ?label . + FILTER(STRSTARTS(STR(?type), "https://vocab.eccenca.com/di/functions/")) + }} + }} + """ + + result = json.loads(post_select(query=type_query)) + + try: + plugin_type = result["results"]["bindings"][0]["type"]["value"] + except IndexError: + plugin.log.warning("Could not add provenance data to output graph.") + return + plugin_label = result["results"]["bindings"][0]["label"]["value"] + + 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)}' + result = json.loads(post_select(query=parameter_query)) + param_sparql = "" + for binding in result["results"]["bindings"]: + param_iri = binding["parameter"]["value"] + param_val = plugin.__dict__[binding["parameter"]["value"].split(param_split)[1]] + param_sparql += f'\n<{new_plugin_iri}> <{param_iri}> "{param_val}" .' + + insert_query = f""" + INSERT DATA {{ + GRAPH <{plugin.output_graph_iri}> {{ + <{plugin.output_graph_iri}> + <{new_plugin_iri}> . + <{new_plugin_iri}> a <{plugin_type}>, . + <{new_plugin_iri}> "{plugin_label}" . + {param_sparql} + }} + }} + """ + + post_update(query=insert_query) diff --git a/cmem_plugin_reason/validate.png b/cmem_plugin_reason/validate.png new file mode 100644 index 0000000..5e9fb8c Binary files /dev/null and b/cmem_plugin_reason/validate.png differ diff --git a/poetry.lock b/poetry.lock index 61c0e7c..2db8076 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "certifi" -version = "2024.6.2" +version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"}, - {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, + {file = 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b/tests/test_elk.ttl index 8eb0e56..0bac834 100644 --- a/tests/test_elk.ttl +++ b/tests/test_elk.ttl @@ -12,8 +12,7 @@ owl:imports vocab: ; rdfs:comment "Reasoning result set of and "@en ; prov:wasDerivedFrom - , ; - prov:wasGeneratedBy "cmem-plugin-reason (elk)"@en . + , . ################################################################# # Individuals diff --git a/tests/test_emr.ttl b/tests/test_emr.ttl index bb10014..2ddd71a 100644 --- a/tests/test_emr.ttl +++ b/tests/test_emr.ttl @@ -12,8 +12,7 @@ owl:imports vocab: ; rdfs:comment "Reasoning result set of and "@en ; prov:wasDerivedFrom - , ; - prov:wasGeneratedBy "cmem-plugin-reason (emr)"@en . + , . ################################################################# # Individuals diff --git a/tests/test_hermit.ttl b/tests/test_hermit.ttl index e1e865e..a81aaf7 100644 --- a/tests/test_hermit.ttl +++ b/tests/test_hermit.ttl @@ -12,8 +12,7 @@ owl:imports vocab: ; rdfs:comment "Reasoning result set of and "@en ; prov:wasDerivedFrom - , ; - prov:wasGeneratedBy "cmem-plugin-reason (hermit)"@en . + , . ################################################################# # Individuals diff --git a/tests/test_jfact.ttl b/tests/test_jfact.ttl index f13d8f3..a81aaf7 100644 --- a/tests/test_jfact.ttl +++ b/tests/test_jfact.ttl @@ -12,8 +12,7 @@ owl:imports vocab: ; rdfs:comment "Reasoning result set of and "@en ; prov:wasDerivedFrom - , ; - prov:wasGeneratedBy "cmem-plugin-reason (jfact)"@en . + , . ################################################################# # Individuals diff --git a/tests/test_reason.py b/tests/test_reason.py index b3050c5..0a1d718 100644 --- a/tests/test_reason.py +++ b/tests/test_reason.py @@ -71,7 +71,7 @@ def test_reasoner(reasoner: str, err_list: list) -> list: ReasonPlugin( data_graph_iri=REASON_DATA_GRAPH_IRI, ontology_graph_iri=REASON_ONTOLOGY_GRAPH_IRI, - result_graph_iri=REASON_RESULT_GRAPH_IRI, + output_graph_iri=REASON_RESULT_GRAPH_IRI, reasoner=reasoner, sub_class=False, class_assertion=True, diff --git a/tests/test_structural.ttl b/tests/test_structural.ttl index 8d7f980..587f20b 100644 --- a/tests/test_structural.ttl +++ b/tests/test_structural.ttl @@ -12,8 +12,7 @@ owl:imports vocab: ; rdfs:comment "Reasoning result set of and "@en ; prov:wasDerivedFrom - , ; - prov:wasGeneratedBy "cmem-plugin-reason (structural)"@en . + , . ################################################################# # Individuals diff --git a/tests/test_validate_output.ttl b/tests/test_validate_output.ttl index 6c7508b..b9b5886 100644 --- a/tests/test_validate_output.ttl +++ b/tests/test_validate_output.ttl @@ -7,8 +7,7 @@ a owl:Ontology ; rdfs:comment "Ontology validation of "@en ; - prov:wasDerivedFrom ; - prov:wasGeneratedBy "cmem-plugin-validate (elk)"@en . + prov:wasDerivedFrom . a owl:NamedIndividual, . diff --git a/tests/test_whelk.ttl b/tests/test_whelk.ttl index 8212b53..2247138 100644 --- a/tests/test_whelk.ttl +++ b/tests/test_whelk.ttl @@ -12,8 +12,7 @@ owl:imports vocab: ; rdfs:comment "Reasoning result set of and "@en ; prov:wasDerivedFrom - , ; - prov:wasGeneratedBy "cmem-plugin-reason (whelk)"@en . + , . ################################################################# # Individuals