diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 21be052..e3986f2 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -31,7 +31,7 @@ jobs: strategy: matrix: python-version: - - '3.7' + - '3.8' - '3.11' steps: diff --git a/.github/workflows/supply-chain.yml b/.github/workflows/supply-chain.yml new file mode 100644 index 0000000..54e932b --- /dev/null +++ b/.github/workflows/supply-chain.yml @@ -0,0 +1,38 @@ +# This software was developed at the National Institute of Standards +# and Technology by employees of the Federal Government in the course +# of their official duties. Pursuant to title 17 Section 105 of the +# United States Code this software is not subject to copyright +# protection and is in the public domain. NIST assumes no +# responsibility whatsoever for its use by other parties, and makes +# no guarantees, expressed or implied, about its quality, +# reliability, or any other characteristic. +# +# We would appreciate acknowledgement if the software is used. + +# This workflow uses Make to review direct dependencies of this +# repository. + +name: Continuous Integration + +on: + schedule: + - cron: '15 5 * * 1,2,3,4,5' + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: + - '3.8' + - '3.11' + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - name: Review dependencies + run: make check-supply-chain diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5460c07..7e3c8d9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,15 +11,15 @@ repos: - repo: https://github.com/psf/black - rev: 22.10.0 + rev: 23.3.0 hooks: - id: black - repo: https://github.com/pycqa/flake8 - rev: 5.0.4 + rev: 6.0.0 hooks: - id: flake8 - repo: https://github.com/pycqa/isort - rev: 5.10.1 + rev: 5.12.0 hooks: - id: isort name: isort (python) diff --git a/Makefile b/Makefile index ef5f220..2435b8d 100644 --- a/Makefile +++ b/Makefile @@ -25,6 +25,8 @@ all: \ --directory figures .PHONY: \ + check-supply-chain \ + check-supply-chain-pre-commit \ clean-figures \ clean-tests @@ -72,6 +74,18 @@ check: \ --directory tests \ check +# This target's dependencies potentially modify the working directory's Git state, so it is intentionally not a dependency of check. +check-supply-chain: \ + check-supply-chain-pre-commit + +check-supply-chain-pre-commit: \ + .venv-pre-commit/var/.pre-commit-built.log + source .venv-pre-commit/bin/activate \ + && pre-commit autoupdate + git diff \ + --exit-code \ + .pre-commit-config.yaml + clean: \ clean-figures \ clean-tests diff --git a/README.md b/README.md index 0a21b52..3dd43e7 100644 --- a/README.md +++ b/README.md @@ -68,8 +68,8 @@ This project follows [SEMVER 2.0.0](https://semver.org/) where versions are decl This repository supports the CASE and UCO ontology versions that are distributed with the [CASE-Utilities-Python repository](https://github.com/casework/CASE-Utilities-Python), at the newest version below a ceiling-pin in [setup.cfg](setup.cfg). Currently, those ontology versions are: -* CASE 1.0.0 -* UCO 1.0.0 +* CASE 1.2.0 +* UCO 1.2.0 ## Repository locations diff --git a/case_prov/__init__.py b/case_prov/__init__.py index 6c4a7a7..139dc85 100644 --- a/case_prov/__init__.py +++ b/case_prov/__init__.py @@ -11,4 +11,4 @@ # # We would appreciate acknowledgement if the software is used. -__version__ = "0.6.0" +__version__ = "0.7.0" diff --git a/case_prov/case_prov_dot.py b/case_prov/case_prov_dot.py index 9814a2e..45e16cb 100644 --- a/case_prov/case_prov_dot.py +++ b/case_prov/case_prov_dot.py @@ -21,7 +21,7 @@ # get quoted. This turns out to be a dot syntax error. Need to report # this upstream to pydot. -__version__ = "0.4.0" +__version__ = "0.4.1" import argparse import collections @@ -170,7 +170,7 @@ def main() -> None: ?nEntity prov:wasDerivedFrom prov:EmptyCollection . } """ - for (select_query_label, select_query_text) in [ + for select_query_label, select_query_text in [ ("activities", select_query_actions_text), ("agents", select_query_agents_text), ("entities", select_query_entities_text), @@ -180,7 +180,9 @@ def main() -> None: select_query_text, initNs=nsdict ) for record in graph.query(select_query_object): - (n_include,) = record + assert isinstance(record, rdflib.query.ResultRow) + assert isinstance(record[0], rdflib.term.IdentifiedNode) + n_include = record[0] filter_iri = n_include.toPython() filter_iris.add(filter_iri) _logger.debug("len(filter_iris) = %d.", len(filter_iris)) @@ -200,6 +202,7 @@ def main() -> None: query_ancestry_text, initNs=nsdict ) for result in graph.query(query_ancestry_object): + assert isinstance(result, rdflib.query.ResultRow) for result_member in result: if not isinstance(result_member, rdflib.URIRef): raise ValueError( @@ -245,7 +248,7 @@ def main() -> None: ?nEndIRI prov:wasDerivedFrom* ?nPrecedingEntity . } """ - for (select_query_label, select_query_text) in [ + for select_query_label, select_query_text in [ ("activities", select_query_actions_text), ("agents", select_query_agents_text), ("entities", select_query_entities_text), @@ -260,7 +263,9 @@ def main() -> None: select_query_object, initBindings={"nEndIRI": rdflib.URIRef(terminal_iri)}, ): - (n_include,) = record + assert isinstance(record, rdflib.query.ResultRow) + assert isinstance(record[0], rdflib.term.IdentifiedNode) + n_include = record[0] filter_iri = n_include.toPython() filter_iris.add(filter_iri) _logger.debug("len(filter_iris) = %d.", len(filter_iris)) @@ -316,8 +321,14 @@ def main() -> None: select_query_object = rdflib.plugins.sparql.processor.prepareQuery( select_query_text, initNs=nsdict ) - for record in graph.query(select_query_object): - (n_agent, l_label, l_comment) = record + for result in graph.query(select_query_object): + assert isinstance(result, rdflib.query.ResultRow) + assert isinstance(result[0], rdflib.term.IdentifiedNode) + assert result[1] is None or isinstance(result[1], rdflib.Literal) + assert result[2] is None or isinstance(result[2], rdflib.Literal) + n_agent = result[0] + l_label = result[1] + l_comment = result[2] agent_iri = n_agent.toPython() dot_label = "ID - " + graph.namespace_manager.qname(agent_iri) if l_label is not None: @@ -327,9 +338,9 @@ def main() -> None: kwargs = clone_style(prov.constants.PROV_AGENT) kwargs["label"] = dot_label # _logger.debug("Agent %r.", agent_iri) - record = (iri_to_gv_node_id(agent_iri), kwargs) - nodes[agent_iri] = record - nodes_agents[agent_iri] = record + node_record = (iri_to_gv_node_id(agent_iri), kwargs) + nodes[agent_iri] = node_record + nodes_agents[agent_iri] = node_record # _logger.debug("nodes = %s." % pprint.pformat(nodes)) # Find Collections, to adjust Entity rendering in the next block. @@ -344,7 +355,9 @@ def main() -> None: select_query_text, initNs=nsdict ) for record in graph.query(select_query_object): - (n_collection,) = record + assert isinstance(record, rdflib.query.ResultRow) + assert isinstance(record[0], rdflib.term.IdentifiedNode) + n_collection = record[0] collection_iri = n_collection.toPython() collection_iris.add(collection_iri) # _logger.debug("len(collection_iris) = %d.", len(collection_iris)) @@ -354,9 +367,9 @@ def main() -> None: entity_iri_to_label_comment: typing.Dict[ str, typing.Tuple[ - typing.Optional[str], - typing.Optional[str], - typing.Optional[str], + typing.Optional[rdflib.Literal], + typing.Optional[rdflib.Literal], + typing.Optional[rdflib.Literal], ], ] = dict() if not args.omit_empty_set: @@ -386,28 +399,48 @@ def main() -> None: select_query_object = rdflib.plugins.sparql.processor.prepareQuery( select_query_text, initNs=nsdict ) + l_entity_label: typing.Optional[rdflib.Literal] + l_entity_comment: typing.Optional[rdflib.Literal] + l_entity_exhibit_number: typing.Optional[rdflib.Literal] for record in graph.query(select_query_object): - (n_entity, l_label, l_comment, l_exhibit_number) = record + assert isinstance(record, rdflib.query.ResultRow) + assert isinstance(record[0], rdflib.term.IdentifiedNode) + assert record[1] is None or isinstance(record[1], rdflib.Literal) + assert record[2] is None or isinstance(record[2], rdflib.Literal) + assert record[3] is None or isinstance(record[3], rdflib.Literal) + n_entity = record[0] + l_entity_label = record[1] + l_entity_comment = record[2] + l_entity_exhibit_number = record[3] + entity_iri = n_entity.toPython() - entity_iri_to_label_comment[entity_iri] = (l_label, l_comment, l_exhibit_number) + entity_iri_to_label_comment[entity_iri] = ( + l_entity_label, + l_entity_comment, + l_entity_exhibit_number, + ) for entity_iri in sorted(entity_iri_to_label_comment): - (l_label, l_comment, l_exhibit_number) = entity_iri_to_label_comment[entity_iri] + ( + l_entity_label, + l_entity_comment, + l_entity_exhibit_number, + ) = entity_iri_to_label_comment[entity_iri] dot_label = "ID - " + graph.namespace_manager.qname(entity_iri) - if l_exhibit_number is not None: - dot_label += "\nExhibit - " + l_exhibit_number.toPython() - if l_label is not None: - dot_label += "\n" + l_label.toPython() - if l_comment is not None: - dot_label += "\n\n" + "\n".join(wrapper.wrap((l_comment.toPython()))) + if l_entity_exhibit_number is not None: + dot_label += "\nExhibit - " + l_entity_exhibit_number.toPython() + if l_entity_label is not None: + dot_label += "\n" + l_entity_label.toPython() + if l_entity_comment is not None: + dot_label += "\n\n" + "\n".join(wrapper.wrap((l_entity_comment.toPython()))) if entity_iri in collection_iris: kwargs = clone_style(PROV_COLLECTION) else: kwargs = clone_style(prov.constants.PROV_ENTITY) kwargs["label"] = dot_label # _logger.debug("Entity %r.", entity_iri) - record = (iri_to_gv_node_id(entity_iri), kwargs) - nodes[entity_iri] = record - nodes_entities[entity_iri] = record + entity_record = (iri_to_gv_node_id(entity_iri), kwargs) + nodes[entity_iri] = entity_record + nodes_entities[entity_iri] = entity_record # Render Activities. select_query_text = """\ @@ -436,7 +469,18 @@ def main() -> None: select_query_text, initNs=nsdict ) for record in graph.query(select_query_object): - (n_activity, l_label, l_comment, l_start_time, l_end_time) = record + assert isinstance(record, rdflib.query.ResultRow) + assert isinstance(record[0], rdflib.term.IdentifiedNode) + assert record[1] is None or isinstance(record[1], rdflib.Literal) + assert record[2] is None or isinstance(record[2], rdflib.Literal) + assert record[3] is None or isinstance(record[3], rdflib.Literal) + assert record[4] is None or isinstance(record[4], rdflib.Literal) + n_activity = record[0] + l_label = record[1] + l_comment = record[2] + l_start_time = record[3] + l_end_time = record[4] + activity_iri = n_activity.toPython() dot_label = "ID - " + graph.namespace_manager.qname(activity_iri) if l_label is not None: @@ -455,9 +499,9 @@ def main() -> None: kwargs = clone_style(prov.constants.PROV_ACTIVITY) kwargs["label"] = dot_label # _logger.debug("Activity %r.", activity_iri) - record = (iri_to_gv_node_id(activity_iri), kwargs) - nodes[activity_iri] = record - nodes_activities[activity_iri] = record + activity_record = (iri_to_gv_node_id(activity_iri), kwargs) + nodes[activity_iri] = activity_record + nodes_activities[activity_iri] = activity_record def _render_edges( select_query_text: str, @@ -469,15 +513,22 @@ def _render_edges( select_query_text, initNs=nsdict ) for record in graph.query(select_query_object): - (n_thing_1, n_thing_2) = record + assert isinstance(record, rdflib.query.ResultRow) + assert isinstance(record[0], rdflib.term.IdentifiedNode) + assert isinstance(record[1], rdflib.term.IdentifiedNode) + n_thing_1 = record[0] + n_thing_2 = record[1] + thing_1_iri = n_thing_1.toPython() thing_2_iri = n_thing_2.toPython() gv_node_id_1 = iri_to_gv_node_id(thing_1_iri) gv_node_id_2 = iri_to_gv_node_id(thing_2_iri) - record = (gv_node_id_1, gv_node_id_2, kwargs) - edges[thing_1_iri][thing_2_iri][short_edge_label] = record + edge_record = (gv_node_id_1, gv_node_id_2, kwargs) + edges[thing_1_iri][thing_2_iri][short_edge_label] = edge_record if supplemental_dict is not None: - supplemental_dict[thing_1_iri][thing_2_iri][short_edge_label] = record + supplemental_dict[thing_1_iri][thing_2_iri][ + short_edge_label + ] = edge_record # Render actedOnBehalfOf. select_query_text = """\ @@ -772,10 +823,10 @@ def _render_edges( continue for short_edge_label in sorted(edges[iri_1][iri_2]): # short_edge_label is intentionally not used aside from as a selector. Edge labelling is left to pydot. - record = edges[iri_1][iri_2][short_edge_label] - node_id_1 = record[0] - node_id_2 = record[1] - kwargs = record[2] + edge_record = edges[iri_1][iri_2][short_edge_label] + node_id_1 = edge_record[0] + node_id_2 = edge_record[1] + kwargs = edge_record[2] dot_edge = pydot.Edge(node_id_1, node_id_2, **kwargs) dot_graph.add_edge(dot_edge) diff --git a/case_prov/case_prov_rdf.py b/case_prov/case_prov_rdf.py index 27ee8d0..9c0dbdf 100644 --- a/case_prov/case_prov_rdf.py +++ b/case_prov/case_prov_rdf.py @@ -15,7 +15,7 @@ This script executes CONSTRUCT queries, returning a supplemental graph. """ -__version__ = "0.3.0" +__version__ = "0.3.1" import argparse import importlib.resources @@ -86,11 +86,13 @@ def main() -> None: # https://rdfextras.readthedocs.io/en/latest/working_with.html construct_query_result = in_graph.query(construct_query_object) _logger.debug("len(construct_query_result) = %d." % len(construct_query_result)) - for (row_no, row) in enumerate(construct_query_result): + for row_no, row in enumerate(construct_query_result): if row_no == 0: _logger.debug("row[0] = %r." % (row,)) tally = row_no + 1 - out_graph.add(row) + # TODO: Handle type review with implementation to RDFLib Issue 2283. + # https://github.com/RDFLib/rdflib/issues/2283 + out_graph.add(row) # type: ignore if tally == 0: if not args.allow_empty_results: raise ValueError("Failed to construct any results.") diff --git a/case_prov/shapes/Makefile b/case_prov/shapes/Makefile index 5859f23..8e09ae6 100644 --- a/case_prov/shapes/Makefile +++ b/case_prov/shapes/Makefile @@ -31,7 +31,7 @@ all: \ .%.ttl-check: \ %.ttl \ $(top_srcdir)/.git_submodule_init.done.log - java -jar $(top_srcdir)/dependencies/CASE-Examples-QC/dependencies/CASE-Examples/dependencies/UCO-develop/lib/rdf-toolkit.jar \ + java -jar $(top_srcdir)/dependencies/CASE-Examples-QC/dependencies/CASE-Examples/dependencies/CASE-develop/dependencies/UCO/lib/rdf-toolkit.jar \ --inline-blank-nodes \ --source $< \ --source-format turtle \ diff --git a/dependencies/CASE-Examples-QC b/dependencies/CASE-Examples-QC index 0056275..7bda777 160000 --- a/dependencies/CASE-Examples-QC +++ b/dependencies/CASE-Examples-QC @@ -1 +1 @@ -Subproject commit 005627542a4bd4e152bb0e70a15393d0b1fcb38d +Subproject commit 7bda777f24ab946ddd11c758719f72c34c6ca90f diff --git a/figures/readme-activities.svg b/figures/readme-activities.svg index e9c9bf8..df3da71 100644 --- a/figures/readme-activities.svg +++ b/figures/readme-activities.svg @@ -1,7 +1,7 @@ - _1dc69e0ebb51673345ae966d7c1ed38f939e9f2a3eb4c3753722e4a4aab66fb1->_dfa40afa8223607a4487772fe58783fb86ed8b6c03657ebaf7603a06c87ac4cd - - + + wasInformedBy @@ -40,8 +40,8 @@ _526944cfe3743b492c3f7751131a98aa3eb5bc97b4085097a36a0eda13b85b9d->_1dc69e0ebb51673345ae966d7c1ed38f939e9f2a3eb4c3753722e4a4aab66fb1 - - + + wasInformedBy diff --git a/figures/readme-attribution.svg b/figures/readme-attribution.svg index 412d7f4..4cecfc6 100644 --- a/figures/readme-attribution.svg +++ b/figures/readme-attribution.svg @@ -1,7 +1,7 @@ - _b3e54d5a1184906f1df8e89ec65665c571405b0d8a37d02c3a00fbd34397b3df->_d35f749b2a59a4c852425d8a45c5c57b6daa5cf2eaa3376a61840d5af32e6a4a - - + + wasAttributedTo @@ -37,8 +37,8 @@ _480bdfd1fe5b252217b8998900a58a6d302338c1e59158f5873f5cd0cafc676e->_d35f749b2a59a4c852425d8a45c5c57b6daa5cf2eaa3376a61840d5af32e6a4a - - + + wasAttributedTo diff --git a/figures/readme-provenance-records.svg b/figures/readme-provenance-records.svg index abb4655..bd46f0c 100644 --- a/figures/readme-provenance-records.svg +++ b/figures/readme-provenance-records.svg @@ -1,7 +1,7 @@ - _4ff8676506e04e724db6c9ed5b76dc39beeefd767b66036056fbce3593ded3dc->_75447935a41fb2b4562606fec9bace2054521fecb4e82258780e1adacf20741f - - + + hadMember diff --git a/setup.cfg b/setup.cfg index 3ae8768..343615a 100644 --- a/setup.cfg +++ b/setup.cfg @@ -19,11 +19,11 @@ license_files = [options] include_package_data = true install_requires = - case_utils >=0.9.0,< 0.10.0 + case_utils >=0.10.0,< 0.11.0 prov pydot packages = find: -python_requires = >=3.7 +python_requires = >=3.8 [options.entry_points] console_scripts = diff --git a/tests/CASE-Examples/examples/illustrations/src/illustration.mk b/tests/CASE-Examples/examples/illustrations/src/illustration.mk index 0d601c7..693ea79 100644 --- a/tests/CASE-Examples/examples/illustrations/src/illustration.mk +++ b/tests/CASE-Examples/examples/illustrations/src/illustration.mk @@ -21,7 +21,7 @@ qc_srcdir := $(top_srcdir)/dependencies/CASE-Examples-QC example_srcdir := $(qc_srcdir)/dependencies/CASE-Examples/examples/illustrations/$(subjectdir_basename) -rdf_toolkit_jar := $(qc_srcdir)/dependencies/CASE-Examples/dependencies/UCO-develop/lib/rdf-toolkit.jar +rdf_toolkit_jar := $(qc_srcdir)/dependencies/CASE-Examples/dependencies/CASE-develop/dependencies/UCO/lib/rdf-toolkit.jar subject_json := $(example_srcdir)/$(subjectdir_basename).json diff --git a/tests/casework.github.io/examples/src/example.mk b/tests/casework.github.io/examples/src/example.mk index bf0b7c6..779d57a 100644 --- a/tests/casework.github.io/examples/src/example.mk +++ b/tests/casework.github.io/examples/src/example.mk @@ -21,7 +21,7 @@ qc_srcdir := $(top_srcdir)/dependencies/CASE-Examples-QC example_srcdir := $(qc_srcdir)/dependencies/casework.github.io/examples/$(subjectdir_basename) -rdf_toolkit_jar := $(qc_srcdir)/dependencies/CASE-Examples/dependencies/UCO-develop/lib/rdf-toolkit.jar +rdf_toolkit_jar := $(qc_srcdir)/dependencies/CASE-Examples/dependencies/CASE-develop/dependencies/UCO/lib/rdf-toolkit.jar subject_json := $(example_srcdir)/$(subjectdir_basename).json diff --git a/tests/casework.github.io/examples/urgent_evidence/test_urgent_evidence.py b/tests/casework.github.io/examples/urgent_evidence/test_urgent_evidence.py index 94b2194..7e32029 100644 --- a/tests/casework.github.io/examples/urgent_evidence/test_urgent_evidence.py +++ b/tests/casework.github.io/examples/urgent_evidence/test_urgent_evidence.py @@ -30,6 +30,8 @@ def test_chain_of_communication() -> None: } """ for result in graph.query(query_all): + assert isinstance(result, rdflib.query.ResultRow) + assert isinstance(result[0], rdflib.term.IdentifiedNode) computed_all.add(result[0].toPython()) query_linked = """\ SELECT ?nActivity @@ -38,6 +40,8 @@ def test_chain_of_communication() -> None: } """ for result in graph.query(query_linked): + assert isinstance(result, rdflib.query.ResultRow) + assert isinstance(result[0], rdflib.term.IdentifiedNode) computed_linked.add(result[0].toPython()) computed = computed_all - computed_linked assert expected == computed @@ -57,6 +61,8 @@ def test_chain_of_derivation() -> None: } """ for result in graph.query(query_all): + assert isinstance(result, rdflib.query.ResultRow) + assert isinstance(result[0], rdflib.term.IdentifiedNode) computed_all.add(result[0].toPython()) query_linked = """\ SELECT ?nEntity @@ -65,6 +71,8 @@ def test_chain_of_derivation() -> None: } """ for result in graph.query(query_linked): + assert isinstance(result, rdflib.query.ResultRow) + assert isinstance(result[0], rdflib.term.IdentifiedNode) computed_linked.add(result[0].toPython()) computed = computed_all - computed_linked diff --git a/tests/casework.github.io/examples/urgent_evidence/urgent_evidence-prov-activities.svg b/tests/casework.github.io/examples/urgent_evidence/urgent_evidence-prov-activities.svg index 769d76e..d98c707 100644 --- a/tests/casework.github.io/examples/urgent_evidence/urgent_evidence-prov-activities.svg +++ b/tests/casework.github.io/examples/urgent_evidence/urgent_evidence-prov-activities.svg @@ -1,7 +1,7 @@ - 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