diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f877cf0..cff6b45 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -6,7 +6,7 @@ In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, -level of experience, education, socio-economic status, nationality, personal +level of experience, education, socioeconomic status, nationality, personal appearance, race, religion, or sexual identity and orientation. ## Our Standards diff --git a/poetry.lock b/poetry.lock index 7b87a86..ef48b44 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "airium" version = "0.2.6" description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies." -category = "main" optional = false python-versions = "*" files = [ @@ -20,7 +19,6 @@ parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"] name = "alabaster" version = "0.7.16" description = "A light, configurable Sphinx theme" -category = "dev" optional = false python-versions = ">=3.9" files = [ @@ -30,21 +28,19 @@ files = [ [[package]] name = "annotated-types" -version = "0.6.0" +version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" -category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, - {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, ] [[package]] name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" -category = "main" optional = false python-versions = "*" files = [ @@ -53,14 +49,13 @@ files = [ [[package]] name = "anyio" -version = "4.3.0" +version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" -category = "dev" optional = false python-versions = ">=3.8" files = [ - 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"docopt", "pytest (<7.0.0)"] [[package]] name = "jinja2" -version = "3.1.3" +version = "3.1.4" description = "A very fast and expressive template engine." -category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"}, - {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"}, + {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, + {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, ] [package.dependencies] @@ -1784,26 +1697,10 @@ MarkupSafe = ">=2.0" [package.extras] i18n = ["Babel (>=2.7)"] -[[package]] -name = "jsbeautifier" -version = "1.15.1" -description = "JavaScript unobfuscator and beautifier." -category = "main" -optional = false -python-versions = "*" 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hash = "sha256:0c6d2c09117550c089995247f605ae4cf77dd1533041d366351f6f298822ea74"}, +] + +[package.dependencies] +attrs = ">=19.2.0" + [[package]] name = "jsonpatch" version = "1.33" description = "Apply JSON-Patches (RFC 6902)" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*" files = [ @@ -1876,7 +1780,6 @@ jsonpointer = ">=1.9" name = "jsonpath-ng" version = "1.6.1" description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming." -category = "main" optional = false python-versions = "*" files = [ @@ -1889,26 +1792,24 @@ ply = "*" [[package]] name = "jsonpointer" -version = "2.4" +version = "3.0.0" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, 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(>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [extras] docs = [] diff --git a/pyproject.toml b/pyproject.toml index b03f8f9..49a1c75 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,4 +64,4 @@ mariadb = ["mariadb"] skip = '.git,*.lock,resources' check-hidden = true ignore-regex = '\bOGER\b' -ignore-words-list = 'sie' +ignore-words-list = 'sie,assertIn' diff --git a/schema_automator/cli.py b/schema_automator/cli.py index 18c33ef..92cbbef 100644 --- a/schema_automator/cli.py +++ b/schema_automator/cli.py @@ -454,6 +454,10 @@ def import_owl(owlfile, output, **args): See :ref:`importers` for more on the importer framework + For a list of caveats on LinkML to OWL mapping, see: + + - https://linkml.io/linkml/generators/owl.html + Example: schemauto import-owl prov.ofn -o my.yaml diff --git a/schema_automator/importers/owl_import_engine.py b/schema_automator/importers/owl_import_engine.py index 487a9bd..921923c 100644 --- a/schema_automator/importers/owl_import_engine.py +++ b/schema_automator/importers/owl_import_engine.py @@ -266,7 +266,10 @@ def set_cardinality(p, min_card, max_card): val = a.value.v if isinstance(sub, IRI): sub = self.iri_to_name(sub) - if isinstance(val, Literal): + if isinstance(val, AnonymousIndividual): + logging.info(f'Ignoring anonymous individuals: {sub} {strp} {val}') + continue + elif isinstance(val, Literal): val = str(val.v) elif isinstance(val, IRI): val = val.v diff --git a/tests/resources/test-anon-individual.ofn b/tests/resources/test-anon-individual.ofn new file mode 100644 index 0000000..d906c26 --- /dev/null +++ b/tests/resources/test-anon-individual.ofn @@ -0,0 +1,123 @@ +Prefix(:=) +Prefix(sh:=) +Prefix(dct:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) +Prefix(vaem:=) + + +Ontology( +Annotation( "admin") +Annotation(dct:contributor "admin") +Annotation(dct:created "2024-07-16T13:56:07.545Z"^^xsd:dateTime) +Annotation(dct:creator "admin") +Annotation(dct:modified "2024-07-17T13:31:13.848Z"^^xsd:dateTime) +Annotation(dct:title "Test Ontology"@en) +Annotation( ) +Annotation(vaem:namespace ) +Annotation(rdfs:label "Test Ontology"@en) +Annotation(owl:priorVersion ) +Annotation(owl:versionInfo "0.2") + +Declaration(Class(sh:NodeShape)) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(DataProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(dct:contributor)) +Declaration(AnnotationProperty(dct:created)) +Declaration(AnnotationProperty(dct:creator)) +Declaration(AnnotationProperty(dct:modified)) +Declaration(AnnotationProperty(dct:title)) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(vaem:namespace)) +Declaration(AnnotationProperty(sh:class)) +Declaration(AnnotationProperty(sh:datatype)) +Declaration(AnnotationProperty(sh:path)) +Declaration(AnnotationProperty(sh:property)) +Declaration(AnnotationProperty(sh:targetClass)) + +############################ +# Object Properties +############################ + +# Object Property: (contains) + +AnnotationAssertion( "admin") +AnnotationAssertion(dct:contributor "admin") +AnnotationAssertion(dct:created "2024-07-17T13:31:13.848Z"^^xsd:dateTime) +AnnotationAssertion(dct:creator "admin") +AnnotationAssertion(dct:modified "2024-07-17T13:31:13.848Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "contains") + + +############################ +# Data Properties +############################ + +# Data Property: (name) + +AnnotationAssertion( "admin") +AnnotationAssertion(dct:contributor "admin") +AnnotationAssertion(dct:created "2024-07-16T13:57:08.281Z"^^xsd:dateTime) +AnnotationAssertion(dct:creator "admin") +AnnotationAssertion(dct:modified "2024-07-16T13:57:08.281Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "name") + + + +############################ +# Classes +############################ + +# Class: (Person) + +AnnotationAssertion( "admin") +AnnotationAssertion(dct:contributor "admin") +AnnotationAssertion(dct:created "2024-07-16T13:57:08.281Z"^^xsd:dateTime) +AnnotationAssertion(dct:creator "admin") +AnnotationAssertion(dct:modified "2024-07-16T13:57:08.281Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Person"@en) + +# Class: (Team) + +AnnotationAssertion( "admin") +AnnotationAssertion(dct:contributor "admin") +AnnotationAssertion(dct:created "2024-07-17T13:31:13.848Z"^^xsd:dateTime) +AnnotationAssertion(dct:creator "admin") +AnnotationAssertion(dct:modified "2024-07-17T13:31:13.848Z"^^xsd:dateTime) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "Team"@en) + + +############################ +# Named Individuals +############################ + +# Individual: () + +AnnotationAssertion(sh:property _:genid2147483649) +AnnotationAssertion(sh:targetClass ) +ClassAssertion(sh:NodeShape ) + +# Individual: () + +AnnotationAssertion(sh:property _:genid2147483648) +AnnotationAssertion(sh:targetClass ) +ClassAssertion(sh:NodeShape ) + + +AnnotationAssertion(sh:class _:genid2147483648 ) +AnnotationAssertion(sh:path _:genid2147483648 ) +AnnotationAssertion(sh:datatype _:genid2147483649 xsd:string) +AnnotationAssertion(sh:path _:genid2147483649 rdfs:label) +) \ No newline at end of file diff --git a/tests/test_importers/test_owl_importer.py b/tests/test_importers/test_owl_importer.py index afc958a..77b72b6 100644 --- a/tests/test_importers/test_owl_importer.py +++ b/tests/test_importers/test_owl_importer.py @@ -28,4 +28,12 @@ def test_from_owl(self): with open(OUTSCHEMA_ENHANCED, 'w') as stream: stream.write(s) + def test_anon_individuals(self): + """ + Test that anonymous individuals are handled correctly + """ + oie = OwlImportEngine() + schema = oie.convert(os.path.join(INPUT_DIR, 'test-anon-individual.ofn'), name='anon_individuals') + write_schema(schema, os.path.join(OUTPUT_DIR, 'anon-individual-from-owl.yaml')) +