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Merge pull request #174 from linkml/adding-example-tests
Adding examples to test
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‎Makefile‎

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@@ -74,17 +74,18 @@ gen-doc:
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rm -rf $(DOCDIR)/$(PYMODEL)/model/docs
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cp README.md $(DOCDIR)
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test: test-schema test-python test-validate-schema
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test: test-schema test-python test-validate-schema test-examples
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test-schema:
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$(RUN) gen-project -d tmp $(SOURCE_SCHEMA_PATH)
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test-python:
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$(RUN) python -m unittest discover
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# TODO: switch to linkml-run-examples when normalize is implemented
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test-examples:
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test-examples: $(SOURCE_SCHEMA_PATH)
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$(RUN) linkml-validate -s $(SOURCE_SCHEMA_PATH) tests/input/examples/schema_definition-*.yaml
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# $(RUN) linkml-run-examples -s $(SOURCE_SCHEMA_PATH) -e tests/input/examples -d /tmp/
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find tests/input/examples | ./utils/run-examples.pl
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# find tests/input/examples | ./utils/run-examples.pl
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test-validate-schema:
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$(RUN) linkml-normalize -s $(SOURCE_SCHEMA_PATH) $(SOURCE_SCHEMA_PATH) -o /tmp/schema

‎tests/input/examples/schema_definition-dynamic-enums.yaml‎

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id: https://w3id.org/linkml/examples/enums
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title: Dynamic Enums Example
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name: dynamicenums-example
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description: This demonstrates the use of dynamic enums
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license: https://creativecommons.org/publicdomain/zero/1.0/
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prefixes:
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linkml: https://w3id.org/linkml/
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ex: https://w3id.org/linkml/examples/enums/
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sh: https://w3id.org/shacl/
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bioregistry: https://bioregistry.io/registry/
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MONDO: http://purl.obolibrary.org/obo/MONDO_
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NCIT: http://purl.obolibrary.org/obo/NCIT_
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loinc: http://loinc.org/
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default_prefix: ex
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default_range: string
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default_curi_maps:
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- semweb_context
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emit_prefixes:
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- linkml
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- rdf
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- rdfs
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- xsd
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- owl
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imports:
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- linkml:types
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#==================================
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# Classes #
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#==================================
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classes:
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HumanSample:
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slots:
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- name
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- disease
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#==================================
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# Slots #
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#==================================
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slots:
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name:
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range: string
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disease:
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range: HumanDisease
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vital_status:
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enum_range:
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permissible_values:
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LIVING:
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DEAD:
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UNDEAD:
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#==================================
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# Enums
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#==================================
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enums:
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Disease:
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reachable_from:
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source_ontology: bioregistry:mondo
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source_nodes:
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- MONDO:0000001 ## disease or disorder
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is_direct: false
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relationship_types:
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- rdfs:subClassOf
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minus:
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- permissible_values:
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root_node:
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meaning: MONDO:0000001 ## disease or disorder
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HumanDisease:
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description: Extends the Disease value set, including NCIT neoplasms, excluding non-human diseases
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inherits:
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- Disease
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include:
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- reachable_from:
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source_ontology: bioregistry:ncit
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source_nodes:
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- NCIT:C3262
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minus:
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- reachable_from:
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source_ontology: bioregistry:mondo
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source_nodes:
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- MONDO:0005583 ## non-human animal disease
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relationship_types:
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- rdfs:subClassOf
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- permissible_values:
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NOT_THIS_ONE:
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meaning: MONDO:9999
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description: Example of excluding a single node
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LoincExample:
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enum_uri: http://hl7.org/fhir/ValueSet/example-intensional
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see_also:
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- https://build.fhir.org/valueset-example-intensional.json.html
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include:
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- reachable_from:
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source_ontology: "loinc:"
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source_nodes:
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- loinc:LP43571-6
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is_direct: true
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minus:
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- concepts:
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- LOINC:5932-9
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HCAExample:
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see_also:
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- https://github.com/linkml/linkml/issues/274
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include:
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- reachable_from:
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source_ontology: bioregistry:go
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source_nodes:
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- GO:0007049
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- GO:0022403
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include_self: false
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relationship_types:
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- rdfs:subClassOf
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minus:
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- concepts:
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- LOINC:5932-9
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BodyPartEnum:
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reachable_from:
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source_ontology: obo:cl
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source_nodes:
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- CL:0000540 ## neuron
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include_self: false
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relationship_types:
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- rdfs:subClassOf
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Brand:
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enum_uri: wikidata:Q431289
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include:
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- reachable_from:
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source_ontology: bioregistry:wikidata
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source_nodes:
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- wikidata:Q431289
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include_self: false
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relationship_types:
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- wdp:P31
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- wdp:P279
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SerumCholesterolExample:
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description: >
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This is an example value set that includes all the LOINC codes for serum/plasma cholesterol from v2.36.
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code_set: http://hl7.org/fhir/ValueSet/serum-cholesterol
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code_set_version: "1.0.0"
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pv_formula: CODE
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include:
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- concepts:
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- LP43571-6
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minus:
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- concepts:
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- 5932-9
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reachable_from:
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source_ontology: http://loinc.org
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source_nodes:
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- LP43571-6
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relationship_types: null
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is_direct: true
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include_self: true
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traverse_up: false
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concepts:
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- http://loinc.org/LP43571-6

‎tests/input/examples/schema_definition-instantiates.yaml‎

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id: https://w3id.org/linkml/examples/enums
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title: Dynamic Enums Example
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name: dynamicenums-example
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description: This demonstrates the use of dynamic enums
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license: https://creativecommons.org/publicdomain/zero/1.0/
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prefixes:
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linkml: https://w3id.org/linkml/
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ex: https://w3id.org/linkml/examples/enums/
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mymetamodel: https://w3id.org/linkml/examples/mymetamodel/
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sh: https://w3id.org/shacl/
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bioregistry: https://bioregistry.io/registry/
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MONDO: http://purl.obolibrary.org/obo/MONDO_
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NCIT: http://purl.obolibrary.org/obo/NCIT_
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loinc: http://loinc.org/
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default_prefix: ex
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default_range: string
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default_curi_maps:
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- semweb_context
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imports:
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- linkml:types
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#==================================
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# Classes #
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#==================================
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classes:
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Person:
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instantiates:
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- mymetamodel:Reviewable
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annotations:
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review.desc: A very useful class that is well defined
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attributes:
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id:
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name:
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address:
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Reviewable:
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class_uri: mymetamodel:Reviewable
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attributes:
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description: an expert review of a schema element
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review: Review
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Review:
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class_uri: mymetamodel:Review
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attributes:
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desc:
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score:
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range: float

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