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Remove if absent annotations causing downstream issues in python dataclasses #1528

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merged 3 commits into from
Oct 10, 2024
Merged

Remove if absent annotations causing downstream issues in python dataclasses #1528

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dedddf5
remove failing ifabsent annotations
sierra-moxon Oct 10, 2024
d12796f
regenerate project files
sierra-moxon Oct 10, 2024
fd47554
update linkml
sierra-moxon Oct 10, 2024
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5 changes: 5 additions & 0 deletions ChangeLog
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
CHANGES
=======
4.2.5
-----
* remove if_absent annotations on KL/AT that result in downstream enumeration errors in python dataclasses
representation of the model, see: https://github.com/linkml/linkml/pull/2329 and associated ticket for more details

4.2.4
-----
* regenerating artifacts
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -124,7 +124,7 @@ gen-project: $(PYMODEL)
-d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink-model-prefix-map.json
mv $(PYMODEL)/biolink*.py $(PYMODEL)/model.py
$(RUN) gen-pydantic src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py
$(RUN) gen-pydantic --meta None src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py
$(RUN) gen-owl --mergeimports --no-metaclasses --no-type-objects --add-root-classes --mixins-as-expressions src/biolink_model/schema/biolink_model.yaml > $(DEST)/owl/biolink_model.owl.ttl
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
$(MAKE) id-prefixes
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2 changes: 0 additions & 2 deletions biolink-model.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6138,7 +6138,6 @@ slots:
range: KnowledgeLevelEnum
multivalued: false
required: true
ifabsent: string(not_provided)
examples:
- value: knowledge_assertion
- value: prediction
Expand Down Expand Up @@ -6166,7 +6165,6 @@ slots:
range: AgentTypeEnum
multivalued: false
required: true
ifabsent: string(not_provided)
examples:
- value: manual_agent
- value: automated_agent
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17 changes: 9 additions & 8 deletions poetry.lock
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2 changes: 2 additions & 0 deletions project/graphql/biolink_model.graphql
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
# metamodel_version: 1.7.0
# version: 4.2.4
type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass
{
id: String!
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45 changes: 13 additions & 32 deletions project/jsonld/biolink_model.context.jsonld
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2024-10-10T17:38:44",
"generation_date": "2024-10-10T16:37:53",
"source": "biolink_model.yaml"
},
"@context": {
"xsd": "http://www.w3.org/2001/XMLSchema#",
"AGRKB": "https://www.alliancegenome.org/",
"APO": {
"@id": "http://purl.obolibrary.org/obo/APO_",
Expand Down Expand Up @@ -578,7 +579,6 @@
"@id": "http://www.w3.org/2003/01/geo/wgs84_pos",
"@prefix": true
},
"xsd": "http://www.w3.org/2001/XMLSchema#",
"@vocab": "https://w3id.org/biolink/vocab/",
"active_in": {
"@type": "@id",
Expand Down Expand Up @@ -644,12 +644,11 @@
"@id": "affects_response_to"
},
"affiliation": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "affiliation"
},
"agent_type": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -733,7 +732,6 @@
},
"available_from": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -790,12 +788,11 @@
"@id": "catalyzes"
},
"category": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "category"
},
"causal_mechanism_qualifier": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -829,7 +826,6 @@
},
"clinical_approval_status": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -1026,7 +1022,6 @@
},
"drug_regulatory_status_world_wide": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -1092,7 +1087,6 @@
},
"FDA_adverse_event_level": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -1146,7 +1140,6 @@
},
"genome_build": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -1469,7 +1462,6 @@
},
"highest_FDA_approval_status": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -1643,7 +1635,6 @@
},
"knowledge_level": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -1702,7 +1693,6 @@
},
"logical_interpretation": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand All @@ -1722,7 +1712,6 @@
},
"max_research_phase": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand All @@ -1749,7 +1738,7 @@
"@id": "mentions"
},
"mesh_terms": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "mesh_terms"
},
"missing_from": {
Expand Down Expand Up @@ -1830,7 +1819,6 @@
},
"object_direction_qualifier": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -1877,7 +1865,7 @@
"@id": "original_object"
},
"original_predicate": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "original_predicate"
},
"original_subject": {
Expand Down Expand Up @@ -1915,7 +1903,6 @@
},
"phase": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -2003,7 +1990,7 @@
"@id": "publications"
},
"published_in": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "published_in"
},
"publisher": {
Expand All @@ -2030,7 +2017,6 @@
},
"reaction_direction": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand All @@ -2039,7 +2025,6 @@
},
"reaction_side": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -2094,12 +2079,11 @@
"@id": "resistance_associated_with"
},
"resource_id": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "resource_id"
},
"resource_role": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -2131,7 +2115,6 @@
},
"routes_of_delivery": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -2204,7 +2187,6 @@
},
"strand": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -2245,7 +2227,6 @@
},
"subject_direction_qualifier": {
"@context": {
"@vocab": "@null",
"text": "skos:notation",
"description": "skos:prefLabel",
"meaning": "@id"
Expand Down Expand Up @@ -2296,7 +2277,7 @@
"@id": "supporting_document_year"
},
"supporting_documents": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "supporting_documents"
},
"supporting_study_cohort": {
Expand All @@ -2312,11 +2293,11 @@
"@id": "supporting_study_metadata"
},
"supporting_study_method_description": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "supporting_study_method_description"
},
"supporting_study_method_type": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "supporting_study_method_type"
},
"supporting_study_size": {
Expand Down Expand Up @@ -2421,7 +2402,7 @@
"@id": "update_date"
},
"upstream_resource_ids": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "upstream_resource_ids"
},
"url": {
Expand All @@ -2446,7 +2427,7 @@
"@id": "xenologous_to"
},
"xref": {
"@type": "@id",
"@type": "xsd:anyURI",
"@id": "xref"
},
"AccessibleDnaRegion": {
Expand Down
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