regenerate project files

biolink · Oct 10, 2024 · d12796f · d12796f
1 parent dedddf5
commit d12796f
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Showing 14 changed files with 54,311 additions and 32,771 deletions.
diff --git a/Makefile b/Makefile
@@ -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 --meta NONE 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

diff --git a/project/graphql/biolink_model.graphql b/project/graphql/biolink_model.graphql
@@ -1,3 +1,5 @@
+# metamodel_version: 1.7.0
+# version: 4.2.4
 type AccessibleDnaRegion implements GenomicEntity, ChemicalEntityOrGeneOrGeneProduct, PhysicalEssence, OntologyClass
   {
     id: String!

diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld
@@ -1,10 +1,11 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-10-10T17:38:44",
+      "generation_date": "2024-10-10T16:29:55",
       "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_",
@@ -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",
@@ -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"
@@ -733,7 +732,6 @@
       },
       "available_from": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -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"
@@ -829,7 +826,6 @@
       },
       "clinical_approval_status": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1026,7 +1022,6 @@
       },
       "drug_regulatory_status_world_wide": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1092,7 +1087,6 @@
       },
       "FDA_adverse_event_level": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1146,7 +1140,6 @@
       },
       "genome_build": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1469,7 +1462,6 @@
       },
       "highest_FDA_approval_status": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1643,7 +1635,6 @@
       },
       "knowledge_level": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1702,7 +1693,6 @@
       },
       "logical_interpretation": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1722,7 +1712,6 @@
       },
       "max_research_phase": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1749,7 +1738,7 @@
          "@id": "mentions"
       },
       "mesh_terms": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "mesh_terms"
       },
       "missing_from": {
@@ -1830,7 +1819,6 @@
       },
       "object_direction_qualifier": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -1877,7 +1865,7 @@
          "@id": "original_object"
       },
       "original_predicate": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "original_predicate"
       },
       "original_subject": {
@@ -1915,7 +1903,6 @@
       },
       "phase": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2003,7 +1990,7 @@
          "@id": "publications"
       },
       "published_in": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "published_in"
       },
       "publisher": {
@@ -2030,7 +2017,6 @@
       },
       "reaction_direction": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2039,7 +2025,6 @@
       },
       "reaction_side": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -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"
@@ -2131,7 +2115,6 @@
       },
       "routes_of_delivery": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2204,7 +2187,6 @@
       },
       "strand": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2245,7 +2227,6 @@
       },
       "subject_direction_qualifier": {
          "@context": {
-            "@vocab": "@null",
             "text": "skos:notation",
             "description": "skos:prefLabel",
             "meaning": "@id"
@@ -2296,7 +2277,7 @@
          "@id": "supporting_document_year"
       },
       "supporting_documents": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "supporting_documents"
       },
       "supporting_study_cohort": {
@@ -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": {
@@ -2421,7 +2402,7 @@
          "@id": "update_date"
       },
       "upstream_resource_ids": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "upstream_resource_ids"
       },
       "url": {
@@ -2446,7 +2427,7 @@
          "@id": "xenologous_to"
       },
       "xref": {
-         "@type": "@id",
+         "@type": "xsd:anyURI",
          "@id": "xref"
       },
       "AccessibleDnaRegion": {