add id_prefixes and infores updates to gen-project

Makefile

@@ -99,7 +99,7 @@ infores:
 
 id-prefixes:
 	poetry run gen-python class_prefixes.yaml > src/biolink_model/scripts/classprefixes.py
-	cd scripts && poetry run python id_prefixes.py
+	cd src/biolink_model/scripts/ && poetry run python id_prefixes.py
 
 spell:
 	poetry run codespell
@@ -125,12 +125,12 @@ gen-project: $(PYMODEL)
 		--include python \
 		--include rdf \
 		-d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
-	mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink-model-prefix-map.json
+	mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink_model_prefix_map.json
 	mv $(PYMODEL)/biolink*.py $(PYMODEL)/model.py
-	mv $(DEST)/graphql/biolink_model.yaml $(DEST)/graphql/biolink-model.graphql
 	$(RUN) gen-pydantic --pydantic_version 1 src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel.py
 	$(RUN) gen-pydantic --pydantic_version 2 src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py
 	cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
+	$(MAKE) id-prefixes infores
 
 tests:
 	cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml

class_prefixes.yaml

@@ -0,0 +1,83 @@
+id: biolink-model-class-prefixes
+name: BiolinkClassPrefixes
+description: preferred order identifier prefixes per class in Biolink Model
+license: https://creativecommons.org/publicdomain/zero/1.0/
+
+# Version should be kept in sync with primary Git repository release tag
+
+version: 4.0.0
+
+default_prefix: biolink
+default_range: string
+
+imports:
+  - linkml:types
+
+# 2. The following prefix maps are retrieved from the
+#    specified contexts defined at https://prefixcommons.org/
+default_curi_maps:
+  - obo_context
+  - idot_context
+  - monarch_context
+  - semweb_context
+
+# The following 'standard' prefixes are also used.
+emit_prefixes:
+  - rdf
+  - rdfs
+  - xsd
+  - skos
+  - OIO
+  - BIOGRID
+  - SO
+
+prefixes:
+  linkml: 'https://w3id.org/linkml/'
+
+classes:
+  BiolinkClassPrefixMap:
+    description: preferred order identifier prefixes per class in Biolink Model
+    slots:
+      - prefix_map
+      - class_name
+
+  BiolinkClassPrefixesCollection:
+    description: collection of BiolinkClassPrefixes objects
+    tree_root: true
+    slots:
+      - biolink_class_prefixes
+
+  Prefix:
+    slots:
+        - prefix
+        - base_uri
+        - order
+
+slots:
+  biolink_class_prefixes:
+    multivalued: true
+    range: BiolinkClassPrefixMap
+    inlined: true
+    inlined_as_list: true
+    description: >-
+      A collectionm of GO domain/range constraint shapes where a GO domain/range constraint shape 
+      is defined as the domain, relationship, and range of a GO shape expression rule.
+
+  prefix_map:
+    description: a collection of Prefixes per class
+    range: Prefix
+    multivalued: true
+
+  class_name:
+    description: the name of a class in Biolink Model
+    range: uriorcurie
+
+  base_uri:
+    description: the URI of a prefix
+    range: uri
+
+  prefix:
+    range: string
+
+  order:
+    range: integer

project/jsonld/biolink_model.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-11-29T11:32:20",
+      "generation_date": "2023-11-29T11:58:17",
       "source": "biolink_model.yaml"
    },
    "@context": {

project/jsonld/biolink_model.jsonld

@@ -33272,9 +33272,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "biolink_model.yaml",
-  "source_file_date": "2023-11-29T11:32:09",
+  "source_file_date": "2023-11-29T11:58:11",
   "source_file_size": 362250,
-  "generation_date": "2023-11-29T11:32:23",
+  "generation_date": "2023-11-29T11:58:19",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/biolink_model.context.jsonld",