fix gen-project

linkml · Aug 5, 2024 · 13b32d2 · 13b32d2
1 parent c5f5729
commit 13b32d2
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Showing 12 changed files with 558 additions and 570 deletions.
diff --git a/.env.public b/.env.public
@@ -0,0 +1,27 @@
+# This file is public in git. No sensitive info allowed.
+
+###### schema definition variables, used by makefile
+
+LINKML_SCHEMA_NAME="cmdr"
+LINKML_SCHEMA_AUTHOR="LinkML Team <admin@linkml.org>"
+LINKML_SCHEMA_DESCRIPTION="Core Model for Clinical Data Collection"
+LINKML_SCHEMA_SOURCE_PATH="src/cmdr/schema/cmdr.yaml"
+
+###### linkml generator variables, used by makefile
+
+## gen-project configuration file
+LINKML_GENERATORS_CONFIG_YAML= --config-file config.yaml
+
+## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports)
+LINKML_GENERATORS_DOC_ARGS=
+
+## pass args to workaround genowl rdfs config bug (linkml#1453)
+##   (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs)
+LINKML_GENERATORS_OWL_ARGS=
+
+## pass args to trigger experimental java/typescript generation
+LINKML_GENERATORS_JAVA_ARGS=
+LINKML_GENERATORS_TYPESCRIPT_ARGS=
+
+LINKML_SCHEMA_GOOGLE_SHEET_ID="1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ"
+LINKML_SCHEMA_GOOGLE_SHEET_TABS="personinfo enums"
diff --git a/Makefile b/Makefile
@@ -16,11 +16,20 @@ PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
 DOCDIR = docs
 EXAMPLEDIR = examples
 SHEET_MODULE = from_sheets
-SHEET_ID = $(shell ${SHELL} ./utils/get-value.sh google_sheet_id)
-SHEET_TABS = $(shell ${SHELL} ./utils/get-value.sh google_sheet_tabs)
+SHEET_ID = $(LINKML_SCHEMA_GOOGLE_SHEET_ID)
+SHEET_TABS = $(LINKML_SCHEMA_GOOGLE_SHEET_TABS)
 SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml
+CONFIG_YAML = config.yaml
 
 # environment variables
+
+.EXPORT_ALL_VARIABLES:
+ifdef LINKML_ENVIRONMENT_FILENAME
+include ${LINKML_ENVIRONMENT_FILENAME}
+else
+include .env.public
+endif
+
 GEN_PARGS =
 ifdef LINKML_COOKIECUTTER_GEN_PROJECT_ARGS
 GEN_PARGS = ${LINKML_COOKIECUTTER_GEN_PROJECT_ARGS}
@@ -100,7 +109,7 @@ gen-examples:
 # generates all project files
 
 gen-project: $(PYMODEL)
-	$(RUN) gen-project ${CONFIG_YAML} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
+	$(RUN) gen-project -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
 	$(RUN) gen-pydantic --pydantic-version 2 $(SOURCE_SCHEMA_PATH) > $(PYMODEL)/pydanticmodel_v2.py
 
 # non-empty arg triggers owl (workaround https://github.com/linkml/linkml/issues/1453)

diff --git a/config.yaml b/config.yaml
@@ -1,41 +1,19 @@
 # Configuration of generators (defaults illustrated)
 ---
 generator_args:
-  excel:
-    mergeimports: true
+  jsonschema: {}
   owl:
     mergeimports: true
     metaclasses: true
     type_objects: true
-    # throws 'Cannot handle metadata profile: rdfs'
-    # metadata_profile: rdfs
-  markdown:
-    mergeimports: true
-  graphql:
-    mergeimports: true
-  java:
-    mergeimports: true
-    metadata: true
-  jsonld:
-    mergeimports: true
-  jsonschema:
-    mergeimports: true
-  jsonldcontext:
-    mergeimports: true
-  python:
-    mergeimports: true
-  prefixmap:
-    mergeimports: true
-  proto:
-    mergeimports: true
-  shacl:
-    mergeimports: true
-  shex:
-    mergeimports: true
-  sqlddl:
-    mergeimports: true
-  typescript:
-    mergeimports: true
-    metadata: true
-
-...
+  includes:
+    - jsonschema
+    - python
+    - owl
+    - shex
+    - shacl
+    - prefixmap
+  excludes:
+    - graphql
+    - sqlschema
+    - protobuf
diff --git a/project/jsonld/cmdr.context.jsonld b/project/jsonld/cmdr.context.jsonld
@@ -1,115 +1,27 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2023-03-07T15:54:05",
+      "generation_date": "2024-08-05T13:47:38",
       "source": "cmdr.yaml"
    },
    "@context": {
-      "OBI": {
-         "@id": "http://purl.obolibrary.org/obo/OBI_",
-         "@prefix": true
-      },
+      "OBI": "http://example.org/UNKNOWN/OBI/",
       "PATO": {
          "@id": "http://purl.obolibrary.org/obo/PATO_",
          "@prefix": true
       },
-      "TEMP": "https://example.org/TEMP/",
       "biolink": "https://w3id.org/biolink/",
       "cmdr": "https://w3id.org/linkml/cmdr/",
       "example": "https://example.org/",
       "linkml": "https://w3id.org/linkml/",
       "schema": "http://schema.org/",
       "@vocab": "https://w3id.org/linkml/cmdr/",
-      "comparator": {
-         "@id": "TEMP:comparator"
-      },
-      "concentration": {
-         "@id": "TEMP:concentration"
-      },
-      "has_input": {
-         "@id": "TEMP:has_input"
-      },
-      "has_numeric_value": {
-         "@id": "TEMP:has_numeric_value"
-      },
-      "has_output": {
-         "@id": "TEMP:has_output"
-      },
-      "has_raw_value": {
-         "@id": "TEMP:has_raw_value"
-      },
-      "has_unit": {
-         "@id": "TEMP:has_unit"
-      },
       "id": "@id",
-      "includes": {
-         "@id": "TEMP:includes"
-      },
-      "investigations": {
-         "@id": "TEMP:investigations"
-      },
-      "involved_in": {
-         "@id": "TEMP:involved_in"
-      },
-      "material_processings": {
-         "@id": "TEMP:material_processings"
-      },
-      "materials": {
-         "@id": "TEMP:materials"
-      },
-      "name": {
-         "@id": "TEMP:name"
-      },
-      "part_of": {
-         "@id": "TEMP:part_of"
-      },
-      "participations": {
-         "@id": "TEMP:participations"
-      },
-      "source": {
-         "@id": "TEMP:source"
-      },
-      "specimen_collection_processes": {
-         "@id": "TEMP:specimen_collection_processes"
-      },
-      "subjects": {
-         "@id": "TEMP:subjects"
-      },
-      "used_in": {
-         "@id": "TEMP:used_in"
-      },
-      "volume": {
-         "@id": "TEMP:volume"
-      },
-      "Container": {
-         "@id": "TEMP:Container"
-      },
-      "DataObject": {
-         "@id": "TEMP:DataObject"
-      },
-      "Investigation": {
-         "@id": "TEMP:Investigation"
-      },
-      "MaterialEntity": {
-         "@id": "TEMP:MaterialEntity"
-      },
       "MaterialProcessing": {
          "@id": "OBI:0000094"
       },
-      "Participation": {
-         "@id": "TEMP:Participation"
-      },
-      "Process": {
-         "@id": "TEMP:Process"
-      },
-      "Quantity": {
-         "@id": "TEMP:Quantity"
-      },
       "SpecimenCollectionProcess": {
          "@id": "OBI:0000659"
-      },
-      "Subject": {
-         "@id": "TEMP:Subject"
       }
    }
 }