inline list representation fixed

Cellular-Semantics · Sep 16, 2024 · 1d76ba8 · 1d76ba8
1 parent 9175d5f
commit 1d76ba8
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Showing 36 changed files with 200,838 additions and 1,618 deletions.
diff --git a/build/BICAN_schema.yaml b/build/BICAN_schema.yaml
diff --git a/build/CAP_schema.yaml b/build/CAP_schema.yaml
diff --git a/build/general_schema.yaml b/build/general_schema.yaml
diff --git a/project.Makefile b/project.Makefile
@@ -1,6 +1,6 @@
 ## Add your own custom Makefile targets here
 #
-# make build : generates dataclasses and merged schemas
+# make build : generates dataclasses and merged & expanded schemas
 # make gendoc : generates documentation
 # make gen-project : generates project folder contents
 
@@ -10,20 +10,27 @@ BUILD_FOLDER = build
 DOCDIR_BICAN = $(DOCDIR)/bican
 DOCDIR_CAP = $(DOCDIR)/cap
 
-.PHONY: merged_schemas classes build
+SCHEMA_EXPANDER := src/cell_annotation_schema/schema_expander.py
+
+.PHONY: expanded_schemas merged_schemas classes build
 
 merged_schemas:
 	cp $(SCHEMA_FOLDER)/cell_annotation_schema.yaml $(BUILD_FOLDER)/general_schema.yaml
 	$(RUN) gen-linkml $(SCHEMA_FOLDER)/BICAN/BICAN_schema.yaml --output $(BUILD_FOLDER)/BICAN_schema.yaml --mergeimports --format yaml --no-materialize-attributes
 	$(RUN) gen-linkml $(SCHEMA_FOLDER)/CAP/CAP_schema.yaml --output $(BUILD_FOLDER)/CAP_schema.yaml --mergeimports --format yaml --no-materialize-attributes
 
-classes: merged_schemas
+expanded_schemas: merged_schemas
+	$(RUN) python $(SCHEMA_EXPANDER) expand -i $(BUILD_FOLDER)/general_schema.yaml -o $(BUILD_FOLDER)/general_schema.yaml
+	$(RUN) python $(SCHEMA_EXPANDER) expand -i $(BUILD_FOLDER)/BICAN_schema.yaml -o $(BUILD_FOLDER)/BICAN_schema.yaml
+	$(RUN) python $(SCHEMA_EXPANDER) expand -i $(BUILD_FOLDER)/CAP_schema.yaml -o $(BUILD_FOLDER)/CAP_schema.yaml
+
+classes: expanded_schemas
 #	gen-python $(BUILD_FOLDER)/general_schema.yaml --no-slots > $(PYMODEL)/cell_annotation_schema.py
 #	gen-python $(BUILD_FOLDER)/BICAN_schema.yaml --no-slots > $(PYMODEL)/bican/cell_annotation_schema.py
 #	gen-python $(BUILD_FOLDER)/CAP_schema.yaml --no-slots > $(PYMODEL)/cap/cell_annotation_schema.py
 	$(RUN) python src/cell_annotation_schema/generator/dataclassgen.py
 
-build: merged_schemas classes
+build: expanded_schemas classes
 	echo "Release products generated."
 
 # mkdocs generation

diff --git a/project/excel/BICAN_schema.xlsx b/project/excel/BICAN_schema.xlsx
diff --git a/project/excel/CAP_schema.xlsx b/project/excel/CAP_schema.xlsx
diff --git a/project/excel/general_schema.xlsx b/project/excel/general_schema.xlsx
diff --git a/project/jsonld/BICAN_schema.context.jsonld b/project/jsonld/BICAN_schema.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-08-06T17:24:36",
+      "generation_date": "2024-09-16T15:21:14",
       "source": "BICAN_schema.yaml"
    },
    "@context": {

diff --git a/project/jsonld/BICAN_schema.jsonld b/project/jsonld/BICAN_schema.jsonld
diff --git a/project/jsonld/CAP_schema.context.jsonld b/project/jsonld/CAP_schema.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-08-06T17:24:38",
+      "generation_date": "2024-09-16T15:21:21",
       "source": "CAP_schema.yaml"
    },
    "@context": {

diff --git a/project/jsonld/CAP_schema.jsonld b/project/jsonld/CAP_schema.jsonld
diff --git a/project/jsonld/general_schema.context.jsonld b/project/jsonld/general_schema.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-08-06T17:24:34",
+      "generation_date": "2024-09-16T15:21:08",
       "source": "general_schema.yaml"
    },
    "@context": {