Merge pull request #871 from GenomicsStandardsConsortium/standardize-linkml-and-yaml

YAML and LinkML auto-formatting and enumeration auto-describing

Author: turbomam

.yamlfmt

@@ -0,0 +1,4 @@
+formatter:
+  type: basic
+  include_document_start: true
+  max_line_length: 0

Makefile

@@ -85,6 +85,40 @@ examples/output: src/mixs/schema/mixs.yaml
 		--output-directory $@ \
 		--schema $< > $@/README.md
 
+.PHONY: standardize-schema
+
+#  |\
+  #	yamlfmt -in -conf .yamlfmt >
+
+standardize-schema:
+	$(RUN) python src/scripts/describe_enums_by_slots_using.py \
+    --schema_file src/mixs/schema/mixs.yaml \
+    --output_file src/mixs/schema/mixs_with_enum_descriptions.yaml
+	$(RUN) gen-linkml \
+		--format yaml \
+		--no-mergeimports \
+		--no-materialize-attributes \
+		--materialize-patterns src/mixs/schema/mixs_with_enum_descriptions.yaml |\
+	yq eval '(.. | select(has("from_schema")) | .from_schema) style="" | del(.. | select(has("from_schema")).from_schema)' |\
+	yq eval '.classes[] |= select(has("annotations")).annotations |= map_values(.value)' |\
+	yq eval '.prefixes |= map_values(.prefix_reference)' |\
+	yq eval '.settings |= map_values(.setting_value)'  |\
+	yq eval '.slots[] |= select(has("annotations")).annotations |= map_values(.value)' |\
+	yq eval 'del(.classes.[].name)' |\
+	yq eval 'del(.classes.[].slot_usage.[].name)'  |\
+	yq eval 'del(.enums.[].name)'  |\
+	yq eval 'del(.enums.[].permissible_values.[].text)' |\
+	yq eval 'del(.slots.[].domain)'  |\
+	yq eval 'del(.slots.[].name)' |\
+	yq eval 'del(.source_file)'  |\
+	yq eval 'del(.subsets.[].name)' | cat > src/mixs/schema/mixs_standardized.yaml
+	mv src/mixs/schema/mixs_standardized.yaml src/mixs/schema/mixs.yaml
+	rm -rf src/mixs/schema/mixs_standardized.yaml src/mixs/schema/mixs_with_enum_descriptions.yaml
+
+test1:
+	echo $$PATH
+	yamlfmt  -conf .yamlfmt src/mixs/schema/mixs.yaml >  src/mixs/schema/mixs_standardized.yam
+
 # Test documentation locally
 serve: mkd-serve