manual merge

Author: turbomam

.gitignore

@@ -5,6 +5,8 @@ generated/docs
 mkdocs_html
 node_modules
 
+.idea
+
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

Makefile

@@ -2,10 +2,10 @@
 
 RUN=poetry run
 
-.PHONY: all clean gh_docs docserve
+.PHONY: all clean gh_docs docserve value_syntax_research
 
 # html_docs
-all: clean generated/mixs.py mkdocs_html/index.html
+all: clean clean_diff_stuff alldiffs value_syntax_research model/schema/mixs.yaml generated/mixs.py mkdocs_html/index.html
 
 # ---------------------------------------
 # TSVs from google drive
@@ -17,25 +17,26 @@ clean:
 	rm -rf generated/*
 	rm -rf logs/*
 	rm -rf mkdocs_html/
-	#rm -rf model/schema/*yaml
+	rm -rf model/schema/*.yaml
+	rm -rf downloads/*.*sv
 
-#model/schema/mixs.yaml: downloads/mixs6.tsv downloads/mixs6_core.tsv
-#	$(RUN) python -m gsctools.mixs_converter  2>&1 | tee -a logs/sheet2linkml.log
-#
-#downloads/mixs6.tsv:
-#	curl -L -s 'https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?format=tsv&gid=750683809' > $@
-#downloads/mixs6_core.tsv:
-#	curl -L -s 'https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?format=tsv&gid=178015749' > $@
+model/schema/mixs.yaml: downloads/mixs6.tsv downloads/mixs6_core.tsv
+	$(RUN) python -m gsctools.mixs_converter  2>&1 | tee -a logs/sheet2linkml.log
+
+downloads/mixs6.tsv:
+	curl -L -s 'https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?format=tsv&gid=750683809' > $@
+downloads/mixs6_core.tsv:
+	curl -L -s 'https://docs.google.com/spreadsheets/d/1QDeeUcDqXes69Y2RjU2aWgOpCVWo5OVsBX9MKmMqi_o/export?format=tsv&gid=178015749' > $@
 
 # todo add owl back in and make it awesome
-# todo derive output path from target file name
 # 		--exclude owl \
 
 generated/mixs.py: model/schema/mixs.yaml
 	$(RUN) gen-project \
 		--exclude excel \
 		--exclude java \
 		--exclude markdown \
+		--exclude owl \
 		--dir $(dir $@) $< 2>&1 | tee -a logs/linkml_artifact_generation.log
 #	mkdir generated/excel
 #	$(RUN) gen-excel --output generated/excel/mixs.xlsx $<
@@ -129,3 +130,7 @@ gsc_vs_nmdc_core: downloads/gsc_mixs6_core.csv downloads/nmdc_mixs6_core.csv
 		--primary-key 1 \
 		--format word-diff $^ > generated/gsc_vs_nmdc_core.txt
 # --format string         Available (rowmark|json|legacy-json|diff|word-diff|color-words) (default "diff")
+
+value_syntax_research: downloads/mixs6.tsv downloads/mixs6_core.tsv
+	poetry run python gsctools/value_syntaxes.py
+