#97 minimal_markers template merged with class template

obophenotype · Sep 8, 2021 · 29ac975 · 29ac975
1 parent 930edaa
commit 29ac975
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Showing 10 changed files with 190 additions and 403 deletions.
diff --git a/src/dendrograms/Makefile b/src/dendrograms/Makefile
@@ -1,20 +1,19 @@
 JOBS = CCN202002013 #CCN201912131 CCN201912132 CCN201908210 CCN201810310 CCN201908211
 
 TEMPLATE_FILES = $(patsubst %, ../templates/%.tsv, $(JOBS))
-TEMPLATE_CLASS_FILES = $(patsubst %, ../patterns/data/bds/%_class.tsv, $(JOBS))
+TEMPLATE_CLASS_FILES = $(patsubst %, ../patterns/data/default/%_class.tsv, $(JOBS))
 MARKER_DENORMALIZED_FILES = $(patsubst %, ../markers/%_markers_denormalized.tsv, $(JOBS))
 EQUIVALENT_CLASS_MARKER_FILES = $(patsubst %, ../templates/%_equivalent_markers.tsv, $(JOBS))
-EQUIVALENT_CLASS_REIFICATION_FILES = $(patsubst %, ../patterns/data/bds/%_equivalent_reification.tsv, $(JOBS))
-TEMPLATE_MINIMAL_MARKER_FILES = $(patsubst %, ../patterns/data/bds/%_minimal_markers.tsv, $(JOBS))
-NOMENCLATURE_TEMPLATE_FILES = $(patsubst %, ../patterns/data/bds/%_non_taxonomy_classification.tsv, $(JOBS))
+EQUIVALENT_CLASS_REIFICATION_FILES = $(patsubst %, ../patterns/data/default/%_equivalent_reification.tsv, $(JOBS))
+NOMENCLATURE_TEMPLATE_FILES = $(patsubst %, ../patterns/data/default/%_non_taxonomy_classification.tsv, $(JOBS))
 
 
-all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_FILES) $(MARKER_DENORMALIZED_FILES) $(EQUIVALENT_CLASS_MARKER_FILES) $(EQUIVALENT_CLASS_REIFICATION_FILES) $(TEMPLATE_MINIMAL_MARKER_FILES) $(NOMENCLATURE_TEMPLATE_FILES)
+all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_FILES) $(MARKER_DENORMALIZED_FILES) $(EQUIVALENT_CLASS_MARKER_FILES) $(EQUIVALENT_CLASS_REIFICATION_FILES) $(NOMENCLATURE_TEMPLATE_FILES)
 
 ../templates/%.tsv: %.json
 	python ../scripts/template_runner.py $< $@
 
-../patterns/data/bds/%_class.tsv: %.json
+../patterns/data/default/%_class.tsv: %.json
 	python ../scripts/template_runner.py -c $< $@
 
 ../markers/%_markers_denormalized.tsv: %.json
@@ -23,12 +22,9 @@ all: $(TEMPLATE_FILES) $(TEMPLATE_CLASS_FILES) $(MARKER_DENORMALIZED_FILES) $(EQ
 ../templates/%_equivalent_markers.tsv: %.json
 	python ../scripts/template_runner.py -em $< $@
 
-../patterns/data/bds/%_equivalent_reification.tsv: %.json
+../patterns/data/default/%_equivalent_reification.tsv: %.json
 	python ../scripts/template_runner.py -er $< $@
 
-../patterns/data/bds/%_minimal_markers.tsv: %.json
-	python ../scripts/template_runner.py -mm $< $@
-
-../patterns/data/bds/%_non_taxonomy_classification.tsv: %.json
+../patterns/data/default/%_non_taxonomy_classification.tsv: %.json
 	python ../scripts/template_runner.py -n $< $@
 
diff --git a/src/ontology/bdscratch.Makefile b/src/ontology/bdscratch.Makefile
@@ -12,7 +12,6 @@ OWL_FILES = $(patsubst %, components/%.owl, $(JOBS))
 OWL_CLASS_FILES = $(patsubst %, components/%_class.owl, $(JOBS))
 OWL_EQUIVALENT_CLASS_FILES = $(patsubst %, components/%_equivalent_class.owl, $(JOBS))
 GENE_FILES = $(patsubst %, mirror/%.owl, $(JOBS))
-OWL_MIN_MARKER_FILES = $(patsubst %, components/%_minimal_markers.owl, $(JOBS))
 OWL_NOMENCLATURE_FILES = $(patsubst %, components/%_non_taxonomy_classification.owl, $(JOBS))
 
 #DEND_FILES = $(patsubst %, ../dendrograms/%.json, $(JOBS))
@@ -45,8 +44,7 @@ dosdp_patterns_default: $(SRC) all_imports .FORCE
 $(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/data/default/%.tsv .FORCE
 	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_class.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_class.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/data/default/CCN202002013_class.txt; fi
 	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_equivalent_reification.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_equivalent_class.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/data/default/CCN202002013_equivalent_reification.txt; fi
-	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_minimal_markers.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_minimal_markers.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/data/default/CCN202002013_minimal_markers.txt; fi
-	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_non_taxonomy_classification.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=CCN202002013_non_taxonomy_classification.txt; fi
+	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(PATTERNDIR)/data/default/CCN202002013_non_taxonomy_classification.tsv --template=$(PATTERNDIR)/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml --obo-prefixes=true --prefixes=template_prefixes.yaml --outfile=$(PATTERNDIR)/CCN202002013_non_taxonomy_classification.txt; fi
 
 # hard wiring for now.  Work on patsubst later
 mirror/ensmusg.owl: ../templates/ensmusg.tsv .FORCE
@@ -80,11 +78,6 @@ components/%_equivalent_class.owl: ../patterns/data/default/%_equivalent_reifica
         --infile=$< --template=../patterns/dosdp-patterns/taxonomy_equivalent_class.yaml \
         --ontology=$(SRC) --obo-prefixes=true --outfile=$@
 
-components/%_minimal_markers.owl: ../patterns/data/default/%_minimal_markers.tsv ../patterns/dosdp-patterns/taxonomy_minimal_markers.yaml $(SRC) all_imports .FORCE
-	$(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
-        --infile=$< --template=../patterns/dosdp-patterns/taxonomy_minimal_markers.yaml \
-        --ontology=$(SRC) --obo-prefixes=true --outfile=$@
-
 components/%_non_taxonomy_classification.owl: ../patterns/data/default/%_non_taxonomy_classification.tsv ../patterns/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml $(SRC) all_imports .FORCE
 	$(DOSDPT) generate --catalog=catalog-v001.xml --prefixes=template_prefixes.yaml \
         --infile=$< --template=../patterns/dosdp-patterns/taxonomy_non_taxonomy_classification.yaml \