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Dividing user makefile from release manager makefile, fixes #72
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-33
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Makefile

Lines changed: 14 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -81,22 +81,25 @@ realclean-%:
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# ---
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# Prefixes
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# ---
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# TODO: sync with bioregistry
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# NOTE: move this to build folder
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build_prefixes: $(PREFIX_DIR)/prefixes.csv
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build_prefixes: $(PREFIX_DIR)/prefixes.csv $(PREFIX_DIR)/prefixes.yaml
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#$(PREFIX_DIR)/obo_prefixes.owl:
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# robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
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$(PREFIX_DIR)/obo_prefixes.owl: $(STAMP)
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robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
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#$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
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# sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
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$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
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sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $<
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#$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
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# sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
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$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
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sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
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$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/prefixes_local.csv $(PREFIX_DIR)/obo_prefixes.csv
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cat $^ > $@
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# see https://github.com/INCATools/relation-graph/issues/168
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$(PREFIX_YAML_PATH): $(PREFIX_CSV_PATH)
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grep -v ^prefix, $< | grep -v ^obo, | perl -npe 's@,(.*)@: "$$1"@' > $@.tmp && mv $@.tmp $@
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#$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv#
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# cat $^ > $@
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# ---

src/semsql/builder/build.Makefile

Lines changed: 0 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -86,25 +86,3 @@ PREFIX_YAML_PATH = $(PREFIX_DIR)/prefixes.yaml
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%-properties.txt:
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touch $@
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# ---
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# Prefixes
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# ---
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build_prefixes: $(PREFIX_DIR)/prefixes.csv $(PREFIX_DIR)/prefixes.yaml
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$(PREFIX_DIR)/obo_prefixes.owl:
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robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
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$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
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sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $<
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$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
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sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
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$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/prefixes_local.csv $(PREFIX_DIR)/obo_prefixes.csv
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cat $^ > $@
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# see https://github.com/INCATools/relation-graph/issues/168
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$(PREFIX_YAML_PATH): $(PREFIX_CSV_PATH)
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grep -v ^prefix, $< | grep -v ^obo, | perl -npe 's@,(.*)@: "$$1"@' > $@.tmp && mv $@.tmp $@
110-

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