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Merge pull request #97 from monarch-initiative/fix-imports
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Add a few missing pieces for a working pipeline
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matentzn authored Nov 25, 2024
2 parents 01301c4 + ce7c17a commit 2f56804
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Showing 22 changed files with 202 additions and 175 deletions.
5 changes: 5 additions & 0 deletions .gitignore
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Expand Up @@ -51,3 +51,8 @@ src/ontology/phenio-relation-graph.tar.gz
src/ontology/phenio-relation-graph.tsv
src/ontology/phenio-test.owl
src/ontology/imports/merged_import.owl
phenio.tar.gz
phenio.owl
phenio.json
phenio-test.owl
phenio-relation-graph.tar.gz
1 change: 1 addition & 0 deletions src/ontology/imports/bspo_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/cl-bridge-to-emapa_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/cl-bridge-to-xao_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/fbdv_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/hgnc_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/monochrom_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/mpath.owl_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/nbo.owl_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/ncbigene_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/pr_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/ro_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/so_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/uberon-bridge-to-emapa_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/uberon-bridge-to-xao_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/uberon-cl-bridges_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/upheno-alignments_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/upheno-bridge_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/wbls_terms.txt
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1 change: 1 addition & 0 deletions src/ontology/imports/zfs_terms.txt
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9 changes: 6 additions & 3 deletions src/ontology/phenio.Makefile
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Expand Up @@ -14,7 +14,7 @@ UPDATE_QUERY_PATH= $(TMPDIR)/subq_update.sparql
EXPLAIN_OUT_PATH= $(TMPDIR)/explain_unsat.md
RELEASE_ASSETS_AFTER_RELEASE=$(foreach n,$(RELEASE_ASSETS), ./$(n))

RELEASE_ASSETS = $(ONT).owl $(ONT).json $(ONT)-relation-graph.tar.gz $(ONT)-test.owl
RELEASE_ASSETS = $(ONT).owl.tar.gz $(ONT).json $(ONT)-relation-graph.tar.gz $(ONT)-test.owl

################################################################
#### Components ################################################
Expand Down Expand Up @@ -43,10 +43,10 @@ ifeq ($(strip $(MIR)),true)

ONTS_WITH_NCBIGENE_DATA = $(COMPONENTSDIR)/mondo.owl

$(TMPDIR)/ncbigene_dependencies.txt: # $(ONTS_WITH_NCBIGENE_DATA)
$(TMPDIR)/ncbigene_dependencies.txt: $(ONTS_WITH_NCBIGENE_DATA)
$(ROBOT) merge $(foreach n,$(ONTS_WITH_NCBIGENE_DATA), -i $(n)) \
query --query ../sparql/terms.sparql $(TMPDIR)/all_terms_for_ncbigene_dependencies.txt
tr -d '\r' < $(TMPDIR)/all_terms_for_ncbigene_dependencies.txt | sed 's/.*/<&>/' | grep ncbigene > $@
tr -d '\r' < $(TMPDIR)/all_terms_for_ncbigene_dependencies.txt | sed 's/.*/<&>/' | grep ncbigene | sort | uniq > $@

../sparql/construct-ncbigene.sparql: ../sparql/construct-ncbigene.sparql.template $(TMPDIR)/ncbigene_dependencies.txt
@sed "/{{VALUES}}/r $(TMPDIR)/ncbigene_dependencies.txt" $< | sed '/{{VALUES}}/d' > $@
Expand Down Expand Up @@ -157,6 +157,9 @@ $(ONT)-test.owl: $(ONT).owl
$(ONT)-relation-graph.tar.gz: $(ONT)-relation-graph.tsv
tar -czf $@ $<

$(ONT).owl.tar.gz: $(ONT).owl
tar -czf $@ $<

# Do release to Github
public_release:
@test $(GHVERSION)
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