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Update VBO pipeline to not break OLS deployment
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Previously, when DADIS KEY was not present, the OLS Monarch pipeline would fail building vbo from master..

cc @twhetzel @sabrinatoro
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matentzn committed Jan 30, 2024
1 parent ccfb1a7 commit 56bbd95
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Showing 2 changed files with 12 additions and 2 deletions.
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -37,3 +37,4 @@ src/patterns/data/**/*.ofn
src/patterns/data/**/*.txt
src/patterns/pattern_owl_seed.txt
src/patterns/all_pattern_terms.txt
*.pyc
13 changes: 11 additions & 2 deletions src/ontology/vbo.Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -69,14 +69,23 @@ $(IMPORTDIR)/wikidata_import.owl: $(TMPDIR)/wikidata_labels.ttl
.PHONY: wikidata
wikidata: $(IMPORTDIR)/wikidata_import.owl

ifeq ($(DADIS_API_KEY),)
$(COMPONENTSDIR)/dadisbreedcountry.tsv:
pip install -U pip && pip install pydantic==2.5.3 pandas==2.1.4
@echo "WARNING: DADIS_API_KEY not set, skipping dadisbreedcountry.tsv"

$(COMPONENTSDIR)/dadistransbound.tsv:
@echo "WARNING: DADIS_API_KEY not set, skipping dadistransbound.tsv"

else
$(COMPONENTSDIR)/dadisbreedcountry.tsv:
pip install pydantic>=2.5.3 pandas>=2.1.4
python ../scripts/find_dadis_local_ids.py --input_filename ./components/dadisbreedcountry.tsv --output_filename ./components/dadisbreedcountry.tsv

$(COMPONENTSDIR)/dadistransbound.tsv:
pip install -U pip && pip install pydantic==2.5.3 pandas==2.1.4
pip install pydantic>=2.5.3 pandas>=2.1.4
python ../scripts/find_dadis_transboundary_ids.py --input_filename ./components/dadistransbound.tsv --output_filename ./components/dadistransbound.tsv

endif

.PHONY: dadisbreedcountry
dadis-local-sync: $(COMPONENTSDIR)/dadisbreedcountry.owl
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