diff --git a/.github/workflows/buid_and_release.yml b/.github/workflows/buid_and_release.yml index 58cb191..436ccd4 100644 --- a/.github/workflows/buid_and_release.yml +++ b/.github/workflows/buid_and_release.yml @@ -31,10 +31,11 @@ jobs: automatic_release_tag: "${{ steps.current-time.outputs.formattedTime }}" title: "${{ steps.current-time.outputs.formattedTime }}" prerelease: false - # todo: add back `release/medgen-disease-extract.owl`, pending https://github.com/monarch-initiative/medgen/issues/11 + # todo: add back `release/medgen-disease-extract.owl`?, pending https://github.com/monarch-initiative/medgen/issues/11 # output/release/medgen-disease-extract.owl files: | output/release/medgen.obo + output/release/medgen.owl.gz output/release/medgen-disease-extract.obo output/release/medgen-xrefs.robot.template.tsv output/release/medgen-xrefs-mesh.robot.template.tsv diff --git a/makefile b/makefile index 856fccd..67d29ad 100644 --- a/makefile +++ b/makefile @@ -6,7 +6,8 @@ .PHONY: all build stage stage-% analyze clean deploy-release build-lite minimal sssom sssom-validate OBO=http://purl.obolibrary.org/obo -PRODUCTS=medgen-disease-extract.obo medgen-disease-extract.owl +# todo: medgen-disease-extract.owl.gz? +PRODUCTS=medgen-disease-extract.obo medgen-disease-extract.owl medgen.owl.gz TODAY ?=$(shell date +%Y-%m-%d) VERSION=$(TODAY) @@ -15,9 +16,10 @@ minimal: build-lite stage-lite clean stage-lite: | output/release/ # mv medgen-disease-extract.owl output/release/ mv *.obo output/release/ + mv medgen.owl.gz output/release/ mv *.robot.template.tsv output/release/ mv *.sssom.tsv output/release/ -build-lite: medgen-disease-extract.obo medgen-xrefs.robot.template.tsv umls-hpo.sssom.tsv sssom-validate +build-lite: medgen.owl.gz medgen-disease-extract.obo medgen-xrefs.robot.template.tsv umls-hpo.sssom.tsv sssom-validate all: build stage clean analyze # analyze: runs more than just this file; that goal creates multiple files @@ -68,6 +70,12 @@ ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt: ftp.ncbi.nlm.nih.gov/ medgen.obo: ftp.ncbi.nlm.nih.gov/ uid2cui.tsv ./src/medgen2obo.pl > $@.tmp && mv $@.tmp $@ +medgen.owl: medgen.obo + robot convert --input $< --output $@ --format owl + +medgen.owl.gz: medgen.owl + gzip -c $< > $@ + # We only care about diseases for now # - NOTE: some cancers seem to appear under Neoplastic-Process x-%.obo: medgen.obo