diff --git a/.github/workflows/buid_and_release.yml b/.github/workflows/buid_and_release.yml index 58cb191..7bf3125 100644 --- a/.github/workflows/buid_and_release.yml +++ b/.github/workflows/buid_and_release.yml @@ -17,7 +17,7 @@ jobs: - name: build # todo: reactivate `make all`, pending pending https://github.com/monarch-initiative/medgen/issues/11 # run: make all - run: make minimal + run: export ROBOT_JAVA_ARGS=-Xmx15G; make minimal - name: Get current time uses: josStorer/get-current-time@v2.0.2 id: current-time @@ -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..9427aa6 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.ttl.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.ttl: medgen.obo + export ROBOT_JAVA_ARGS=-Xmx15G; robot convert --input $< --output $@ --format ttl + +medgen.ttl.gz: medgen.ttl + gzip -c $< > $@ + # We only care about diseases for now # - NOTE: some cancers seem to appear under Neoplastic-Process x-%.obo: medgen.obo @@ -76,9 +84,7 @@ x-%.obo: medgen.obo medgen-disease-extract.obo: x-Disease-or-Syndrome.obo x-Neoplastic-Process.obo owltools $^ --merge-support-ontologies -o -f obo $@ -medgen-disease-extract.json: medgen-disease-extract.obo - owltools $< -o -f json $@ - +# todo: change this to robot convert w/ format ttl, lower memory usage? output/medgen-disease-extract.owl: medgen-disease-extract.obo | output/ owltools $< -o $@ @@ -92,6 +98,8 @@ sssom-validate: umls-hpo.sssom.tsv # todo: Address GH action build heap space err: # https://github.com/monarch-initiative/medgen/actions/runs/9150396559/job/25155114016 # Don't need to fix until the case where we need to use `make all` or otherwise need this file. +#medgen-disease-extract.json: medgen-disease-extract.obo +# owltools $< -o -f json $@ output/medgen.obographs.json: output/medgen-disease-extract.owl | output/ robot convert -i $< -o $@