Alternate format for OLS

- Add: Goal for medgen.owl.gz, along with additional intermediate goals and updates to build goals and GH action for this.

.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=-Xmx12G; make minimal
     - name: Get current time
       uses: josStorer/[email protected]
       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

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=-Xmx12G; 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 $@