From 701595390634b09bb70a0ffdf7b5be0f803e752b Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sun, 12 Jan 2025 00:24:30 +0200 Subject: [PATCH] Makefile MISC refactor --- src/ontology/upheno.Makefile | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/src/ontology/upheno.Makefile b/src/ontology/upheno.Makefile index 9e4f868..8b55e80 100644 --- a/src/ontology/upheno.Makefile +++ b/src/ontology/upheno.Makefile @@ -215,6 +215,8 @@ $(TEMPLATEDIR)/phenotype-top-level.tsv: $(TEMPLATEDIR)/root-alignments.tsv: wget "https://docs.google.com/spreadsheets/d/1TDDGUKLME28ZLE5YayXNOwAkBD7jDoAgLPuTkYoMAs0/pub?gid=1260598340&single=true&output=tsv" -O $@ +$(TEMPLATEDIR)/axiom-injections.tsv: + wget "https://docs.google.com/spreadsheets/d/e/2PACX-1vRx0gi2I-Ks14LGNibiy6YzW-3A45_jZOnYsBNmaIjF3M8vrXboJwBYle525RXVscXhGGlOzGe05VhX/pub?gid=1825106877&single=true&output=tsv" -O $@ $(COMPONENTSDIR)/upheno-species-neutral.owl: $(ROBOT) merge -i ../curation/upheno-release-prepare/all/upheno_layer.owl \ @@ -232,6 +234,12 @@ $(COMPONENTSDIR)/upheno-bridge.owl: $(SRC) $(MAPPINGDIR)/upheno-species-independ ###### Import preparation ########## #################################### +# go has to be relaxed before it can be merged +mirror-go: | $(TMPDIR) + curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 400 && \ + $(ROBOT) relax -i $(TMPDIR)/go-download.owl convert -o $(TMPDIR)/$@.owl + + $(IMPORTDIR)/all_phenotype_terms.txt: mirror/merged.owl $(ROBOT) query -f csv -i $< --query ../sparql/all_phenotype_terms.sparql $@ sed -i 's/[?]//g' $@ @@ -328,3 +336,27 @@ obsolete_fillers: base_report: $(MAKE) IMP=false PAT=false MIR=false upheno-base.owl -B $(ROBOT) report -i upheno-base.owl $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o tmp/$@.tsv + +################################# +## Patterns managed on GDocs #### +################################# + +abnormalCellularComponent=https://docs.google.com/spreadsheets/d/e/2PACX-1vRx0gi2I-Ks14LGNibiy6YzW-3A45_jZOnYsBNmaIjF3M8vrXboJwBYle525RXVscXhGGlOzGe05VhX/pub?gid=1218954488&single=true&output=tsv + +$(PATTERNDIR)/data/automatic/abnormalCellularComponent.tsv: + wget "$(abnormalCellularComponent)" -O $@ + +prepare_release: + @echo "WARNING WARNING WARNING: DO NOT USE THIS COMMAND, use sh prepare_release.sh instead!" + +.PHONY: prepare_release_customised +prepare_release_customised: all_odk + rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ + mkdir -p $(RELEASEDIR)/patterns && cp -rf $(PATTERN_RELEASE_FILES) $(RELEASEDIR)/patterns &&\ + rm -f $(CLEANFILES) &&\ + echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release \ + on your git hosting site such as GitHub or GitLab" + +.PHONY: prepare_release_fast +prepare_release_fast: + $(MAKE) prepare_release_customised IMP=false PAT=false MIR=false COMP=false