Merge pull request #121 from geneontology/noctua-issue-902b

Use functional syntax instead of OBO

Makefile

@@ -1,16 +1,18 @@
 OBO = http://purl.obolibrary.org/obo
 
-all: target all_obo neo.obo neo.owl
+all: target all_ofn neo.obo neo.owl
 
 clean:
 	rm trigger datasets.json mirror/*gz mirror/*tmp target/*.obo || echo "not all files present, perhaps last build did not complete"
 
 TEST_SRCS ?= sgd pombase
 SRCS ?= sgd pombase mgi zfin rgd dictybase fb tair wb goa_human goa_human_complex goa_human_rna goa_human_isoform goa_pig xenbase pseudocap ecocyc goa_sars-cov-2 uniprot_reviewed
+ROBOT_ENV = ROBOT_JAVA_ARGS=-Xmx12G
+ROBOT = $(ROBOT_ENV) robot
 
-OBO_SRCS = $(patsubst %,target/neo-%.obo,$(SRCS))
-all_obo: $(OBO_SRCS)
-test_obo: target $(patsubst %,target/neo-%.obo,$(TEST_SRCS))
+OFN_SRCS = $(patsubst %,target/neo-%.ofn,$(SRCS))
+all_ofn: $(OFN_SRCS)
+test_ofn: target $(patsubst %,target/neo-%.ofn,$(TEST_SRCS))
 
 #test: touch_trigger test_obo
 test:
@@ -23,8 +25,8 @@ trigger:
 	touch $@
 
 IMPORTS = imports/pr_import.obo
-neo.obo:  $(OBO_SRCS) $(IMPORTS)
-	owltools --create-ontology http://purl.obolibrary.org/obo/go/noctua/neo.owl $^ --merge-support-ontologies  -o -f obo $@.tmp && grep -v ^owl-axioms $@.tmp > $@
+neo.owl: $(OFN_SRCS) $(IMPORTS)
+	$(ROBOT) merge $(addprefix -i ,$^) annotate --ontology-iri 'http://purl.obolibrary.org/obo/go/noctua/neo.owl' convert -f owl -o $@.tmp && mv $@.tmp $@
 
 ## datasets.json is created as a throwaway in the NEO versions of the
 ## pipeline and is based on the go-site master data.
@@ -41,8 +43,8 @@ foo:
 # BUG: temporary hardcode until https://github.com/geneontology/go-site/issues/1431 is resolved and stable GPI URL is established
 mirror/goa_sars-cov-2.gpi.gz:
 	wget --no-check-certificate https://raw.githubusercontent.com/Knowledge-Graph-Hub/kg-covid-19/master/curated/ORFs/uniprot_sars-cov-2.gpi -O mirror/goa_sars-cov-2.gpi && gzip mirror/goa_sars-cov-2.gpi
-target/neo-goa_sars-cov-2.obo: mirror/goa_sars-cov-2.gpi.gz
-	gzip -dc $< | ./gpi2obo.pl -s Scov2 -n sars-cov-2 > $@.tmp && mv $@.tmp $@
+target/neo-goa_sars-cov-2.ofn: mirror/goa_sars-cov-2.gpi.gz
+	gzip -dc $< | ./gpi2ofn.pl -s Scov2 -n sars-cov-2 > $@.tmp && mv $@.tmp $@
 
 # ## In support of including viruses and bacteria
 # ## (https://github.com/geneontology/neo/issues/77).
@@ -64,8 +66,8 @@ mirror/uniprot_reviewed.gpi.gz: datasets.json
 	perl filter.pl -v --metadata datasets.json --filter filter_list.txt --input mirror/uniprot_reviewed.gpi.tmp > mirror/filtered_uniprot_reviewed.gpi.tmp
 	gzip -c mirror/filtered_uniprot_reviewed.gpi.tmp > mirror/filtered_uniprot_reviewed.gpi.gz.tmp
 	mv mirror/filtered_uniprot_reviewed.gpi.gz.tmp mirror/uniprot_reviewed.gpi.gz
-target/neo-uniprot_reviewed.obo: mirror/uniprot_reviewed.gpi.gz
-	gzip -dc $< | ./gpi2obo.pl -F -n reviewed > $@.tmp && mv $@.tmp $@
+target/neo-uniprot_reviewed.ofn: mirror/uniprot_reviewed.gpi.gz
+	gzip -dc $< | ./gpi2ofn.pl -F -n reviewed > $@.tmp && mv $@.tmp $@
 
 # Sub-makefile
 #
@@ -75,20 +77,13 @@ target/neo-uniprot_reviewed.obo: mirror/uniprot_reviewed.gpi.gz
 # see below for regenerating this
 include Makefile-gafs
 
-# This is very hacky:
-#  - The neo solr index has an ID field (which is a CURIE), but no URI
-#  - Minerva requires OWL which uses URIs
+#  The neo solr index has an ID field (which is a CURIE), but no URI
+#  Minerva requires OWL which uses URIs
 #
 # When loading solr, owltools will use the oboInOwl:id field as priority to load the ID field (see https://github.com/owlcollab/owltools/pull/247)
 # Otherwise, the owltools built-in URI contraction method is used, which assumes OBO purls, with unpredictable behavior non-OBO PURLs
-#
-# Neo entities are NOT OBO ontologies, so they have a mix of prefixes, including identifiers.org
-#
-# Our hack is as follows. The perl code first generates an OBO file with CURIEs like FlyBase:FBgn111
-# The default owltools expansion makes this an OBO PURLs
-# We then "reverse" this with some hacky regexes...
-neo.owl: neo.obo
-	owltools $< -o $@.tmp && ./bin/fix-obo-uris.pl $@.tmp > $@.tmp2 && mv $@.tmp2 $@
+neo.obo: neo.owl
+	$(ROBOT) convert -i $< -o $@.tmp -f obo && grep -v ^owl-axioms $@.tmp >$@
 
 Makefile-gafs: datasets.json
 	./build-neo-makefile.py -i $< > $@.tmp && mv $@.tmp $@
@@ -107,10 +102,8 @@ rnacentral.gpi.gz:
 rnacentral.gpi: rnacentral.gpi.gz
 	gzip -dc $< > $@
 
-target/neo-rnac.obo: rnacentral.gpi.gz
-	gzip -dc $< | ./rnacgpi2obo.pl > $@.tmp && mv $@.tmp $@
+target/neo-rnac.ofn: rnacentral.gpi.gz
+	gzip -dc $< | ./rnacgpi2ofn.pl > $@.tmp && mv $@.tmp $@
 
-target/xneo-%.owl: target/neo-%.obo
-	owltools $< -o $@.tmp && mv $@.tmp $@
-target/neo-%.owl: target/xneo-%.owl
-	./bin/fix-obo-uris.pl $< >  $@.tmp && mv $@.tmp $@
+target/neo-%.owl: target/neo-%.ofn
+	$(ROBOT) convert -i $< -o $@.tmp -f owl && mv $@.tmp $@