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add build for reacto.owl and go-lego-reacto.owl to stage_release #19288

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Apr 21, 2020
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add build for reacto.owl and go-lego-reacto.owl to stage_release #19288

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15 changes: 14 additions & 1 deletion src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,7 @@ GO_MAIN_RELATIONS = $(GO_BASIC_RELATIONS) BFO:0000051 BFO:0000066 RO:0002091 RO:
GO_PLUS = extensions/go-plus
GO_GAF = extensions/go-gaf
GO_LEGO = extensions/go-lego
GO_LEGO_REACTO = extensions/go-lego-reacto

SPARQLDIR = ../sparql
REPORTDIR = $(RELEASEDIR)/reports
Expand All @@ -79,7 +80,7 @@ REPORTDIR = $(RELEASEDIR)/reports
# TOP LEVEL TARGETS
# ----------------------------------------

stage_release: imports/reactome_xrefs_import.owl test $(ONT).owl $(ONT).obo $(ONT).json.gz $(GO_PLUS).owl $(GO_PLUS).json.gz go-base.owl $(GO_GAF).owl $(GO_LEGO).owl go-basic.obo go-basic.json.gz subset-reports generate-mappings
stage_release: imports/reactome_xrefs_import.owl test $(ONT).owl $(ONT).obo $(ONT).json.gz $(GO_PLUS).owl $(GO_PLUS).json.gz go-base.owl $(GO_GAF).owl $(GO_LEGO).owl $(GO_LEGO_REACTO).owl go-basic.obo go-basic.json.gz subset-reports generate-mappings

test: $(SRC)-check sparql_test change-report.txt reasoned.owl unsatisfiable

Expand Down Expand Up @@ -216,6 +217,18 @@ $(GO_GAF).owl: extensions/go-gaf-edit.ofn $(GO_PLUS).owl extensions/gorel.owl mi
$(GO_LEGO).owl: extensions/go-lego-edit.ofn $(GO_PLUS).owl mirror/ro-download.owl extensions/legorel.owl extensions/go-bfo-bridge.owl mirror/taxslim.owl mirror/taxslim-disjoint-over-in-taxon.owl
$(ROBOT) merge -i $< --collapse-import-closure true --include-annotations false reason -r ELK --exclude-duplicate-axioms true --remove-redundant-subclass-axioms true --exclude-tautologies structural relax reduce --named-classes-only true annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@

extensions/reacto.owl: $(GO_LEGO).owl mirror/chebi.owl
mkdir -p reacto-tmp
wget -O ./reacto-tmp/biopax2go.jar --no-check-certificate https://github.com/geneontology/pathways2GO/releases/download/v0.1.0/biopax2go.jar
wget -O ./reacto-tmp/biopax.zip --no-check-certificate https://reactome.org/download/current/biopax.zip
unzip -o ./reacto-tmp/biopax.zip -d ./reacto-tmp/
java -jar -Xmx8G ./reacto-tmp/biopax2go.jar -b ./reacto-tmp/Homo_sapiens.owl -reacto ./extensions/reacto -lego $(GO_LEGO).owl -chebi ./mirror/chebi.owl
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Does -jar need to go just before the specified jar?

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It works as is, tested. I usually do it that way. I guess it might also work with the memory allocation argument right after java ?

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Interesting, I just always thought that the jar file was an argument to -jar.

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I think it is indeed an argument to -jar. I guess its clever enough to deal with both. I poked around a little and see examples of both patterns all over.

rm ./reacto-tmp/*
rmdir ./reacto-tmp

$(GO_LEGO_REACTO).owl: extensions/go-lego-reacto-edit.ofn $(GO_LEGO).owl extensions/reacto.owl
$(ROBOT) merge -i $< --collapse-import-closure true --include-annotations false reason -r ELK --exclude-duplicate-axioms true --remove-redundant-subclass-axioms true --exclude-tautologies structural relax reduce --named-classes-only true annotate -O $(BASE)/$@ -V $(RELEASE_URIBASE)/$@ -o $@

# ----------------------------------------
# OBO and subsets
# ----------------------------------------
Expand Down
2 changes: 2 additions & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -41,4 +41,6 @@
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/gorel.owl" uri="imports/gorel.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/x-disjoint.owl" uri="imports/x-disjoint.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/imports/reactome_xrefs_import.owl" uri="imports/reactome_xrefs_import.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/go-lego.owl" uri="extensions/go-lego.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/go/extensions/reacto.owl" uri="extensions/reacto.owl"/>
</catalog>
13 changes: 13 additions & 0 deletions src/ontology/extensions/go-lego-reacto-edit.ofn
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@@ -0,0 +1,13 @@
Prefix(:=<http://purl.obolibrary.org/obo/go/extensions/go-lego.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl>
Import(<http://purl.obolibrary.org/obo/go/extensions/go-lego.owl>)
Import(<http://purl.obolibrary.org/obo/go/extensions/reacto.owl>)
Annotation(rdfs:comment "This ontology extends go-lego (the core ontology underlying GO-CAMs, with classes representing entities in Reactome.)")
)