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Changed makefile

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matentzn committed Aug 12, 2019
1 parent 2db5e28 commit d08a5880caa1f9085e49bbacf0a3631671cdd356
Showing with 1,904 additions and 1,900 deletions.
  1. +1 −1 patterns/definitions.owl
  2. +6 −3 src/ontology/cl.Makefile
  3. +1,896 −1,895 src/ontology/ontologyterms.txt
  4. +1 −1 src/patterns/definitions.owl
@@ -7,6 +7,6 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/cl/patterns/definitions.owl>
<http://purl.obolibrary.org/obo/cl/releases/2019-08-09/patterns/definitions.owl>
<http://purl.obolibrary.org/obo/cl/releases/2019-08-12/patterns/definitions.owl>

)
@@ -66,7 +66,9 @@ tmp/asserted-subclass-of-axioms.obo: $(SRC) tmp/cl_terms.txt

# All this terrible OBO file hacking is necessary to make sure downstream tools can actually compile something resembling valid OBO (oort!).
#http://purl.obolibrary.org/obo/UBERON_0004370 EquivalentTo basement membrane needs fixing

# Removing drains CARO relationship is a necessary hack because of an OBO bug that turns universals
# into existentials on roundtrip

tmp/source-merged.obo: $(SRC) tmp/asserted-subclass-of-axioms.obo
$(ROBOT) merge --input $< \
reason --reasoner ELK \
@@ -75,9 +77,10 @@ tmp/source-merged.obo: $(SRC) tmp/asserted-subclass-of-axioms.obo
merge -i tmp/asserted-subclass-of-axioms.obo \
convert --check false -f obo $(OBO_FORMAT_OPTIONS) -o tmp/source-merged.owl.obo &&\
grep -v ^owl-axioms tmp/source-merged.owl.obo > tmp/source-stripped2.obo &&\
grep -v '^def[:][ ]["]x[ ]only[ ]in[ ]taxon' tmp/source-stripped2.obo > tmp/source-stripped.obo &&\
grep -v '^def[:][ ]["]x[ ]only[ ]in[ ]taxon' tmp/source-stripped2.obo > tmp/source-stripped3.obo &&\
grep -v '^relationship[:][ ]drains[ ]CARO' tmp/source-stripped3.obo > tmp/source-stripped.obo &&\
cat tmp/source-stripped.obo | perl -0777 -e '$$_ = <>; s/name[:].*\nname[:]/name:/g; print' | perl -0777 -e '$$_ = <>; s/range[:].*\nrange[:]/range:/g; print' | perl -0777 -e '$$_ = <>; s/domain[:].*\ndomain[:]/domain:/g; print' | perl -0777 -e '$$_ = <>; s/comment[:].*\ncomment[:]/comment:/g; print' | perl -0777 -e '$$_ = <>; s/def[:].*\ndef[:]/def:/g; print' > $@ &&\
rm tmp/source-merged.owl.obo tmp/source-stripped.obo tmp/source-stripped2.obo
rm tmp/source-merged.owl.obo tmp/source-stripped.obo tmp/source-stripped2.obo tmp/source-stripped3.obo

oort: tmp/source-merged.obo
ontology-release-runner --reasoner elk $< --no-subsets --skip-ontology-checks --allow-equivalent-pairs --simple --relaxed --asserted --allow-overwrite --outdir oort

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