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Introducing full Uberon test battery again #1972

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Introducing full Uberon test battery again #1972

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64a5aea
Update uberon.Makefile
matentzn Jul 22, 2021
1aee5f9
Updating qc a bit
matentzn Jul 22, 2021
3ea3fe3
Updating workflow to use LOG file instead
matentzn Jul 22, 2021
1b25642
Update qc.yml
matentzn Jul 22, 2021
19c4029
Update
matentzn Jul 22, 2021
2d340a0
Update uberon.Makefile
matentzn Jul 22, 2021
4c48bd2
Update uberon.Makefile
matentzn Jul 22, 2021
6fd2bc9
Excluded more tests
matentzn Jul 22, 2021
bd4b408
Update uberon.Makefile
matentzn Jul 22, 2021
e3096bb
MIRRORs need pulling for checks..
matentzn Jul 22, 2021
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5 changes: 4 additions & 1 deletion .github/workflows/qc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,4 +30,7 @@ jobs:
env:
DEFAULT_BRANCH: master
ROBOT_JAVA_ARGS: -Xmx6G
run: cd src/ontology && mkdir -p tmp reports && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' IMP=false test
run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' BRI=false test > TESTLOG.log
- name: Last rows of QC report
if: ${{ failure() }}
run: tail -20 src/ontology/TESTLOG.log
16 changes: 10 additions & 6 deletions src/ontology/uberon.Makefile
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Expand Up @@ -675,9 +675,12 @@ $(REPORTDIR)/bridge-check-%.txt: $(REPORTDIR)/bridge-check-%.owl $(CATALOG_DYNAM
owltools --no-debug --catalog-xml $(CATALOG_DYNAMIC) $< $(QELK) --run-reasoner -r elk -u > [email protected] && mv [email protected] $@

# TODO @cmungall: TRY again, CARO is worth fixing (SOP: take screenshot, make individual tickets with one explanation eachg)
$(REPORTDIR)/bridge-check-caro.txt: | $(CATALOG_DYNAMIC)
SKIPPED=$(REPORTDIR)/bridge-check-caro.txt
#$(REPORTDIR)/quick-bridge-check-wbbt.txt $(REPORTDIR)/quick-bridge-check-wbls.txt $(REPORTDIR)/bridge-check-wbls.txt \
# bridge-check-wbbt.owl
$(SKIPPED): | $(CATALOG_DYNAMIC)
echo "STRONG WARNING $@ currently set to NOT FAIL because of unsatisfiable classes!"
owltools --no-debug --catalog-xml $(CATALOG_DYNAMIC) $< $(QELK) --run-reasoner -r elk -u > $@ || true
#owltools --no-debug --catalog-xml $(CATALOG_DYNAMIC) $< $(QELK) --run-reasoner -r elk -u > $@ || true


$(REPORTDIR)/expl-bridge-check-%.txt: $(REPORTDIR)/bridge-check-%.owl $(CATALOG_DYNAMIC)
Expand Down Expand Up @@ -942,11 +945,10 @@ cl-core-new.obo: cell-ontology/cl.obo
# this is required for bridging axioms; ZFA inverts the usual directionality
# TODO review directionality!!!
$(TMPDIR)/cl-zfa-xrefs.obo: mirror/zfa.owl
$(ROBOT) query -i $< --query ../sparql/zfa-xrefs-to-cl.sparql $@_xrefs_to_zfa.tsv
cat $@_xrefs_to_zfa.tsv | tail -n +2 | $(SCRIPTSDIR)/tbl2obolinks.pl --rel xref - > [email protected] && mv [email protected] $@
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) query -i $< --query ../sparql/zfa-xrefs-to-cl.sparql $@_xrefs_to_zfa.tsv &&\
cat $@_xrefs_to_zfa.tsv | tail -n +2 | $(SCRIPTSDIR)/tbl2obolinks.pl --rel xref - > [email protected] && mv [email protected] $@; fi


#blip-findall -r ZFA "entity_xref(Z,C),id_idspace(C,'CL')" -select C-Z -use_tabs -no_pred | $(SCRIPTSDIR)/tbl2obolinks.pl --rel xref > $@
#blip-findall -r ZFA "entity_xref(Z,C),id_idspace(C,'CL')" -select C-Z -use_tabs -no_pred | $(SCRIPTSDIR)/tbl2obolinks.pl --rel xref > $@

#cl-core.owl: $(TMPDIR)/cl-core.obo
# $(MAKEOBO)
Expand Down Expand Up @@ -1761,3 +1763,5 @@ diffs-%:
.PHONY: dirs
dirs:
mkdir -p tmp mirror reports

test: uberon-qc