From e2f89fbd0364a1492806ac20a3703983664c48a5 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Mon, 23 May 2022 16:22:02 +0300 Subject: [PATCH 1/2] Update uberon.Makefile --- src/ontology/uberon.Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index c2a2cd624f..e06cfa12b5 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -634,8 +634,8 @@ $(TMPDIR)/uberon-edit-plus-tax-equivs.owl: $(OWLSRC) $(TMPDIR)/external-disjoint # see above $(REPORTDIR)/taxon-constraint-check.txt: $(TMPDIR)/uberon-edit-plus-tax-equivs.owl $(CATALOG_DYNAMIC) - #$(OWLTOOLS_CAT_DYNAMIC) $< $(QELK) --run-reasoner -r elk -u > $@.tmp && mv $@.tmp $@ - echo "STRONG WARNING: Skipped $@." + $(OWLTOOLS_CAT_DYNAMIC) $< $(QELK) --run-reasoner -r elk -u > $@.tmp && mv $@.tmp $@ + #echo "STRONG WARNING: Skipped $@." # BRIDGE CHECKS. # these can be used to validate on a per-bridge file basis. There are a variety of flavours: @@ -710,7 +710,7 @@ $(REPORTDIR)/full-bridge-check-caro.txt: | $(CATALOG_DYNAMIC) $(OWLTOOLS_CAT_DYNAMIC) --no-debug $< $(URIBASE)/$*.owl $(BRIDGEDIR)/uberon-bridge-to-$*.owl $(TMPDIR)/external-disjoints.owl --merge-support-ontologies $(QELK) --run-reasoner -r elk -u -m $(REPORTDIR)/debug-full-bridge-check-$*.owl > $@ || true # TODO @cmungall says: worth fixing -$(REPORTDIR)/full-bridge-check-wbls.txt: | $(CATALOG_DYNAMIC) +$(REPORTDIR)/full-bridge-check-wbls.txt: ext.owl | $(CATALOG_DYNAMIC) echo "STRONG WARNING $@ currently set to NOT FAIL because of unsatisfiable classes!" $(OWLTOOLS_CAT_DYNAMIC) --no-debug $< $(URIBASE)/$*.owl $(BRIDGEDIR)/uberon-bridge-to-$*.owl $(TMPDIR)/external-disjoints.owl --merge-support-ontologies $(QELK) --run-reasoner -r elk -u -m $(REPORTDIR)/debug-full-bridge-check-$*.owl > $@ || true From 52f6d4612b2a05f8d96811ee99aaeeb31974d17f Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Mon, 23 May 2022 16:32:52 +0300 Subject: [PATCH 2/2] Update uberon.Makefile --- src/ontology/uberon.Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index e06cfa12b5..f6c81bd522 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -710,7 +710,7 @@ $(REPORTDIR)/full-bridge-check-caro.txt: | $(CATALOG_DYNAMIC) $(OWLTOOLS_CAT_DYNAMIC) --no-debug $< $(URIBASE)/$*.owl $(BRIDGEDIR)/uberon-bridge-to-$*.owl $(TMPDIR)/external-disjoints.owl --merge-support-ontologies $(QELK) --run-reasoner -r elk -u -m $(REPORTDIR)/debug-full-bridge-check-$*.owl > $@ || true # TODO @cmungall says: worth fixing -$(REPORTDIR)/full-bridge-check-wbls.txt: ext.owl | $(CATALOG_DYNAMIC) +$(REPORTDIR)/full-bridge-check-wbls.txt: | $(CATALOG_DYNAMIC) echo "STRONG WARNING $@ currently set to NOT FAIL because of unsatisfiable classes!" $(OWLTOOLS_CAT_DYNAMIC) --no-debug $< $(URIBASE)/$*.owl $(BRIDGEDIR)/uberon-bridge-to-$*.owl $(TMPDIR)/external-disjoints.owl --merge-support-ontologies $(QELK) --run-reasoner -r elk -u -m $(REPORTDIR)/debug-full-bridge-check-$*.owl > $@ || true