diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 64342f751e..257dad319d 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.4.1 + container: obolibrary/odkfull:v1.4.3 # Steps represent a sequence of tasks that will be executed as part of the job steps: @@ -30,7 +30,7 @@ jobs: env: DEFAULT_BRANCH: master ROBOT_JAVA_ARGS: -Xmx6G - run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' BRI=false MIR=false IMP=false test > TESTLOG.log + run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' GH_ACTION=true BRI=false MIR=false IMP=false test > TESTLOG.log - name: Last rows of QC report if: ${{ failure() }} run: tail -20 src/ontology/TESTLOG.log \ No newline at end of file diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 909913e3ca..3951dcad80 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for uberon # Generated using ontology-development-kit -# ODK Version: v1.4.2 +# ODK Version: v1.4.3 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead @@ -44,7 +44,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format SPARQL_EXPORTS = basic-report -ODK_VERSION_MAKEFILE = v1.4.2 +ODK_VERSION_MAKEFILE = v1.4.3 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 803292caac..502c9c140a 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -124,11 +124,15 @@ $(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-g # For the temporary injection of property chains, see # DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl +ifeq ($(GH_ACTION),true) +MATERIALIZE= +else +MATERIALIZE = materialize -T $(CONFIGDIR)/basic_properties.txt -r elk +endif uberon.owl: $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl $(DEVELOPS_FROM_CHAIN) $(ROBOT) merge -i $(OWLSRC) -i $(BRIDGEDIR)/uberon-bridge-to-bfo.owl \ -i $(DEVELOPS_FROM_CHAIN) \ - relax \ - materialize -T $(CONFIGDIR)/basic_properties.txt -r elk \ + relax $(MATERIALIZE) \ reason -r elk --exclude-duplicate-axioms true \ --equivalent-classes-allowed asserted-only \ unmerge -i $(DEVELOPS_FROM_CHAIN) \