Update ODK image to v1.4.3 in QC (#3087)

* update ODK image in QC

* increase ROBOT_JAVA_ARGS in qc

* change to macos runner and increase memory

* setup macos runner in qc

* increase memory

* decrease memory

* decrease memory

* change image to odkfull

* decrease memory

* roll back qc to use ubuntu runner

* add conditional use not to materialize when running qc

---------

Co-authored-by: Anita Caron <anitacaron@users.noreply.github.com>

.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

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')

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
 # <https://github.com/obophenotype/uberon/issues/2381>
 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) \