Merge pull request #7 from luis-gonzalez-m/main

New Lepidoptera-specific terms added.
insect-morphology · Nov 17, 2021 · 79de312 · 79de312
2 parents 7af72e5 + ca876af
commit 79de312
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Showing 12 changed files with 130,765 additions and 49,870 deletions.
diff --git a/lepao-base.obo b/lepao-base.obo
diff --git a/lepao-base.owl b/lepao-base.owl
diff --git a/lepao-full.obo b/lepao-full.obo
diff --git a/lepao-full.owl b/lepao-full.owl
diff --git a/lepao.obo b/lepao.obo
diff --git a/lepao.owl b/lepao.owl
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for lepao
 # Generated using ontology-development-kit
-# ODK Version: v1.2.29
+# ODK Version: v1.2.30
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use lepao.Makefile instead
 
@@ -35,7 +35,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =   equivalent-classes owldef-self-reference
 SPARQL_EXPORTS =             basic-report class-count-by-prefix edges xrefs obsoletes synonyms
-ODK_VERSION_MAKEFILE =      v1.2.29
+ODK_VERSION_MAKEFILE =      v1.2.30
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -247,7 +247,7 @@ mirror/aism.trigger: $(SRC)
 
 mirror/aism.owl: mirror/aism.trigger
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/insect-morphology/aism/master/aism.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/%.owl
+.PRECIOUS: mirror/aism.owl
 
 
 
@@ -294,6 +294,10 @@ endif
 # ----------------------------------------
 # ROBOT report
 # ----------------------------------------
+
+$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
+	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
+
 $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
 	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
 
@@ -305,7 +309,7 @@ SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql
 # This combines all into one single command
 
 .PHONY: all_reports_onestep
-all_reports_onestep: $(SRC)
+all_reports_onestep: $(SRC) | $(REPORTDIR)
 ifneq ($(SPARQL_EXPORTS_ARGS),)
 	$(ROBOT) query -f tsv -i $< $(SPARQL_EXPORTS_ARGS)
 endif

diff --git a/src/ontology/imports/aism_import.owl b/src/ontology/imports/aism_import.owl
diff --git a/src/ontology/lepao-edit.owl b/src/ontology/lepao-edit.owl
diff --git a/src/ontology/reports/lepao-edit.owl-obo-report.tsv b/src/ontology/reports/lepao-edit.owl-obo-report.tsv
diff --git a/src/ontology/run.sh b/src/ontology/run.sh
@@ -9,4 +9,7 @@
 # we therefore map the whole repo (../..) to a docker volume.
 #
 # See README-editors.md for more details.
-docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='' -e JAVA_OPTS='' --rm -ti obolibrary/odkfull "$@"
+
+IMAGE=${IMAGE:-odkfull}
+
+docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='' -e JAVA_OPTS='' --rm -ti obolibrary/$IMAGE "$@"
diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh
@@ -11,7 +11,7 @@ CONFIG=$OID"-odk.yaml"
 
 rm -rf target
 mkdir target
-/tools/odk.py seed -c -g False -C $CONFIG
+/tools/odk.py seed -c -g -C $CONFIG
 ls -l target/$OID/src
 ls -l $SRCDIR/
 cp target/$OID/src/scripts/update_repo.sh $SRCDIR/scripts/