ODK 1.4 migration

obophenotype · Feb 19, 2023 · 4ec7348 · 4ec7348
1 parent be85492
commit 4ec7348
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Showing 3 changed files with 29 additions and 13 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for oba
 # Generated using ontology-development-kit
-# ODK Version: v1.4-dev
+# ODK Version: v1.4
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use oba.Makefile instead
 
@@ -44,20 +44,20 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.4-dev
+ODK_VERSION_MAKEFILE =      v1.4
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
-ANNOTATE_CONVERT_FILE =		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
+ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
 OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/obsoletes.owl $(COMPONENTSDIR)/synonyms.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
-EDIT_PREPROCESSED = 		$(TMPDIR)/$(ONT)-preprocess.owl
+EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
-PATTERN_TESTER=              dosdp validate -i
-DOSDPT=                      dosdp-tools
-PATTERN_RELEASE_FILES=       $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.owl
+PATTERN_TESTER=             dosdp validate -i
+DOSDPT=                     dosdp-tools
+PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.owl
 
 
 FORMATS = $(sort  owl obo json owl)
@@ -137,6 +137,19 @@ SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n
 .PHONY: all_subsets
 all_subsets: $(SUBSET_FILES)
 
+# ----------------------------------------
+# Mapping assets
+# ----------------------------------------
+
+
+MAPPINGS = 
+
+MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS))
+
+.PHONY: all_mappings
+all_mappings: $(MAPPING_FILES)
+
+
 # ----------------------------------------
 # QC Reports & Utilities
 # ----------------------------------------
@@ -173,9 +186,10 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt
 
 SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql)
 
-sparql_test: $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR)
+sparql_test:  $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR)
 ifneq ($(SPARQL_VALIDATION_QUERIES),)
-	$(ROBOT) verify  --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
+
+	$(ROBOT) verify  --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
 endif
 
 # ----------------------------------------
@@ -197,7 +211,8 @@ ASSETS = \
   $(MAIN_FILES) \
   $(PATTERN_RELEASE_FILES) \
   $(REPORT_FILES) \
-  $(SUBSET_FILES)
+  $(SUBSET_FILES) \
+  $(MAPPING_FILES)
 
 RELEASE_ASSETS = \
   $(MAIN_FILES) \
@@ -723,7 +738,7 @@ $(ONT).owl: $(ONT)-full.owl
 
 $(ONT).obo: $(ONT).owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
-$(ONT).json: $(ONT)-full.owl
+$(ONT).json: $(ONT).owl
 	$(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
@@ -905,6 +920,7 @@ Additional build commands (advanced users)
 * custom_reports:	Generate all custom sparql reports you have configured in your oba-odk.yaml file.
 * all_assets:		Build all assets
 * show_assets:		Print a list of all assets that would be build by the release pipeline
+* all_mappings:		Update all SSSOM mapping sets
 
 Additional QC commands (advanced users)
 * robot_reports:	Run all configured ROBOT reports

diff --git a/src/ontology/run.sh b/src/ontology/run.sh
@@ -59,13 +59,14 @@ fi
 if [ -n "$USE_SINGULARITY" ]; then
 
     singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
         --bind $VOLUME_BIND \
         -W $WORK_DIR \
         docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 else
     BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')"
     docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \
-         \
+        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \
         --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 fi
 

diff --git a/src/ontology/run.sh.conf b/src/ontology/run.sh.conf
@@ -1,4 +1,3 @@
-ODK_TAG=dev
 ODK_DEBUG=yes
 ODK_IMAGE=odkfull
 ODK_JAVA_OPTS=-Xmx18G