From 4ec73481bf74f089f44063a0fb8f3e67cbcfd5e3 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Sun, 19 Feb 2023 14:05:37 +0200 Subject: [PATCH] ODK 1.4 migration --- src/ontology/Makefile | 38 +++++++++++++++++++++++++++----------- src/ontology/run.sh | 3 ++- src/ontology/run.sh.conf | 1 - 3 files changed, 29 insertions(+), 13 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 6bd4416f..acdcd9f8 100644 --- 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 $@ @@ -905,6 +920,7 @@ Additional build commands (advanced users) * custom_reports: Generate all custom sparql reports you have configured in your oba-odk.yaml file. * all_assets: Build all assets * show_assets: Print a list of all assets that would be build by the release pipeline +* all_mappings: Update all SSSOM mapping sets Additional QC commands (advanced users) * robot_reports: Run all configured ROBOT reports diff --git a/src/ontology/run.sh b/src/ontology/run.sh index 895f4345..2718ff67 100755 --- a/src/ontology/run.sh +++ b/src/ontology/run.sh @@ -59,13 +59,14 @@ fi if [ -n "$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 index 0df160a2..375321bb 100644 --- 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 \ No newline at end of file