Remove NCBITAXON again

berkeleybop · Mar 27, 2023 · 322ebe9 · 322ebe9
1 parent 60282a2
commit 322ebe9
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Showing 4 changed files with 32 additions and 23 deletions.
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -22,7 +22,7 @@ These are the current imports in BERO
 | ecocore | http://purl.obolibrary.org/obo/ecocore.owl | None |
 | to | http://purl.obolibrary.org/obo/to.owl | None |
 | chebi | http://purl.obolibrary.org/obo/chebi.owl | None |
-| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon.owl | None |
+| ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None |
 | envo | http://purl.obolibrary.org/obo/envo.owl | None |
 | go | http://purl.obolibrary.org/obo/go.owl | None |
 | ncit | http://purl.obolibrary.org/obo/ncit.owl | custom |

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for bero
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.5
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use bero.Makefile instead
 
@@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.5
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -74,6 +74,10 @@ all_odk: odkversion test all_assets
 test: odkversion reason_test sparql_test robot_reports 
 	echo "Finished running all tests successfully."
 
+.PHONY: test
+test_fast:
+	$(MAKE_FAST) test
+
 .PHONY: release_diff
 release_diff: $(REPORTDIR)/release-diff.md
 
@@ -314,12 +318,6 @@ $(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/chebi.owl $(IMPORTDIR)/chebi_terms_c
 	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) merge -i $<  \
     $(ANNOTATE_CONVERT_FILE); fi
 
-## Module for ontology: ncbitaxon
-
-$(IMPORTDIR)/ncbitaxon_import.owl: $(MIRRORDIR)/ncbitaxon.owl $(IMPORTDIR)/ncbitaxon_terms_combined.txt
-	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) merge -i $<  \
-    $(ANNOTATE_CONVERT_FILE); fi
-
 ## Module for ontology: ncit
 
 $(IMPORTDIR)/ncit_import.owl: $(MIRRORDIR)/ncit.owl
@@ -377,7 +375,7 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports
 mirror-mop: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/mop.owl --create-dirs -o $(MIRRORDIR)/mop.owl --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/mop.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/MOP --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(OBOBASE)/MOP --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
@@ -387,7 +385,7 @@ mirror-mop: | $(TMPDIR)
 mirror-po: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/po.owl --create-dirs -o $(MIRRORDIR)/po.owl --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/po.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(OBOBASE)/PO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
@@ -414,7 +412,7 @@ mirror-ecocore: | $(TMPDIR)
 mirror-to: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/to.owl --create-dirs -o $(MIRRORDIR)/to.owl --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/to.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/TO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(OBOBASE)/TO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
@@ -424,16 +422,15 @@ mirror-to: | $(TMPDIR)
 mirror-chebi: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(OBOBASE)/chebi.owl.gz --create-dirs -o $(MIRRORDIR)/chebi.owl.gz --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/chebi.owl.gz -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CHEBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(OBOBASE)/CHEBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: ncbitaxon
 .PHONY: mirror-ncbitaxon
 .PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl
 mirror-ncbitaxon: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(OBOBASE)/ncbitaxon.owl.gz --create-dirs -o $(MIRRORDIR)/ncbitaxon.owl.gz --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/ncbitaxon.owl.gz -o $@.tmp.owl && \
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl && \
 		$(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/NCBITaxon_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
@@ -460,7 +457,7 @@ mirror-go: | $(TMPDIR)
 mirror-ncit: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(OBOBASE)/ncit.owl --create-dirs -o $(MIRRORDIR)/ncit.owl --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/ncit.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/NCIT --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(OBOBASE)/NCIT --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
@@ -494,7 +491,7 @@ mirror-mesh: | $(TMPDIR)
 mirror-obi: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\
 		$(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/OBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(OBOBASE)/OBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
 		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
@@ -584,9 +581,13 @@ ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $<
 # ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base"
 ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) 
 
-# base: All the axioms as they are editted by the editors, excluding reasoning
-$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
-	$(ROBOT_RELEASE_IMPORT_MODE_BASE) \
+# base: A version of the ontology that does not include any externally imported axioms.
+$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+	reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \
+	relax \
+	reduce -r ELK \
+	remove --base-iri $(URIBASE)/BERO --axioms external --preserve-structure false --trim false \
 	$(SHARED_ROBOT_COMMANDS) \
 	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
 		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
@@ -678,6 +679,7 @@ Core commands:
 * prepare_release_fast:	Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns.
 * update_repo:		Update the ODK repository setup using the config file bero-odk.yaml
 * test:			Running all validation tests
+* test_fast:		Runs the test suite, but without updating imports or components
 * odkversion:		Show the current version of the ODK Makefile and ROBOT.
 * clean:		Delete all temporary files
 * help:			Print ODK Usage information
@@ -695,7 +697,7 @@ Imports management:
 
 Editor utilities:
 * validate_idranges:	Make sure your ID ranges file is formatted correctly
-* normalize_src:	Load and safe your bero-edit file after you to make sure its serialised correctly
+* normalize_src:	Load and save your bero-edit file after you to make sure its serialised correctly
 * explain_unsat:	If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes
 * validate-all-tsv:	Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files
 * validate-tsv:		Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv.

diff --git a/src/ontology/bero-odk.yaml b/src/ontology/bero-odk.yaml
@@ -29,8 +29,7 @@ import_group:
       use_gzipped: TRUE
       make_base: TRUE
     - id: ncbitaxon
-      is_large: TRUE
-      use_gzipped: TRUE
+      mirror_from: http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl
       make_base: TRUE
       base_iris:
         - http://purl.obolibrary.org/obo/NCBITaxon_

diff --git a/src/ontology/run.sh b/src/ontology/run.sh
@@ -40,6 +40,14 @@ ODK_TAG=${ODK_TAG:-latest}
 ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx20G}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
+# Convert OWLAPI_* environment variables to the OWLAPI as Java options
+# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html
+# for a list of allowed options
+OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions
+for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do
+    ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}"
+done
+
 TIMECMD=
 if [ x$ODK_DEBUG = xyes ]; then
     # If you wish to change the format string, take care of using