nmrML · StroemPhi · Mar 18, 2024 · Mar 18, 2024
diff --git a/.github/workflows/qc.yml b/.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:v1.4.3
+    container: obolibrary/odkfull:v1.5
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -29,5 +29,5 @@ jobs:
       - name: Run ontology QC checks
         env:
           DEFAULT_BRANCH: main
-        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 
diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md
@@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
    Just make sure you give GitHub 2-5 minutes to build the pages!
 
 
+
diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md
@@ -2,7 +2,7 @@
 
 ## Updating your ODK repository
 
-Your ODK repositories configuration is managed in `src/ontology/nmrCV-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
+Your ODK repositories configuration is managed in `src/ontology/nmrCV-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:
 
 
 ```

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,14 +1,17 @@
 # ----------------------------------------
 # Makefile for nmrCV
 # Generated using ontology-development-kit
-# ODK Version: v1.4.3
+# ODK Version: v1.5
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use nmrCV.Makefile instead
 
 
 # ----------------------------------------
 # More information: https://github.com/INCATools/ontology-development-kit/
 
+# Fingerprint of the configuration file when this Makefile was last generated
+CONFIG_HASH=                048e86b877413691096fdaf760046bfa1f9cc76be28e57b283a8dd03e21e3213
+
 
 # ----------------------------------------
 # Standard Constants
@@ -41,9 +44,9 @@ REPORT_FAIL_ON =            None
 REPORT_LABEL =              -l true
 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 =      v1.4.3
+SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties 
+SPARQL_EXPORTS =            basic-report edges xrefs obsoletes synonyms 
+ODK_VERSION_MAKEFILE =      v1.5
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -58,6 +61,11 @@ FORMATS = $(sort  owl ttl obo owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
 RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base )
 
+ifeq ($(ODK_DEBUG),yes)
+ODK_DEBUG_FILE = debug.log
+SHELL = $(SCRIPTSDIR)/run-command.sh
+endif
+
 # ----------------------------------------
 # Top-level targets
 # ----------------------------------------
@@ -68,12 +76,16 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base )
 all: all_odk
 
 .PHONY: all_odk
-all_odk: odkversion test all_assets
+all_odk: odkversion config_check test custom_reports all_assets
 
 .PHONY: test
 test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt
 	echo "Finished running all tests successfully."
 
+.PHONY: test
+test_fast:
+	$(MAKE_FAST) test
+
 .PHONY: release_diff
 release_diff: $(REPORTDIR)/release-diff.md
 
@@ -84,13 +96,52 @@ reason_test: $(EDIT_PREPROCESSED)
 
 .PHONY: odkversion
 odkversion:
-	echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \
-        not the version of the ODK you are running)" &&\
-	echo "ROBOT version (ODK): " && $(ROBOT) --version
+	@echo "ODK Makefile $(ODK_VERSION_MAKEFILE)"
+	@odk-info --tools
+.PHONY: config_check
+config_check:
+	@if [ "$$(sha256sum $(ONT)-odk.yaml | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \
+		echo "Repository is up-to-date." ; else \
+		echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi
+
 
 $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR):
 	mkdir -p $@
 
+# ----------------------------------------
+# ODK-managed ROBOT plugins
+# ----------------------------------------
+
+# Make sure ROBOT knows where to find plugins
+export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins
+
+# Override this rule in nmrCV.Makefile to install custom plugins
+.PHONY: custom_robot_plugins
+custom_robot_plugins:
+
+
+.PHONY: extra_robot_plugins
+extra_robot_plugins: 
+
+
+# Install all ROBOT plugins to the runtime plugins directory
+.PHONY: all_robot_plugins
+all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
+		   $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
+		   custom_robot_plugins extra_robot_plugins  \
+
+# Default rule to install plugins
+$(ROBOT_PLUGINS_DIRECTORY)/%.jar:
+	@mkdir -p $(ROBOT_PLUGINS_DIRECTORY)
+	@if [ -f ../../plugins/$*.jar ]; then        \
+		ln ../../plugins/$*.jar $@ ;         \
+	elif [ -f /tools/robot-plugins/$*.jar ]; then \
+		cp /tools/robot-plugins/$*.jar $@ ;  \
+	fi
+
+# Specific rules for supplementary plugins defined in configuration
+
+
 # ----------------------------------------
 # Release assets
 # ----------------------------------------
@@ -180,10 +231,10 @@ 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) | $(REPORTDIR)
 ifneq ($(SPARQL_VALIDATION_QUERIES),)
 
-	$(ROBOT) verify  --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
+	$(ROBOT) verify -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
 endif
 
 # ----------------------------------------
@@ -196,6 +247,10 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
 $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
 	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri $(URIBASE)/NMRCV_ --base-iri $(URIBASE)/nmrCV --print 5 -o $@
 
+check_for_robot_updates:
+	echo "You are not using a custom profile, so you are getting the joy of the latest ROBOT report!"
+
+
 # ----------------------------------------
 # Release assets
 # ----------------------------------------
@@ -212,15 +267,15 @@ RELEASE_ASSETS = \
   $(SUBSET_FILES)
 
 .PHONY: all_assets
-all_assets: $(ASSETS) 
+all_assets: $(ASSETS) check_rdfxml_assets
 
 .PHONY: show_assets
 show_assets:
 	echo $(ASSETS)
 	du -sh $(ASSETS)
 
 check_rdfxml_%: %
-	@check-rdfxml $<
+	@check-rdfxml  $<
 
 .PHONY: check_rdfxml_assets
 check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl)
@@ -350,75 +405,73 @@ IMP=true # Global parameter to bypass import generation
 MIR=true # Global parameter to bypass mirror generation
 IMP_LARGE=true # Global parameter to bypass handling of large imports
 
+ifeq ($(strip $(MIR)),true)
 
 
 ## ONTOLOGY: bfo
 .PHONY: mirror-bfo
 .PRECIOUS: $(MIRRORDIR)/bfo.owl
 mirror-bfo: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(MIRRORDIR)/bfo.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/bfo.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(TMPDIR)/bfo-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/bfo-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: ro
 .PHONY: mirror-ro
 .PRECIOUS: $(MIRRORDIR)/ro.owl
 mirror-ro: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: omo
 .PHONY: mirror-omo
 .PRECIOUS: $(MIRRORDIR)/omo.owl
 mirror-omo: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/omo.owl --create-dirs -o $(TMPDIR)/omo-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: iao
 .PHONY: mirror-iao
 .PRECIOUS: $(MIRRORDIR)/iao.owl
 mirror-iao: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/iao.owl --create-dirs -o $(MIRRORDIR)/iao.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/iao.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: chmo
 .PHONY: mirror-chmo
 .PRECIOUS: $(MIRRORDIR)/chmo.owl
 mirror-chmo: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/chmo.owl --create-dirs -o $(MIRRORDIR)/chmo.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/chmo.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/chmo.owl --create-dirs -o $(TMPDIR)/chmo-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/chmo-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: pato
 .PHONY: mirror-pato
 .PRECIOUS: $(MIRRORDIR)/pato.owl
 mirror-pato: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/pato.owl --create-dirs -o $(TMPDIR)/pato-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/pato-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: obi
 .PHONY: mirror-obi
 .PRECIOUS: $(MIRRORDIR)/obi.owl
 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 &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \
+	$(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl
 
 
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
-	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
+	if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
 
+else # MIR=false
+$(MIRRORDIR)/%.owl:
+	@echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))."
+endif
 
 
 
@@ -497,9 +550,13 @@ 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 asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
+	relax \
+	reduce -r ELK \
+	remove --base-iri $(URIBASE)/NMRCV --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) \
@@ -566,13 +623,16 @@ update_repo:
 update_docs:
 	mkdocs gh-deploy --config-file ../../mkdocs.yaml
 
-# Note to future generations: prepending ./ is a safety measure to ensure that 
-# the environment does not malicously set `CLEANFILES` to `\`.
+# Note to future generations: computing the real path relative to the
+# current directory is a way to ensure we only clean up directories that
+# are located below the current directory, regardless of the contents of
+# the *DIR variables.
 .PHONY: clean
 clean:
-	[ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/*
-	[ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/*
-	[ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/*
+	for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do      \
+		reldir=$$(realpath --relative-to=$$(pwd) $$dir) ;    \
+		case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \
+	done
 	rm -f $(CLEANFILES)
 
 .PHONY: help
@@ -591,6 +651,7 @@ 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 nmrCV-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
@@ -608,7 +669,7 @@ Imports management:
 
 Editor utilities:
 * validate_idranges:	Make sure your ID ranges file is formatted correctly
-* normalize_src:	Load and safe your nmrCV-edit file after you to make sure its serialised correctly
+* normalize_src:	Load and save your nmrCV-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.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
		Just make sure you give GitHub 2-5 minutes to build the pages!
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,7 @@ @@
     ## Updating your ODK repository
-    Your ODK repositories configuration is managed in `src/ontology/nmrCV-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
+    Your ODK repositories configuration is managed in `src/ontology/nmrCV-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:
     ```
@@ Expand Down @@