From 8b8360cfa60e62d1b5aa78f41607acfed87a7e7f Mon Sep 17 00:00:00 2001
From: Nico Matentzoglu <nicolas.matentzoglu@gmail.com>
Date: Sat, 10 Aug 2024 09:45:22 +0300
Subject: [PATCH] Refresh ODK (includes 1.5.2 migration)

---
 .github/workflows/qc.yml                  |   6 +-
 docs/odk-workflows/ManageDocumentation.md |   1 +
 docs/odk-workflows/RepoManagement.md      |   2 +-
 src/ontology/Makefile                     | 164 +++++++++++++++-------
 src/ontology/run.sh                       |  38 ++++-
 src/scripts/run-command.sh                |   4 +
 src/scripts/update_repo.sh                |   5 +-
 src/sparql/class-count-by-prefix.sparql   |   2 +-
 8 files changed, 163 insertions(+), 59 deletions(-)
 create mode 100755 src/scripts/run-command.sh

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
index 21966a7c..ec0efec4 100644
--- a/.github/workflows/qc.yml
+++ b/.github/workflows/qc.yml
@@ -19,15 +19,15 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.3.0
+    container: obolibrary/odkfull:v1.5.2
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
         env:
           DEFAULT_BRANCH: master
-        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
index 7840c1f7..17f986a1 100644
--- 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
index 2934798a..4e4082b7 100644
--- 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/pato-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/pato-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
index a898f8a2..47e44918 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for pato
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.5.2
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use pato.Makefile instead
 
@@ -9,6 +9,9 @@
 # ----------------------------------------
 # More information: https://github.com/INCATools/ontology-development-kit/
 
+# Fingerprint of the configuration file when this Makefile was last generated
+CONFIG_HASH=                8c38f556f1076ce2a46088cd083451de27b8553932affe92d72c22f02b6e92e4
+
 
 # ----------------------------------------
 # Standard Constants
@@ -44,7 +47,7 @@ REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference properties-as-annotation-and-object missing-label illegal-annotation-property orcid-contributor iri-range 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.5.2
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -59,6 +62,11 @@ FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
 RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-simple $(ONT)-full )
 
+ifeq ($(ODK_DEBUG),yes)
+ODK_DEBUG_FILE = debug.log
+SHELL = $(SCRIPTSDIR)/run-command.sh
+endif
+
 # ----------------------------------------
 # Top-level targets
 # ----------------------------------------
@@ -69,12 +77,16 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-simple $(ONT)-full )
 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
 
@@ -85,13 +97,52 @@ 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 pato.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
 # ----------------------------------------
@@ -137,7 +188,7 @@ all_subsets: $(SUBSET_FILES)
 # ----------------------------------------
 
 
-MAPPINGS = 
+MAPPINGS =  pato-to-qudt-quantitykind
 
 MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS))
 
@@ -181,12 +232,12 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt
 
 SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql)
 
-sparql_test:  $(EDIT_PREPROCESSED) pato-base.owl catalog-v001.xml | $(REPORTDIR)
+sparql_test:  $(EDIT_PREPROCESSED) pato-base.owl | $(REPORTDIR)
 ifneq ($(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)
   
-	$(ROBOT) verify  --catalog catalog-v001.xml -i pato-base.owl --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
+	$(ROBOT) verify -i pato-base.owl --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
 endif
 
 # ----------------------------------------
@@ -199,6 +250,14 @@ $(REPORTDIR)/$(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 http://purl.obolibrary.org/obo/PATO_ --base-iri http://purl.obolibrary.org/obo/pato# --print 5 -o $@
 
+check_for_robot_updates:	
+	@cut -f2 "/tools/robot_report_profile.txt" | sort > $(TMPDIR)/sorted_tsv2.txt
+	@cut -f2 "$(ROBOT_PROFILE)" | sort > $(TMPDIR)/sorted_tsv1.txt
+	@comm -23 $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/sorted_tsv1.txt > $(TMPDIR)/missing.txt
+	@echo "Missing tests:"
+	@cat $(TMPDIR)/missing.txt
+	@rm $(TMPDIR)/sorted_tsv1.txt $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/missing.txt $(TMPDIR)/report_profile_robot.txt
+
 # ----------------------------------------
 # Release assets
 # ----------------------------------------
@@ -215,7 +274,7 @@ RELEASE_ASSETS = \
   $(SUBSET_FILES)
 
 .PHONY: all_assets
-all_assets: $(ASSETS) 
+all_assets: $(ASSETS) check_rdfxml_assets
 
 .PHONY: show_assets
 show_assets:
@@ -223,7 +282,7 @@ show_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)
@@ -318,6 +377,7 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_term
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
 		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>"  \
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
+		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
@@ -380,9 +440,9 @@ recreate-%:
 no-mirror-recreate-%:
 	$(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B
 
-$(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
-	touch $@
-.PRECIOUS: $(COMPONENTSDIR)/%
+$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR)
+	test -f $@ || touch $@
+.PRECIOUS: $(COMPONENTSDIR)/%.owl
 
 
 # ----------------------------------------
@@ -393,87 +453,87 @@ 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: ro
 .PHONY: mirror-ro
 .PRECIOUS: $(MIRRORDIR)/ro.owl
 mirror-ro: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/ro/ro-base.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: chebi
 .PHONY: mirror-chebi
 .PRECIOUS: $(MIRRORDIR)/chebi.owl
 mirror-chebi: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/CHEBI --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) remove -I https://raw.githubusercontent.com/obophenotype/chebi_obo_slim/main/chebi_slim.owl --base-iri $(OBOBASE)/CHEBI  --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: go
 .PHONY: mirror-go
 .PRECIOUS: $(MIRRORDIR)/go.owl
 mirror-go: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: pco
 .PHONY: mirror-pco
 .PRECIOUS: $(MIRRORDIR)/pco.owl
 mirror-pco: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pco.owl --create-dirs -o $(MIRRORDIR)/pco.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/pco.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PCO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/pco.owl --create-dirs -o $(TMPDIR)/pco-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) remove -i $(TMPDIR)/pco-download.owl --base-iri $(OBOBASE)/PCO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: uberon
 .PHONY: mirror-uberon
 .PRECIOUS: $(MIRRORDIR)/uberon.owl
 mirror-uberon: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uberon/uberon-base.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/uberon/uberon-base.owl --create-dirs -o $(TMPDIR)/uberon-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) convert -i $(TMPDIR)/uberon-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: cl
 .PHONY: mirror-cl
 .PRECIOUS: $(MIRRORDIR)/cl.owl
 mirror-cl: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/cl/cl-base.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/cl/cl-base.owl --create-dirs -o $(TMPDIR)/cl-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) convert -i $(TMPDIR)/cl-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: ncbitaxon
 .PHONY: mirror-ncbitaxon
 .PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl
 mirror-ncbitaxon: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: pr
 .PHONY: mirror-pr
 .PRECIOUS: $(MIRRORDIR)/pr.owl
 mirror-pr: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PR --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) remove -I https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl --base-iri $(OBOBASE)/PR  --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
 MERGE_MIRRORS = true
 
+ifeq ($(strip $(MERGE_MIRRORS)),true)
 $(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
-	if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) -o $@; fi
+	$(ROBOT) merge $(patsubst %, -i %, $^)  -o $@
 .PRECIOUS: $(MIRRORDIR)/merged.owl
+endif
 
 
 $(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
 
 
 
@@ -562,9 +622,13 @@ 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 http://purl.obolibrary.org/obo/PATO_ --base-iri http://purl.obolibrary.org/obo/pato# --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) \
@@ -581,7 +645,7 @@ $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 #	remove --select imports --trim false
 $(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \
-		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
+		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \
 		relax \
 		remove --axioms equivalent \
 		relax \
@@ -648,13 +712,16 @@ 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
@@ -673,6 +740,7 @@ 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 pato-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
@@ -690,8 +758,8 @@ Imports management:
 
 Editor utilities:
 * validate_idranges:	Make sure your ID ranges file is formatted correctly
-* normalize_src:	Load and safe your pato-edit file after you to make sure its serialised correctly
-* normalize_obo_src:	Load and safe your pato-edit.obo file after you to merge duplicate annotation assertions
+* normalize_src:	Load and save your pato-edit file after you to make sure its serialised correctly
+* normalize_obo_src:	Load and save your pato-edit.obo file after you to merge duplicate annotation assertions
 * 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/run.sh b/src/ontology/run.sh
index cebc839b..833f7e6c 100755
--- a/src/ontology/run.sh
+++ b/src/ontology/run.sh
@@ -14,6 +14,8 @@
 #
 # See README-editors.md for more details.
 
+set -e
+
 if [ -f run.sh.conf ]; then
     . ./run.sh.conf
 fi
@@ -29,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok
     GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token")
 fi
 
+# SSH agent socket
+# On macOS, we cannot use $SSH_AUTH_SOCK directly,
+# we need to use a "magic" socket instead.
+case "$(uname)" in
+Darwin)
+    ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock
+    ;;
+*)
+    ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK
+    ;;
+esac
+ODK_SSH_BIND=
+if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then
+    ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock"
+fi
+
 ODK_IMAGE=${ODK_IMAGE:-odkfull}
 TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
 if [ -n "$TAG_IN_IMAGE" ]; then
@@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest}
 ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx12G}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
+ODK_USER_ID=${ODK_USER_ID:-$(id -u)}
+ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)}
+
+# 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
     # non-breaking spaces (U+00A0) instead of normal spaces, to
     # prevent the shell from tokenizing the format string.
-    echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
+    echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps."
     TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
 fi
+rm -f tmp/debug.log
 
-VOLUME_BIND=$PWD/../../:/work
+VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND
 WORK_DIR=/work/src/ontology
 
 if [ -n "$ODK_BINDS" ]; then
@@ -59,14 +89,14 @@ fi
 if [ -n "$USE_SINGULARITY" ]; then
     
     singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
-        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \
         --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="$ODK_JAVA_OPTS" \
+        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \
         --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 fi
 
diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh
new file mode 100755
index 00000000..45d431d1
--- /dev/null
+++ b/src/scripts/run-command.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log}
+echo "Command: sh $@" >> $ODK_DEBUG_FILE
+/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@"
diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh
index 42278403..085abe4d 100644
--- a/src/scripts/update_repo.sh
+++ b/src/scripts/update_repo.sh
@@ -26,7 +26,8 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/
 cp -r target/$OID/src/sparql/* $SRCDIR/sparql/
 mkdir -p $ROOTDIR/.github
 mkdir -p $ROOTDIR/.github/workflows
-cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+
 
 
 cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
@@ -35,5 +36,5 @@ cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
 cp -n target/$OID/mkdocs.yaml $ROOTDIR/
 
 echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)"
-echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml."
+
 echo "Ontology repository update successfully completed."
\ No newline at end of file
diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql
index 0c4d2844..a6a4851e 100644
--- a/src/sparql/class-count-by-prefix.sparql
+++ b/src/sparql/class-count-by-prefix.sparql
@@ -7,4 +7,4 @@ SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE
   FILTER (!isBlank(?cls))
   BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix)
 }
-GROUP BY ?prefix
+GROUP BY ?prefix
\ No newline at end of file