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Experimental migration to ODK 1.5 #228

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Experimental migration to ODK 1.5 #228

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53 changes: 28 additions & 25 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# ----------------------------------------
# Makefile for oba
# 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 oba.Makefile instead

Expand Down Expand Up @@ -44,7 +44,7 @@ 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
ODK_VERSION_MAKEFILE = v1.5

TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
Expand All @@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.

FORMATS = $(sort owl obo json owl)
FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-basic $(ONT)-baseplus )
RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-basic $(ONT)-baselite )

# ----------------------------------------
# Top-level targets
Expand All @@ -80,6 +80,10 @@ all_odk: odkversion test all_assets release_diff
test: odkversion dosdp_validation 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

Expand Down Expand Up @@ -430,7 +434,7 @@ mirror-ro: | $(TMPDIR)
.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 [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/CHEBI --axioms external --preserve-structure false --trim false -o [email protected] &&\
$(ROBOT) remove -i [email protected] --base-iri $(OBOBASE)/CHEBI --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


Expand Down Expand Up @@ -498,7 +502,7 @@ mirror-ncbitaxon: | $(TMPDIR)
mirror-uberon: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/uberon.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/UBERON --axioms external --preserve-structure false --trim false -o [email protected] &&\
$(ROBOT) remove -i [email protected] --base-iri $(OBOBASE)/UBERON --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


Expand All @@ -523,7 +527,7 @@ mirror-nbo: | $(TMPDIR)
.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 [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/PR --axioms external --preserve-structure false --trim false -o [email protected] &&\
$(ROBOT) remove -i [email protected] --base-iri $(OBOBASE)/PR --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


Expand All @@ -533,7 +537,7 @@ mirror-pr: | $(TMPDIR)
mirror-so: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/so.owl --create-dirs -o $(MIRRORDIR)/so.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/so.owl -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/SO --axioms external --preserve-structure false --trim false -o [email protected] &&\
$(ROBOT) remove -i [email protected] --base-iri $(OBOBASE)/SO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


Expand All @@ -543,7 +547,7 @@ mirror-so: | $(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 [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/PO --axioms external --preserve-structure false --trim false -o [email protected] &&\
$(ROBOT) remove -i [email protected] --base-iri $(OBOBASE)/PO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi


Expand All @@ -553,14 +557,14 @@ mirror-po: | $(TMPDIR)
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 [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/BFO --axioms external --preserve-structure false --trim false -o [email protected] &&\
$(ROBOT) remove -i [email protected] --base-iri $(OBOBASE)/BFO --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi

ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
MERGE_MIRRORS = true

$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) -o $@; fi
if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) remove --axioms equivalent --preserve-structure false -o $@; fi
.PRECIOUS: $(MIRRORDIR)/merged.owl


Expand Down Expand Up @@ -722,9 +726,9 @@ $(ONT)-basic.json: $(ONT)-basic.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
mv [email protected] $@
$(ONT)-baseplus.obo: $(ONT)-baseplus.owl
$(ONT)-baselite.obo: $(ONT)-baselite.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT)-baseplus.json: $(ONT)-baseplus.owl
$(ONT)-baselite.json: $(ONT)-baselite.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
mv [email protected] $@
Expand Down Expand Up @@ -756,15 +760,8 @@ ROBOT_RELEASE_IMPORT_MODE=$(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
# base: A version of the ontology that does not include any externally imported axioms.
$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
$(ROBOT_RELEASE_IMPORT_MODE_BASE) \
$(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) \
--output [email protected] && mv [email protected] $@
# baseplus: A highly experimental variant of base, UNSTABLE. Only to be used experimentally (may disappear in future ODK releases).
$(ONT)-baseplus.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
$(ROBOT_RELEASE_IMPORT_MODE) \
reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
relax \
Expand All @@ -774,12 +771,17 @@ $(ONT)-baseplus.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output [email protected] && mv [email protected] $@
# baselite: All the axioms as they are editted by the editors, excluding reasoning. This is currently the same as "base". Only to be used experimentally (may disappear in future ODK releases).
$(ONT)-baselite.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
$(ROBOT_RELEASE_IMPORT_MODE_BASE) \
$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
--output [email protected] && mv [email protected] $@
# Full: The full artefacts with imports merged, reasoned.
$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
$(ROBOT_RELEASE_IMPORT_MODE) \
reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
relax \
reduce -r ELK \
reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
relax \
reduce -r ELK \
$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@

# foo-basic: A version of -simple containing only relationships using relations on a configurable whitelist (default = BFO:0000050 (?)).
Expand Down Expand Up @@ -881,6 +883,7 @@ 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 oba-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
Expand All @@ -907,8 +910,8 @@ DOSDP templates

Editor utilities:
* validate_idranges: Make sure your ID ranges file is formatted correctly
* normalize_src: Load and safe your oba-edit file after you to make sure its serialised correctly
* normalize_obo_src: Load and safe your oba-edit.obo file after you to merge duplicate annotation assertions
* normalize_src: Load and save your oba-edit file after you to make sure its serialised correctly
* normalize_obo_src: Load and save your oba-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.
Expand Down
2 changes: 1 addition & 1 deletion src/ontology/oba-odk.yaml
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Expand Up @@ -17,7 +17,7 @@ release_artefacts:
- base
- full
- basic
- baseplus
- baselite
primary_release: full
import_group:
use_base_merging: TRUE
Expand Down
8 changes: 8 additions & 0 deletions src/ontology/run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,14 @@ ODK_TAG=${ODK_TAG:-latest}
ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G}
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
Expand Down