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Makefile
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# ----------------------------------------
# Makefile for cl
# Generated using ontology-development-kit
# ODK Version: v1.3.1
# ----------------------------------------
# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use cl.Makefile instead
# ----------------------------------------
# More information: https://github.com/INCATools/ontology-development-kit/
# ----------------------------------------
# Standard Constants
# ----------------------------------------
# these can be overwritten on the command line
URIBASE= http://purl.obolibrary.org/obo
ONT= cl
ONTBASE= $(URIBASE)/$(ONT)
EDIT_FORMAT= owl
SRC = $(ONT)-edit.$(EDIT_FORMAT)
CATALOG= catalog-v001.xml
ROBOT= robot --catalog $(CATALOG)
OWLTOOLS= owltools --use-catalog
RELEASEDIR= ../..
REPORTDIR= reports
TEMPLATEDIR= ../templates
TMPDIR= tmp
MIRRORDIR= mirror
IMPORTDIR= imports
SUBSETDIR= subsets
SCRIPTSDIR= ../scripts
SPARQLDIR = ../sparql
COMPONENTSDIR = components
REPORT_FAIL_ON = ERROR
REPORT_LABEL =
REPORT_PROFILE_OPTS =
OBO_FORMAT_OPTIONS =
SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by
SPARQL_EXPORTS = basic-report
ODK_VERSION_MAKEFILE = v1.3.1
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)
OTHER_SRC = $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl
ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt
PATTERNDIR= ../patterns
PATTERN_TESTER= dosdp validate -i
DOSDPT= dosdp-tools
PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.owl
FORMATS = $(sort owl obo json owl)
FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic $(ONT)-non-classified $(ONT)-base $(ONT)-full)
# ----------------------------------------
# Top-level targets
# ----------------------------------------
.PHONY: .FORCE
.PHONY: all
all: all_odk
.PHONY: all_odk
all_odk: odkversion test all_assets
.PHONY: test
test: odkversion dosdp_validation sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt
$(ROBOT) reason --input $(SRC) --reasoner ELK --equivalent-classes-allowed asserted-only \
--exclude-tautologies structural --output test.owl && rm test.owl &&\
echo "Success"
.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
$(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR):
mkdir -p $@
# ----------------------------------------
# Release assets
# ----------------------------------------
MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(r)) $(ONT))
MAIN_GZIPPED =
MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED)
SRCMERGED = $(TMPDIR)/merged-$(SRC)
.PHONY: all_main
all_main: $(MAIN_FILES)
# ----------------------------------------
# Import assets
# ----------------------------------------
IMPORTS = pr go caro uberon ro chebi pato ncbitaxon
IMPORT_ROOTS = $(IMPORTDIR)/merged_import
IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
IMPORT_FILES = $(IMPORT_OWL_FILES)
.PHONY: all_imports
all_imports: $(IMPORT_FILES)
# ----------------------------------------
# Subset assets
# ----------------------------------------
SUBSETS = BDS_subset
SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS))
SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f)))
.PHONY: all_subsets
all_subsets: $(SUBSET_FILES)
# ----------------------------------------
# QC Reports & Utilities
# ----------------------------------------
OBO_REPORT = $(SRC)-obo-report
REPORTS = $(OBO_REPORT)
REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS))
.PHONY: robot_reports
robot_reports: $(REPORT_FILES)
.PHONY: all_reports
all_reports: custom_reports robot_reports
# ----------------------------------------
# ROBOT OWL Profile checking
# ----------------------------------------
# The conversion to functional syntax is necessary to avoid undeclared entity violations.
$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) $(TMPDIR)
$(ROBOT) merge -i $< convert -f ofn -o $(TMPDIR)/validate.ofn
$(ROBOT) validate-profile --profile DL -i $(TMPDIR)/validate.ofn -o $@ || { cat $@ && exit 1; }
.PRECIOUS: $(REPORTDIR)/validate_profile_owl2dl_%.txt
validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt
echo "$* profile validation completed."
# ----------------------------------------
# Sparql queries: Q/C
# ----------------------------------------
# these live in the ../sparql directory, and have suffix -violation.sparql
# adding the name here will make the violation check live.
SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql)
sparql_test: $(SRC) catalog-v001.xml | $(REPORTDIR)
ifneq ($(SPARQL_VALIDATION_QUERIES),)
$(ROBOT) verify --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
endif
# ----------------------------------------
# ROBOT report
# ----------------------------------------
$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
# ----------------------------------------
# Release assets
# ----------------------------------------
ASSETS = \
$(IMPORT_FILES) \
$(MAIN_FILES) \
$(PATTERN_RELEASE_FILES) \
$(REPORT_FILES) \
$(SUBSET_FILES)
RELEASE_ASSETS = \
$(MAIN_FILES) \
$(SUBSET_FILES)
.PHONY: all_assets
all_assets: $(ASSETS)
.PHONY: show_assets
show_assets:
echo $(ASSETS)
du -sh $(ASSETS)
# ----------------------------------------
# Release Management
# ----------------------------------------
KEEPRELATIONS=keeprelations.txt
CLEANFILES=$(MAIN_FILES) $(SRCMERGED)
# This should be executed by the release manager whenever time comes to make a release.
# It will ensure that all assets/files are fresh, and will copy to release folder
.PHONY: prepare_release
prepare_release: all_odk
rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\
mkdir -p $(RELEASEDIR)/patterns && cp -rf $(PATTERN_RELEASE_FILES) $(RELEASEDIR)/patterns &&\
rm -f $(CLEANFILES) &&\
echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release \
on your git hosting site such as GitHub or GitLab"
.PHONY: prepare_initial_release
prepare_initial_release: all_assets
rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\
mkdir -p $(RELEASEDIR)/patterns && cp -rf $(PATTERN_RELEASE_FILES) $(RELEASEDIR)/patterns &&\
rm -f $(patsubst %, ./%, $(CLEANFILES)) &&\
cd $(RELEASEDIR) && git add $(RELEASE_ASSETS)
.PHONY: prepare_release_fast
prepare_release_fast:
$(MAKE) prepare_release IMP=false PAT=false MIR=false COMP=false
# ------------------------
# Imports: Seeding system
# ------------------------
# seed.txt contains all referenced entities
IMPORTSEED=$(TMPDIR)/seed.txt
PRESEED=$(TMPDIR)/pre_seed.txt
$(SRCMERGED): $(SRC) $(OTHER_SRC)
$(ROBOT) remove --input $< --select imports --trim false \
merge $(patsubst %, -i %, $(OTHER_SRC)) -o $@
$(PRESEED): $(SRCMERGED)
$(ROBOT) query -f csv -i $< --query ../sparql/terms.sparql [email protected] &&\
cat [email protected] | sort | uniq > $@
SIMPLESEED=$(TMPDIR)/simple_seed.txt
$(SIMPLESEED): $(SRCMERGED) $(ONTOLOGYTERMS)
$(ROBOT) query -f csv -i $< --query ../sparql/simple-seed.sparql [email protected] &&\
cat [email protected] $(ONTOLOGYTERMS) | sort | uniq > $@ &&\
echo "http://www.geneontology.org/formats/oboInOwl#SubsetProperty" >> $@ &&\
echo "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty" >> $@
ALLSEED = $(PRESEED) $(TMPDIR)/all_pattern_terms.txt \
$(IMPORTSEED): $(ALLSEED) | $(TMPDIR)
if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi
ANNOTATION_PROPERTIES=rdfs:label IAO:0000115
# ----------------------------------------
# Import modules
# ----------------------------------------
# Most ontologies are modularly constructed using portions of other ontologies
# These live in the imports/ folder
# This pattern uses ROBOT to generate an import module
# Should be able to drop this if robot can just take a big messy list of terms as input.
$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt
if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi
ALL_TERMS_COMBINED = $(patsubst %, $(IMPORTDIR)/%_terms_combined.txt, $(IMPORTS))
$(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi
$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
remove --select "<http://www.informatics.jax.org/marker/MGI:*>" remove --select "<http://purl.obolibrary.org/obo/OBA_*>" remove --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove --select "<http://purl.obolibrary.org/obo/OBI_*>" remove --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove --select "<http://purl.obolibrary.org/obo/CLO_*>" remove --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>" \
extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@; fi
$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@; fi
.PRECIOUS: $(IMPORTDIR)/%_import.owl
## Module for ontology: pr
$(IMPORTDIR)/pr_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/pr_terms_combined.txt
if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/pr_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@; fi
## Module for ontology: chebi
$(IMPORTDIR)/chebi_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/chebi_terms_combined.txt
if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/chebi_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@; fi
.PHONY: refresh-imports
refresh-imports:
$(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B
.PHONY: no-mirror-refresh-imports
no-mirror-refresh-imports:
$(MAKE) IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B
.PHONY: refresh-imports-excluding-large
refresh-imports-excluding-large:
$(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B
.PHONY: refresh-%
refresh-%:
$(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B
.PHONY: no-mirror-refresh-%
no-mirror-refresh-%:
$(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B
# ----------------------------------------
# Components
# ----------------------------------------
# Some ontologies contain external and internal components. A component is included in the ontology in its entirety.
COMP=true # Global parameter to bypass component generation
.PHONY: all_components
all_components: $(OTHER_SRC)
.PHONY: recreate-components
recreate-components:
$(MAKE) IMP=true MIR=true PAT=true IMP_LARGE=true all_components -B
.PHONY: recreate-%
recreate-%:
$(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B
$(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
touch $@
.PRECIOUS: $(COMPONENTSDIR)/%
# ----------------------------------------
# Mirroring upstream ontologies
# ----------------------------------------
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
## ONTOLOGY: pr
.PHONY: mirror-pr
.PRECIOUS: $(MIRRORDIR)/pr.owl
mirror-pr: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = 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] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: go
.PHONY: mirror-go
.PRECIOUS: $(MIRRORDIR)/go.owl
mirror-go: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/go/go-base.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/go.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: caro
.PHONY: mirror-caro
.PRECIOUS: $(MIRRORDIR)/caro.owl
mirror-caro: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/caro/caro-base.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: uberon
.PHONY: mirror-uberon
.PRECIOUS: $(MIRRORDIR)/uberon.owl
mirror-uberon: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/uberon/uberon-base.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: ro
.PHONY: mirror-ro
.PRECIOUS: $(MIRRORDIR)/ro.owl
mirror-ro: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: chebi
.PHONY: mirror-chebi
.PRECIOUS: $(MIRRORDIR)/chebi.owl
mirror-chebi: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(URIBASE)/chebi.owl.gz --create-dirs -o $(MIRRORDIR)/chebi.owl.gz --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/chebi.owl.gz -o [email protected] && \
$(ROBOT) remove -i [email protected] --base-iri $(URIBASE)/CHEBI --axioms external --preserve-structure false --trim false -o [email protected] &&\
mv [email protected] $(TMPDIR)/[email protected]; fi
## ONTOLOGY: pato
.PHONY: mirror-pato
.PRECIOUS: $(MIRRORDIR)/pato.owl
mirror-pato: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/pato/pato-base.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 &&\
$(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
## 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 [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
.PRECIOUS: $(MIRRORDIR)/merged.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." &&\
cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
# ----------------------------------------
# Subsets
# ----------------------------------------
$(SUBSETDIR)/%.tsv: $(SUBSETDIR)/%.owl
$(ROBOT) query -f tsv -i $< -s ../sparql/labels.sparql $@
.PRECIOUS: $(SUBSETDIR)/%.tsv
$(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR)
$(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset $* -o [email protected] && mv [email protected] $@ &&\
$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o [email protected] && mv [email protected] $@
.PRECIOUS: $(SUBSETDIR)/%.owl
$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(SUBSETDIR)/%.json: $(SUBSETDIR)/%.owl
$(ROBOT) convert --input $< --check false -f json -o [email protected] &&\
jq -S 'walk(if type == "array" then sort else . end)' [email protected] > $@ && rm [email protected]
# ---------------------------------------------
# Sparql queries: Table exports / Query Reports
# ---------------------------------------------
SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql $(REPORTDIR)/$(V).tsv)
# This combines all into one single command
.PHONY: custom_reports
custom_reports: $(SRC) | $(REPORTDIR)
ifneq ($(SPARQL_EXPORTS_ARGS),)
$(ROBOT) query -f tsv --use-graphs true -i $< $(SPARQL_EXPORTS_ARGS)
endif
# ----------------------------------------
# DOSDP Templates/Patterns
# ----------------------------------------
PAT=true # Global parameter to bypass pattern generation
ALL_PATTERN_FILES=$(wildcard $(PATTERNDIR)/dosdp-patterns/*.yaml)
ALL_PATTERN_NAMES=$(strip $(patsubst %.yaml,%, $(notdir $(wildcard $(PATTERNDIR)/dosdp-patterns/*.yaml))))
PATTERN_CLEAN_FILES=../patterns/all_pattern_terms.txt \
$(DOSDP_OWL_FILES_DEFAULT) $(DOSDP_TERM_FILES_DEFAULT) \
$(DOSDP_OWL_FILES_CLUSTERING) $(DOSDP_TERM_FILES_CLUSTERING)
# Note to future generations: prepending ./ is a safety measure to ensure that
# the environment does not malicously set `PATTERN_CLEAN_FILES` to `\`.
.PHONY: pattern_clean
pattern_clean:
rm -f $(PATTERN_CLEAN_FILES)
.PHONY: patterns
patterns dosdp:
echo "Validating all DOSDP templates"
$(MAKE) dosdp_validation
echo "Building $(PATTERNDIR)/definitions.owl"
$(MAKE) $(PATTERNDIR)/pattern.owl $(PATTERNDIR)/definitions.owl
# DOSDP Template Validation
$(TMPDIR)/pattern_schema_checks: $(ALL_PATTERN_FILES) | $(TMPDIR)
$(PATTERN_TESTER) $(PATTERNDIR)/dosdp-patterns/ && touch $@
.PHONY: pattern_schema_checks
pattern_schema_checks dosdp_validation: $(TMPDIR)/pattern_schema_checks
.PHONY: update_patterns
update_patterns: download_patterns
cp -r $(TMPDIR)/dosdp/*.yaml $(PATTERNDIR)/dosdp-patterns
# This command is a workaround for the absence of -N and -i in wget of alpine (the one ODK depend on now).
# It downloads all patterns specified in external.txt
.PHONY: download_patterns
download_patterns:
if [ $(PAT) = true ]; then rm -f $(TMPDIR)/dosdp/*.yaml.1 || true; fi
if [ $(PAT) = true ] && [ -s $(PATTERNDIR)/dosdp-patterns/external.txt ]; then wget -i $(PATTERNDIR)/dosdp-patterns/external.txt --backups=1 -P $(TMPDIR)/dosdp; fi
if [ $(PAT) = true ]; then rm -f $(TMPDIR)/dosdp/*.yaml.1 || true; fi
$(PATTERNDIR)/dospd-patterns/%.yml: download_patterns
if [ $(PAT) = true ] ; then if cmp -s $(TMPDIR)/dosdp-$*.yml $@ ; then echo "DOSDP templates identical."; else echo "DOSDP templates different, updating." &&\
cp $(TMPDIR)/dosdp-$*.yml $@; fi; fi
# DOSDP Template: Pipelines
# Each pipeline gets its own directory structure
# DOSDP default pipeline
DOSDP_TSV_FILES_DEFAULT = $(wildcard $(PATTERNDIR)/data/default/*.tsv)
DOSDP_OWL_FILES_DEFAULT = $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.ofn, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))
DOSDP_TERM_FILES_DEFAULT = $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.txt, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))
DOSDP_PATTERN_NAMES_DEFAULT = $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv))))
$(DOSDP_OWL_FILES_DEFAULT): $(SRC) $(DOSDP_TSV_FILES_DEFAULT) $(ALL_PATTERN_FILES)
if [ $(PAT) = true ] && [ "${DOSDP_PATTERN_NAMES_DEFAULT}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml \
--infile=$(PATTERNDIR)/data/default/ --template=$(PATTERNDIR)/dosdp-patterns --batch-patterns="$(DOSDP_PATTERN_NAMES_DEFAULT)" \
--ontology=$< --obo-prefixes=true --outfile=$(PATTERNDIR)/data/default; fi
# DOSDP clustering pipeline
DOSDP_OWL_FILES_CLUSTERING = $(patsubst %.tsv, $(PATTERNDIR)/data/clustering/%.ofn, $(notdir $(wildcard $(PATTERNDIR)/data/clustering/*.tsv)))
DOSDP_TERM_FILES_CLUSTERING = $(patsubst %.tsv, $(PATTERNDIR)/data/clustering/%.txt, $(notdir $(wildcard $(PATTERNDIR)/data/clustering/*.tsv)))
DOSDP_TSV_FILES_CLUSTERING = $(wildcard $(PATTERNDIR)/data/clustering/*.tsv)
DOSDP_PATTERN_NAMES_CLUSTERING = $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/clustering/*.tsv))))
$(DOSDP_OWL_FILES_CLUSTERING): $(SRC) $(DOSDP_TSV_FILES_CLUSTERING) $(ALL_PATTERN_FILES)
if [ $(PAT) = true ] && [ "${DOSDP_PATTERN_NAMES_CLUSTERING}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml \
--infile=$(PATTERNDIR)/data/clustering --template=$(PATTERNDIR)/dosdp-patterns/ --batch-patterns="$(DOSDP_PATTERN_NAMES_CLUSTERING)" \
--ontology=$< --obo-prefixes=true --outfile=$(PATTERNDIR)/data/clustering; fi
# Generate template file seeds
## Generate template file seeds
$(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERNDIR)/data/default/%.tsv
if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi
$(PATTERNDIR)/data/clustering/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERNDIR)/data/clustering/%.tsv
if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi
# Generating the seed file from all the TSVs. If Pattern generation is deactivated, we still extract a seed from definitions.owl
$(TMPDIR)/all_pattern_terms.txt: $(DOSDP_TERM_FILES_DEFAULT) $(DOSDP_TERM_FILES_CLUSTERING) $(TMPDIR)/pattern_owl_seed.txt
if [ $(PAT) = true ]; then cat $^ | sort | uniq > $@; else $(ROBOT) query --use-graphs true -f csv -i $(PATTERNDIR)/definitions.owl \
--query ../sparql/terms.sparql $@; fi
$(TMPDIR)/pattern_owl_seed.txt: $(PATTERNDIR)/pattern.owl
if [ $(PAT) = true ]; then $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/terms.sparql $@; fi
# Pattern pipeline main targets: the generated OWL files
# Create pattern.owl, an ontology of all DOSDP patterns
$(PATTERNDIR)/pattern.owl: $(ALL_PATTERN_FILES)
if [ $(PAT) = true ]; then $(DOSDPT) prototype --obo-prefixes true --template=$(PATTERNDIR)/dosdp-patterns --outfile=$@; fi
# Generating the individual pattern modules and merging them into definitions.owl
$(PATTERNDIR)/definitions.owl: $(DOSDP_OWL_FILES_DEFAULT) $(DOSDP_OWL_FILES_CLUSTERING)
if [ $(PAT) = true ] && [ "${DOSDP_PATTERN_NAMES_DEFAULT}" ] || [ "${DOSDP_PATTERN_NAMES_CLUSTERING}" ] && [ $(PAT) = true ]; then $(ROBOT) merge $(addprefix -i , $^) \
annotate --ontology-iri $(ONTBASE)/patterns/definitions.owl --version-iri $(ONTBASE)/releases/$(TODAY)/patterns/definitions.owl \
--annotation owl:versionInfo $(VERSION) -o definitions.ofn && mv definitions.ofn $@; fi
# ----------------------------------------
# Release artefacts: export formats
# ----------------------------------------
$(ONT)-base.obo: $(ONT)-base.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT)-base.json: $(ONT)-base.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
jq -S 'walk(if type == "array" then sort else . end)' [email protected] > $@ && rm [email protected]
$(ONT)-full.obo: $(ONT)-full.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT)-full.json: $(ONT)-full.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
jq -S 'walk(if type == "array" then sort else . end)' [email protected] > $@ && rm [email protected]
$(ONT)-simple.obo: $(ONT)-simple.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT)-simple.json: $(ONT)-simple.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
jq -S 'walk(if type == "array" then sort else . end)' [email protected] > $@ && rm [email protected]
$(ONT)-basic.obo: $(ONT)-basic.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT)-basic.json: $(ONT)-basic.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
jq -S 'walk(if type == "array" then sort else . end)' [email protected] > $@ && rm [email protected]
$(ONT)-non-classified.obo: $(ONT)-non-classified.owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT)-non-classified.json: $(ONT)-non-classified.owl
$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] &&\
jq -S 'walk(if type == "array" then sort else . end)' [email protected] > $@ && rm [email protected]
# ----------------------------------------
# Release artefacts: main release artefacts
# ----------------------------------------
$(ONT).owl: $(ONT)-full.owl
$(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert -o [email protected] && mv [email protected] $@
$(ONT).obo: $(ONT).owl
$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o [email protected] && grep -v ^owl-axioms [email protected] > $@ && rm [email protected]
$(ONT).json: $(ONT)-full.owl
$(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
convert --check false -f json -o [email protected] && \
jq -S 'walk(if type == "array" then sort else . end)' [email protected] > $@ && rm [email protected]
# -----------------------------------------------------
# Release artefacts: variants (base, full, simple, etc)
# -----------------------------------------------------
SHARED_ROBOT_COMMANDS =
$(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC)
touch $(ONTOLOGYTERMS) && \
$(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/cl_terms.sparql $@
# base: OTHER sources of interest, such as definitions owl
$(ONT)-base.owl: $(SRC) $(OTHER_SRC)
$(ROBOT) remove --input $< --select imports --trim false \
merge $(patsubst %, -i %, $(OTHER_SRC)) \
$(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] $@
# Full: The full artefacts with imports merged, reasoned
$(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES)
$(ROBOT) merge --input $< \
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-non-classified: (edit->imports-merged)
$(ONT)-non-classified.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES)
$(ROBOT) merge --input $< \
$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@
# foo-simple: (edit->reason,relax,reduce,drop imports, drop every axiom which contains an entity outside the "namespaces of interest")
# drop every axiom: filter --term-file keep_terms.txt --trim true
# remove --select imports --trim false
$(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
$(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) \
reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
relax \
remove --axioms equivalent \
relax \
filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
reduce -r ELK \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
$(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 (?)).
# See above (David comment) for explanation.
# removes any axioms that contains one of the ops that not in the whitelist file
$(ONT)-basic.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATIONS) $(IMPORT_FILES)
$(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) \
reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
relax \
remove --axioms equivalent \
remove --axioms disjoint \
remove --term-file $(KEEPRELATIONS) --select complement --select object-properties --trim true \
relax \
filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
reduce -r ELK \
$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output [email protected] && mv [email protected] $@
# ----------------------------------------
# Debugging Tools
# ----------------------------------------
explain_unsat: $(SRC)
$(ROBOT) explain -i $(SRC) -M unsatisfiability --unsatisfiable random:10 --explanation $(TMPDIR)/[email protected]
# ----------------------------------------
# General Validation
# ----------------------------------------
TSV=
ALL_TSV_FILES=$(DOSDP_TSV_FILES_CLUSTERING) $(DOSDP_TSV_FILES_DEFAULT)
validate-tsv: $(TSV) | $(TMPDIR)
for FILE in $< ; do \
tsvalid $$FILE > $(TMPDIR)/validate.txt; \
if [ -s $(TMPDIR)/validate.txt ]; then cat $(TMPDIR)/validate.txt && exit 1; fi ; \
done
validate-all-tsv: $(ALL_TSV_FILES)
$(MAKE) validate-tsv TSV="$^"
# ----------------------------------------
# Editors Utilities
# ----------------------------------------
.PHONY: normalize_src
normalize_src: $(SRC)
$(ROBOT) convert -i $< -f ofn -o $(TMPDIR)/normalise && mv $(TMPDIR)/normalise $<
.PHONY: validate_idranges
validate_idranges:
amm $(SCRIPTSDIR)/validate_id_ranges.sc cl-idranges.owl
.PHONY: update_repo
update_repo:
sh $(SCRIPTSDIR)/update_repo.sh
update_docs:
mkdocs gh-deploy --config-file ../../mkdocs.yaml
# Note to future generations: prepending ./ is a safety measure to ensure that
# the environment does not malicously set `CLEANFILES` to `\`.
.PHONY: clean
clean:
$(MAKE) pattern_clean
[ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/*
[ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/*
rm -f $(CLEANFILES)
.PHONY: help
help:
@echo "$$data"
define data
Usage: [IMAGE=(odklite|odkfull)] [ODK_DEBUG=yes] sh run.sh make [(IMP|MIR|IMP_LARGE|PAT)=(false|true)] command
----------------------------------------
Command reference
----------------------------------------
Core commands:
* prepare_release: Run the entire release pipeline. Use make IMP=false prepare_release to avoid rerunning the imports
* 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 cl-odk.yaml
* test: Running all validation tests
* odkversion: Show the current version of the ODK Makefile and ROBOT.
* clean: Delete all temporary files
* help: Print ODK Usage information
Imports management:
* refresh-imports: Refresh all imports and mirrors.
* refresh-components: Refresh all components.
* no-mirror-refresh-imports: Refresh all imports without downloading mirrors.
* refresh-imports-excluding-large: Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'.
* refresh-%: Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'.
* no-mirror-refresh-%: Refresh a single import without updating the mirror, i.e. refresh-go will refresh 'imports/go_import.owl'.
* mirror-%: Refresh a single mirror.
DOSDP templates
* dosdp: Run the DOSDP patterns pipeline: Run tests, then build OWL files from the tables.
* patterns: Alias of the 'dosdp' command
* pattern_clean: Delete all temporary pattern files
* dosdp_validation: Run all validation checks on DOSDP template files and tables
* pattern_schema_checks: Alias of the 'dosdp_validation' command
* update_patterns: Pull updated patterns listed in dosdp-patterns/external.txt
* dosdp-matches-%: Run the DOSDP matches/query pipeline as configured in your cl-odk.yaml file.
Editor utilities:
* validate_idranges: Make sure your ID ranges file is formatted correctly
* normalize_src: Load and safe your cl-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.
Additional build commands (advanced users)
* all: Run the entire pipeline (like prepare_release), but without copying the release files to the release directory.
* all_subsets: Build all subsets
* custom_reports: Generate all custom sparql reports you have configured in your cl-odk.yaml file.
* all_assets: Build all assets
* show_assets: Print a list of all assets that would be build by the release pipeline
Additional QC commands (advanced users)
* robot_reports: Run all configured ROBOT reports
* validate_profile_%: Run an OWL2 DL profile validation check, for example validate_profile_cl-edit.owl.
Examples:
* sh run.sh make IMP=false prepare_release
* sh run.sh make update_repo
* sh run.sh make test
Tricks:
* Add -B to the end of your command to force re-running it even if nothing has changed
* Use the IMAGE parameter to the run.sh script to use a different image like odklite
* Use ODK_DEBUG=yes sh run.sh make ... to print information about timing and debugging
endef
export data
include cl.Makefile