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create new release
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@ramonawalls
ramonawalls committed Jan 1, 2022
1 parent 9b0906d commit 02f2412
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Showing 17 changed files with 165,340 additions and 155,724 deletions.
95 changes: 11 additions & 84 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,8 @@ 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
OTHER_SRC =
ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt
PATTERNDIR= ../patterns
DOSDP_SCHEMA= http:// # change to PURL when ready.
PATTERN_TESTER= simple_pattern_tester.py
DOSDPT= dosdp-tools
PATTERN_RELEASE_FILES= $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.owl



FORMATS = $(sort owl owl)
FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
Expand All @@ -64,7 +57,7 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-full $(ONT)-base $(ONT)-base $(ONT)-full)
.PHONY: .FORCE

.PHONY: all
all: odkversion all_imports patterns all_main all_subsets sparql_test all_reports all_assets
all: odkversion all_imports all_main all_subsets sparql_test all_reports all_assets

.PHONY: test
test: odkversion sparql_test all_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt
Expand Down Expand Up @@ -168,8 +161,6 @@ CLEANFILES=$(MAIN_FILES) $(SRCMERGED)
.PHONY: prepare_release
prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES)
rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\
mkdir -p $(RELEASEDIR)/patterns &&\
cp $(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"

Expand Down Expand Up @@ -202,10 +193,10 @@ $(PRESEED): $(SRCMERGED)



ALLSEED = $(PRESEED) $(PATTERNDIR)/all_pattern_terms.txt \
ALLSEED = $(PRESEED) \


$(IMPORTSEED): prepare_patterns $(ALLSEED)
$(IMPORTSEED): $(ALLSEED)
if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi


Expand All @@ -227,7 +218,7 @@ imports/merged_import.owl: mirror/merged.owl imports/merged_terms_combined.txt

imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt
if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
extract -T imports/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \
extract -T imports/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi

Expand All @@ -236,7 +227,7 @@ imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt
## Module for ontology: chebi

imports/chebi_import.owl: mirror/chebi.owl imports/chebi_terms_combined.txt
if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T imports/chebi_terms_combined.txt --force true --individuals include --method BOT \
if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T imports/chebi_terms_combined.txt --force true --individuals exclude --method BOT \
query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi

Expand Down Expand Up @@ -271,7 +262,7 @@ no-mirror-refresh-%:
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
PAT=true # Global parameter to bypass pattern generation


## ONTOLOGY: bco
## Copy of bco is re-downloaded whenever source changes
Expand All @@ -287,7 +278,8 @@ mirror/bco.owl: mirror/bco.trigger
mirror/chebi.trigger: $(SRC)

mirror/chebi.owl: mirror/chebi.trigger
if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(URIBASE)/chebi.owl.gz --create-dirs -o mirror/chebi.owl.gz --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/chebi.owl.gz -o $@.tmp.owl && mv $@.tmp.owl $@; fi
if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(URIBASE)/chebi.owl.gz --create-dirs -o mirror/chebi.owl.gz --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/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 && mv $@.tmp.owl $@; fi
.PRECIOUS: mirror/chebi.owl


Expand Down Expand Up @@ -341,7 +333,7 @@ mirror/pato.owl: mirror/pato.trigger
mirror/pco.trigger: $(SRC)

mirror/pco.owl: mirror/pco.trigger
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/pco.owl --create-dirs -o mirror/pco.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/pco.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/pco/pco-base.owl --create-dirs -o mirror/pco.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/pco.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
.PRECIOUS: mirror/pco.owl


Expand All @@ -359,7 +351,7 @@ mirror/po.owl: mirror/po.trigger
mirror/ro.trigger: $(SRC)

mirror/ro.owl: mirror/ro.trigger
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ro.owl --create-dirs -o mirror/ro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ro/ro-base.owl --create-dirs -o mirror/ro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
.PRECIOUS: mirror/ro.owl


Expand Down Expand Up @@ -442,71 +434,6 @@ all_reports_onestep: $(SRC) | $(REPORTDIR)
ifneq ($(SPARQL_EXPORTS_ARGS),)
$(ROBOT) query -f tsv -i $< $(SPARQL_EXPORTS_ARGS)
endif
# ----------------------------------------
# Patterns (experimental)
# ----------------------------------------

# Test patterns for schema compliance:

.PHONY: patterns
patterns: all_imports $(PATTERNDIR)/pattern.owl $(PATTERNDIR)/definitions.owl

.PHONY: pattern_clean
pattern_clean:
echo "Not implemented"

.PHONY: pattern_schema_checks
pattern_schema_checks: update_patterns
$(PATTERN_TESTER) $(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: update_patterns
update_patterns: .FORCE
if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi
if [ $(PAT) = true ] && [ -s $(PATTERNDIR)/dosdp-patterns/external.txt ]; then wget -i $(PATTERNDIR)/dosdp-patterns/external.txt --backups=1 -P $(PATTERNDIR)/dosdp-patterns; fi
if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi


$(PATTERNDIR)/pattern.owl: pattern_schema_checks update_patterns
if [ $(PAT) = true ]; then $(DOSDPT) prototype --obo-prefixes true --template=$(PATTERNDIR)/dosdp-patterns --outfile=$@; fi

individual_patterns_default := $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.ofn, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))
pattern_term_lists_default := $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.txt, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))





# Generating the individual pattern modules and merging them into definitions.owl
$(PATTERNDIR)/definitions.owl: prepare_patterns update_patterns dosdp_patterns_default
if [ $(PAT) = true ] && [ "${individual_patterns_names_default}" ] && [ $(PAT) = true ]; then $(ROBOT) merge $(addprefix -i , $(individual_patterns_default)) 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

individual_patterns_names_default := $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv))))
dosdp_patterns_default: $(SRC) all_imports .FORCE
if [ $(PAT) = true ] && [ "${individual_patterns_names_default}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --infile=$(PATTERNDIR)/data/default/ --template=$(PATTERNDIR)/dosdp-patterns --batch-patterns="$(individual_patterns_names_default)" --ontology=$< --obo-prefixes=true --outfile=$(PATTERNDIR)/data/default; fi





# Generating the seed file from all the TSVs. If Pattern generation is deactivated, we still extract a seed from definitions.owl
$(PATTERNDIR)/all_pattern_terms.txt: $(pattern_term_lists_default) $(PATTERNDIR)/pattern_owl_seed.txt
if [ $(PAT) = true ]; then cat $^ | sort | uniq > $@; else $(ROBOT) query --use-graphs true -f csv -i ../patterns/definitions.owl --query ../sparql/terms.sparql $@; fi

$(PATTERNDIR)/pattern_owl_seed.txt: $(PATTERNDIR)/pattern.owl
if [ $(PAT) = true ]; then $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/terms.sparql $@; fi

$(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERNDIR)/data/default/%.tsv .FORCE
if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi

.PHONY: prepare_patterns
prepare_patterns:
if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(pattern_term_lists_default) ; fi
if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(individual_patterns_default) ; fi





# ----------------------------------------
# Release artefacts: export formats
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