mirror of
https://github.com/psychoinformatics-de/datalad-concepts.git
synced 2026-05-06 23:23:45 +00:00
Michael Hanke
f09a0efaf1
We use this to ensure testing a consistent set of schemas (and it is also faster). With linkml v1.10, it appears that local schemas are imported relative to CWD -- but only at the first level. When a locally imported schema imports another local schema, the imports are relative to the location of the imported schema (behavior prior v1.10). We mitigate this by changing CWD to the directory of the respective root schema to equalize the conditions again.
312 lines
11 KiB
Makefile
312 lines
11 KiB
Makefile
# this is a shell monster that will fail with exit(125) if a command produces
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# stderr output
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FAILIF_STDERR=bash -c 'fail_if_stderr() (rc=$$({("$$@" 2>&1 >&3 3>&- 4>&-; echo "$$?" >&4) | grep '^' >&2 3>&- 4>&-; } 4>&1); err=$$?; [ "$$rc" -eq 0 ] || exit "$$rc"; [ "$$err" -ne 0 ] || exit 125 ) 3>&1; fail_if_stderr $$@' FAILIF_STDERR
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# no execution when only command printed is wanted
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ifneq (,$(filter n,$(MAKEFLAGS)))
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FAILIF_STDERR=: FAILIF_STDERR
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endif
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try:
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${FAILIF_STDERR} bash -c 'exit 12'
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all: build/mkdocs-site
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build/linkml-docs: \
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build/linkml-docs/s/types/unreleased \
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build/linkml-docs/s/types/v1 \
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build/linkml-docs/s/common-mixin/unreleased \
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build/linkml-docs/s/relations-mixin/unreleased \
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build/linkml-docs/s/things/unreleased \
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build/linkml-docs/s/things/v1 \
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build/linkml-docs/s/things/v2 \
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build/linkml-docs/s/things-properties/unreleased \
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build/linkml-docs/s/things-properties/v1 \
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build/linkml-docs/s/things-data/unreleased \
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build/linkml-docs/s/things-data/v1 \
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build/linkml-docs/s/things-study/unreleased \
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build/linkml-docs/s/things-study/v1 \
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build/linkml-docs/s/things-resources/unreleased \
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build/linkml-docs/s/things-resources/v1 \
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build/linkml-docs/s/things-rules/unreleased \
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build/linkml-docs/s/things-rules/v1 \
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build/linkml-docs/s/things-distributions/unreleased \
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build/linkml-docs/s/things-distributions/v1 \
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build/linkml-docs/s/things-social/unreleased \
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build/linkml-docs/s/things-social/v1 \
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build/linkml-docs/s/things-files/unreleased \
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build/linkml-docs/s/things-files/v1 \
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build/linkml-docs/s/things-publications/unreleased \
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build/linkml-docs/s/things-publications/v1 \
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build/linkml-docs/s/things-prov/unreleased \
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build/linkml-docs/s/things-prov/v1 \
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build/linkml-docs/s/flat/unreleased \
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build/linkml-docs/s/spatial-mixin/unreleased \
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build/linkml-docs/s/temporal-mixin/unreleased \
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build/linkml-docs/s/prov-mixin/unreleased \
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build/linkml-docs/s/flat-prov/unreleased \
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build/linkml-docs/s/publications-mixin/unreleased \
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build/linkml-docs/s/flat-publications/unreleased \
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build/linkml-docs/s/resources-mixin/unreleased \
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build/linkml-docs/s/flat-resources/unreleased \
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build/linkml-docs/s/social-mixin/unreleased \
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build/linkml-docs/s/flat-social/unreleased \
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build/linkml-docs/s/study-mixin/unreleased \
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build/linkml-docs/s/flat-study/unreleased \
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build/linkml-docs/s/identifiers/unreleased \
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build/linkml-docs/s/quantities-mixin/unreleased \
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build/linkml-docs/s/versions-mixin/unreleased \
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build/linkml-docs/s/files-mixin/unreleased \
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build/linkml-docs/s/flat-files/unreleased \
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build/linkml-docs/s/demo-empirical-data/unreleased \
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build/linkml-docs/s/demo-research-assets/unreleased \
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build/linkml-docs/s/demo-research-information/unreleased \
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build/linkml-docs/s/demo-rse-group/unreleased
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build/linkml-docs/s/%: src/%.yaml src/%/extra-docs
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$(MAKE) imports-remote
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# take the YAML schema verbatim
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mkdir -p $(dir $@)
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cp $< $@.yaml
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$(MAKE) imports-local
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gen-doc \
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--hierarchical-class-view \
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--metadata \
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--format markdown \
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--example-directory src/$*/examples/ \
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-d $@ \
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$< \
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&& (cp -r src/$*/extra-docs/*.md $@ || true)
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# try to inject any extra-docs (if any exist)
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schema="$<"; if [ "$${schema##*-mixin}" = "$<" ]; then \
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gen-owl \
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-f owl \
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--mergeimports \
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$< > $@.owl.ttl && \
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gen-jsonld-context \
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--mergeimports \
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$< > $@.context.jsonld && \
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gen-shacl \
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--include-annotations \
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--include-stripped-prefixes \
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--exclude-order \
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$< > $@.shacl.ttl ; \
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dump-things-create-merged-schema \
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$< > $@.static.yaml ; \
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fi
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build/mkdocs-site: build/linkml-docs extra-docs/*.md
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# top-level content
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cp -r extra-docs/*.md $<
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mkdocs build
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check: check-models check-validation
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# add additional schemas to lint here
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check-models: \
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checkmodel/types/unreleased \
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checkmodel/types/v1 \
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checkmodel/common-mixin/unreleased \
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checkmodel/relations-mixin/unreleased \
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checkmodel/things/unreleased \
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checkmodel/things/v1 \
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checkmodel/things/v2 \
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checkmodel/things-properties/unreleased \
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checkmodel/things-properties/v1 \
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checkmodel/things-study/unreleased \
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checkmodel/things-study/v1 \
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checkmodel/things-data/unreleased \
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checkmodel/things-data/v1 \
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checkmodel/things-resources/unreleased \
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checkmodel/things-resources/v1 \
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checkmodel/things-rules/unreleased \
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checkmodel/things-rules/v1 \
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checkmodel/things-distributions/unreleased \
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checkmodel/things-distributions/v1 \
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checkmodel/things-social/unreleased \
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checkmodel/things-social/v1 \
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checkmodel/things-files/unreleased \
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checkmodel/things-files/v1 \
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checkmodel/things-publications/unreleased \
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checkmodel/things-publications/v1 \
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checkmodel/things-prov/unreleased \
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checkmodel/things-prov/v1 \
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checkmodel/flat/unreleased \
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checkmodel/spatial-mixin/unreleased \
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checkmodel/temporal-mixin/unreleased \
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checkmodel/prov-mixin/unreleased \
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checkmodel/flat-prov/unreleased \
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checkmodel/publications-mixin/unreleased \
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checkmodel/flat-publications/unreleased \
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checkmodel/resources-mixin/unreleased \
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checkmodel/flat-resources/unreleased \
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checkmodel/social-mixin/unreleased \
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checkmodel/flat-social/unreleased \
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checkmodel/study-mixin/unreleased \
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checkmodel/flat-study/unreleased \
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checkmodel/identifiers/unreleased \
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checkmodel/quantities-mixin/unreleased \
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checkmodel/versions-mixin/unreleased \
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checkmodel/files-mixin/unreleased \
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checkmodel/flat-files/unreleased \
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checkmodel/demo-empirical-data/unreleased \
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checkmodel/demo-research-assets/unreleased \
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checkmodel/demo-research-information/unreleased \
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checkmodel/demo-rse-group/unreleased
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checkmodel/%: src/%.yaml
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@echo [Check $<]
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@echo "Run linter"
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@linkml-lint \
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--config .linkmllint.yaml \
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--max-warnings 0 \
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--validate \
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$<
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schema="$<"; if [ "$${schema##*-mixin}" = "$<" ]; then $(MAKE) checkmodel-outputs/$*; else echo "Skipping mixin output tests"; fi
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checkmodel-outputs/%: src/%.yaml
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# generate various output formats, they all have the potential to
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# reveal "hidden" issues
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@echo Generate a JSON-LD context
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@${FAILIF_STDERR} gen-jsonld-context \
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--prefixes \
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--model \
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--mergeimports \
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$< > /dev/null
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@echo Generate JSON schema
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@${FAILIF_STDERR} gen-json-schema $< > /dev/null
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@echo Generate OWL
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@${FAILIF_STDERR} gen-owl $< > /dev/null
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@echo Generate Python classes
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@${FAILIF_STDERR} grep -q '^classes:' $< && ( gen-python $< | python ) || true
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# within check-validation, conversion targets must come before the
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# respective validation targets, because some tests rely on these
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# converted formats
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check-validation: \
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convertexamples/things/unreleased \
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checkvalidation/things/unreleased \
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convertexamples/things/v1 \
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checkvalidation/things/v1 \
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convertexamples/things/v2 \
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checkvalidation/things/v2 \
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convertexamples/things-distributions/unreleased \
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checkvalidation/things-distributions/unreleased \
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convertexamples/things-distributions/v1 \
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checkvalidation/things-distributions/v1 \
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convertexamples/things-social/unreleased \
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checkvalidation/things-social/unreleased \
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convertexamples/things-social/v1 \
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checkvalidation/things-social/v1 \
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convertexamples/things-study/unreleased \
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checkvalidation/things-study/unreleased \
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convertexamples/things-study/v1 \
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checkvalidation/things-study/v1 \
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convertexamples/things-data/unreleased \
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checkvalidation/things-data/unreleased \
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convertexamples/things-data/v1 \
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checkvalidation/things-data/v1 \
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convertexamples/things-resources/unreleased \
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checkvalidation/things-resources/unreleased \
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convertexamples/things-resources/v1 \
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checkvalidation/things-resources/v1 \
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convertexamples/things-rules/unreleased \
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checkvalidation/things-rules/unreleased \
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convertexamples/things-rules/v1 \
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checkvalidation/things-rules/v1 \
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convertexamples/things-files/unreleased \
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checkvalidation/things-files/unreleased \
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convertexamples/things-files/v1 \
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checkvalidation/things-files/v1 \
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convertexamples/things-publications/unreleased \
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checkvalidation/things-publications/unreleased \
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convertexamples/things-publications/v1 \
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checkvalidation/things-publications/v1 \
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convertexamples/demo-empirical-data/unreleased \
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checkvalidation/demo-empirical-data/unreleased \
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convertexamples/demo-research-assets/unreleased \
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checkvalidation/demo-research-assets/unreleased \
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convertexamples/demo-research-information/unreleased \
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checkvalidation/demo-research-information/unreleased \
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convertexamples/demo-rse-group/unreleased \
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checkvalidation/demo-rse-group/unreleased
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checkvalidation/%:
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$(MAKE) checkvalid/$* checkinvalid/$*
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checkvalid/%: src/%/validation src/%.yaml
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@for ex in $(wildcard $</*.valid.cfg.yaml); do \
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echo "Validate $$ex" ; \
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linkml-validate --config "$$ex" || exit 5 ; \
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done
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checkinvalid/%: src/%/validation src/%.yaml
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@for ex in $(wildcard $</*.invalid.cfg.yaml); do \
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echo "(In)validate $$ex" ; \
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linkml-validate --config "$$ex" && exit 5 || true; \
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done
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convert-examples: \
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convertexamples/things/unreleased \
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convertexamples/things/v1 \
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convertexamples/things/v2 \
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convertexamples/things-distributions/unreleased \
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convertexamples/things-distributions/v1 \
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convertexamples/things-social/unreleased \
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convertexamples/things-social/v1 \
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convertexamples/things-study/unreleased \
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convertexamples/things-study/v1 \
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convertexamples/things-data/unreleased \
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convertexamples/things-data/v1 \
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convertexamples/things-resources/unreleased \
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convertexamples/things-resources/v1 \
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convertexamples/things-rules/unreleased \
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convertexamples/things-rules/v1 \
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convertexamples/things-files/unreleased \
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convertexamples/things-files/v1 \
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convertexamples/things-publications/unreleased \
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convertexamples/things-publications/v1 \
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convertexamples/flat/unreleased \
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convertexamples/flat-prov/unreleased \
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convertexamples/flat-publications/unreleased \
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convertexamples/flat-resources/unreleased \
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convertexamples/flat-social/unreleased \
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convertexamples/flat-study/unreleased \
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convertexamples/identifiers/unreleased \
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convertexamples/flat-files/unreleased \
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convertexamples/demo-empirical-data/unreleased \
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convertexamples/demo-research-assets/unreleased \
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convertexamples/demo-research-information/unreleased \
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convertexamples/demo-rse-group/unreleased
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convertexamples/%: src/%.yaml src/%/examples
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# loop over all examples, skip the schema file itself
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for ex in $^/*.yaml; do \
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[ "$$ex" = "$<" ] && continue; \
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echo "Converting $$ex" ; \
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for outf in json rdf; do \
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( cd $$(dirname "$<"); linkml-convert \
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-s "$$(basename "$<")" \
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--target-class-from-path \
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--infer \
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-t "$$outf" \
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../../"$$ex" \
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) > $${ex%.yaml}.$${outf}.tmp && \
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mv $${ex%.yaml}.$${outf}.tmp $${ex%.yaml}.$${outf} ; \
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done \
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done
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@git --no-pager diff -- $(filter-out $<,$^)
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@if [ -n "$$(git diff -- $(filter-out $<,$^))" ]; then \
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echo -n 'ERROR: Unexpected modification of example output. ' ; \
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echo 'Inspect and commit changes shown above!' ; \
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exit 22 ; \
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fi
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imports-local:
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@echo "Switch to local imports"
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@sed -i -e 's,- dlschemas:\(.*/.*\)$$,- ../../src/\1,' src/*/*.yaml
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imports-remote:
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@echo "Switch to remote imports"
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@sed -i -e 's,- \.\./\.\./src/\(.*/.*\)$$,- dlschemas:\1,' src/*/*.yaml
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clean:
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rm -rf build
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rm -f *-stamp
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.PHONY: clean check check-models check-validation convert-examples localrefs remoterefs
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