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Makefile
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Makefile
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# All artifacts of the build should be preserved
.SECONDARY:
# It can be fairly expensive to regenerate the various png's in the markdown.
# There are three alternatives:
# 1) make imgflags="-i" -- generate uml images in images subdirectory (default)
# 2) make imgflags="-i --noimages" -- assume uml images already exist and generate links to them
# 3) make imgflags="" -- genrate uml images as inline url's
imgflags?="-i"
# ----------------------------------------
# TOP LEVEL TARGETS
# ----------------------------------------
all: build test
test: pytests
build: metamodel/context.jsonld context.jsonld build_core contrib_build_monarch contrib_build_translator contrib_build_go
build_core: metamodel/docs/index.md biolinkmodel/datamodel.py docs/index.md gen-golr-views \
ontology/biolink.ttl json-schema/biolink-model.json java graphql/biolink-model.graphql proto/biolink-model.proto \
gen-graphviz rdf/meta.ttl shex/meta.ttl rdf/biolink-model.ttl shex/biolink-model.ttl
contrib_build_%: contrib-dir-% contrib/%/docs/index.md contrib/%/datamodel.py contrib-golr-% contrib/%/ontology.ttl \
contrib/%/schema.json contrib-java-% contrib/%/%.graphql contrib/%/shex
echo
install:
pip install -e . --upgrade
# ----------------------------------------
# BUILD/COMPILATION
# ----------------------------------------
# ~~~~~~~~~~~~~~~~~~~~
# CSV
# ~~~~~~~~~~~~~~~~~~~~
kbsync: subsets/biological_entity.csv
cp $< ../translator-knowledge-beacon/api/types.csv
subsets/biological_entity.csv: biolink-model.yaml
gen-csv -r 'biological entity' biolink-model.yaml > $@.tmp && mv $@.tmp $@
biolink-model.tsv: biolink-model.yaml
gen-csv -f tsv biolink-model.yaml > $@.tmp && mv $@.tmp $@
# ~~~~~~~~~~~~~~~~~~~~
# JSON-LD CONTEXT
# ~~~~~~~~~~~~~~~~~~~~
context.jsonld: biolink-model.yaml
gen-jsonld-context $< > $@
metamodel/context.jsonld: meta.yaml
gen-jsonld-context $< > $@
# ~~~~~~~~~~~~~~~~~~~~
# JSONSCHEMA -> Java
# ~~~~~~~~~~~~~~~~~~~~
json-schema/%.json: dir-json-schema %.yaml
gen-json-schema $*.yaml > $@
contrib/%/schema.json: contrib-dir-% contrib/%.yaml
gen-json-schema contrib/$*.yaml > $@
java: dir-java json-schema/biolink-model.json
jsonschema2pojo --source json-schema/biolink-model.json -T JSONSCHEMA -t java
contrib-java-%: contrib-dir-% contrib/%/schema.json
mkdir -p contrib/$*/java
jsonschema2pojo --source contrib/$*/schema.json -T JSONSCHEMA -t contrib/$*/java
# ~~~~~~~~~~~~~~~~~~~~
# DOCS
# ~~~~~~~~~~~~~~~~~~~~
docs/index.md: biolink-model.yaml
gen-markdown --dir docs $(imgflags) $<
metamodel/docs/index.md: meta.yaml
gen-markdown --dir metamodel/docs $(imgflags) $<
contrib/%/docs/index.md: contrib/%.yaml
gen-markdown --dir contrib/$*/docs $<
# ~~~~~~~~~~~~~~~~~~~~
# Ontology
# ~~~~~~~~~~~~~~~~~~~~
ontology/biolink.ttl: dir-ontology biolink-model.yaml
gen-owl -o $@ biolink-model.yaml
contrib/%/ontology.ttl: contrib-dir-% contrib/%.yaml
gen-owl -o $@ contrib/$*.yaml
# ~~~~~~~~~~~~~~~~~~~~
# RDF
# ~~~~~~~~~~~~~~~~~~~~
rdf/%.ttl: dir-rdf metamodel/context.jsonld meta.yaml
gen-rdf $*.yaml -f ttl --context metamodel/context.jsonld > rdf/$*.ttl
contrib/%/datamodel.py: contrib-dir-% contrib/%.yaml
gen-py-classes contrib/$*.yaml > $@
gen-graphviz: dir-graphviz biolink-model.yaml
gen-graphviz -d graphviz biolink-model.yaml
# ~~~~~~~~~~~~~~~~~~~~
# Solr
# ~~~~~~~~~~~~~~~~~~~~
gen-golr-views: dir-golr-views biolink-model.yaml
gen-golr-views -d golr-views biolink-model.yaml
contrib-golr-%: contrib/%.yaml
mkdir -p contrib/$*/golr-views
gen-golr-views -d contrib/$*/golr-views contrib/$*.yaml
# ~~~~~~~~~~~~~~~~~~~~
# Python
# ~~~~~~~~~~~~~~~~~~~~
contrib/%/datamodel.py: contrib-dir-% contrib/%.yaml
gen-py-classes contrib/$*.yaml > $@
# ~~~~~~~~~~~~~~~~~~~~
# ShEx
# ~~~~~~~~~~~~~~~~~~~~
shex/%.ttl: dir-shex %.yaml
gen-shex $*.yaml -f rdf > shex/$*.ttl
gen-shex $*.yaml -f json > shex/$*.json
contrib/%/shex:
mkdir -p contrib/$*/shex
gen-shex contrib/$*.yaml -f rdf > contrib/$*/shex/$*.ttl
gen-shex contrib/$*.yaml -f json > contrib/$*/shex/$*.json
# ~~~~~~~~~~~~~~~~~~~~
# Graphql
# ~~~~~~~~~~~~~~~~~~~~
graphql/biolink-model.graphql: dir-graphql biolink-model.yaml
gen-graphql biolink-model.yaml > $@
proto/biolink-model.proto: dir-proto biolink-model.yaml
gen-proto biolink-model.yaml > $@
contrib/%/%.graphql: contrib-dir-% contrib/%.yaml
gen-graphql contrib/$*.yaml > contrib/$*/$*.graphql
# ----------------------------------------
# Ontology conversion
# ----------------------------------------
ontology/%.json: ontology/%.ttl
owltools $< -o -f json $@
ontology/%.obo: ontology/%.ttl
owltools $< -o -f obo --no-check $@
ontology/%.omn: ontology/%.ttl
owltools $< -o -f omn --prefix '' http://bioentity.io/vocab/ --prefix def http://purl.obolibrary.org/obo/IAO_0000115 $@
ontology/%.tree: ontology/%.json
ogr --showdefs -t tree -r $< % > $@
ontology/%.png: ontology/%.json
ogr-tree -t png -o $@ -r $< %
# ~~~~~~~~~~~~~~~~~~~~
# Update the metamodel - not part of the main build. Use this method when meta.yaml has changed
# ~~~~~~~~~~~~~~~~~~~~
MM = metamodel/metamodel.py
BMM = biolinkmodel/datamodel.py
regen-mm:
gen-py-classes meta.yaml > tmp.py && python tmp.py && cp $(MM) $(MM)-PREV && mv tmp.py $(MM)
gen-py-classes biolink-model.yaml > tmp.py && python tmp.py && cp $(BMM) $(BMM)-PREV && mv tmp.py $(BMM)
# ----------------------------------------
# TESTS
# ----------------------------------------
pytests:
python -m unittest
# ----------------------------------------
# CLEAN
# ----------------------------------------
clean:
rm -rf subsets java shex proto ontology json-schema graphviz graphql golr-views contrib/go contrib/monarch contrib/translator docs/images/* docs/*.md
# ----------------------------------------
# UTILS
# ----------------------------------------
dir-%:
mkdir -p $*
contrib-dir-%:
mkdir -p contrib/$*