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Makefile
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Makefile
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MAKEFLAGS += --warn-undefined-variables
SHELL := bash
.SHELLFLAGS := -eu -o pipefail -c
.DEFAULT_GOAL := help
.DELETE_ON_ERROR:
.SUFFIXES:
.SECONDARY:
RUN = poetry run
# get values from about.yaml file
SCHEMA_NAME = $(shell ${SHELL} ./utils/get-value.sh name)
SOURCE_SCHEMA_PATH = $(shell ${SHELL} ./utils/get-value.sh source_schema_path)
SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
SRC = src
DEST = project
PYMODEL = $(SRC)/biolink_model/datamodel
DOCDIR = docs
EXAMPLEDIR = examples
SHEET_MODULE = personinfo_enums
SHEET_ID = $(shell ${SHELL} ./utils/get-value.sh google_sheet_id)
SHEET_TABS = $(shell ${SHELL} ./utils/get-value.sh google_sheet_tabs)
SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml
TEMPLATEDIR = doc-templates
# environment variables
include config.env
GEN_PARGS =
ifdef LINKML_GENERATORS_PROJECT_ARGS
GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS}
endif
GEN_DARGS =
ifdef LINKML_GENERATORS_MARKDOWN_ARGS
GEN_DARGS = ${LINKML_GENERATORS_MARKDOWN_ARGS}
endif
# basename of a YAML file in model/
.PHONY: all clean
# note: "help" MUST be the first target in the file,
# when the user types "make" they should get help info
help: status
@echo ""
@echo "make site -- makes site locally"
@echo "make install -- install dependencies"
@echo "make test -- runs tests"
@echo "make lint -- perform linting"
@echo "make testdoc -- builds docs and runs local test server"
@echo "make deploy -- deploys site"
@echo "make update -- updates linkml version"
@echo "make help -- show this help"
@echo ""
status: check-config
@echo "Project: $(SCHEMA_NAME)"
@echo "Source: $(SOURCE_SCHEMA_PATH)"
# generate products and add everything to github
setup: install gen-project gen-examples gendoc git-init-add
# install any dependencies required for building
install:
git init
poetry install
.PHONY: install
# ---
# Project Synchronization
# ---
#
# check we are up to date
check: cruft-check
cruft-check:
cruft check
cruft-diff:
cruft diff
update: update-template update-linkml
update-template:
cruft update
# todo: consider pinning to template
update-linkml:
poetry add -D linkml@latest
all: site
site: gen-project gendoc id-prefixes
%.yaml: gen-project
deploy: all mkd-gh-deploy
# In future this will be done by conversion
gen-examples:
cp src/data/examples/* $(EXAMPLEDIR)
id-prefixes:
$(RUN) gen-python class_prefixes.yaml > src/biolink_model/scripts/classprefixes.py
cd src/biolink_model/scripts/ && $(RUN) python id_prefixes.py
spell:
poetry run codespell
# generates all project files
gen-project: $(PYMODEL)
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
# keep these in sync between PROJECT_FOLDERS and the includes/excludes for gen-project and test-schema
$(RUN) gen-project \
--exclude excel \
--include graphql \
--include jsonld \
--exclude markdown \
--include prefixmap \
--include proto \
--include shacl \
--include shex \
--exclude sqlddl \
--include jsonldcontext \
--include jsonschema \
--exclude owl \
--include python \
--include rdf \
-d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
mv $(DEST)/prefixmap/biolink_model.yaml $(DEST)/prefixmap/biolink-model-prefix-map.json
mv $(PYMODEL)/biolink*.py $(PYMODEL)/model.py
$(RUN) gen-pydantic --meta None src/biolink_model/schema/biolink_model.yaml > $(PYMODEL)/pydanticmodel_v2.py
$(RUN) gen-owl --mergeimports --no-metaclasses --no-type-objects --add-root-classes --mixins-as-expressions src/biolink_model/schema/biolink_model.yaml > $(DEST)/owl/biolink_model.owl.ttl
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
$(MAKE) id-prefixes
tests:
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
$(RUN) python -m unittest discover -p 'test_*.py'
$(RUN) codespell
$(RUN) yamllint -c .yamllint-config biolink-model.yaml
test: test-schema test-python test-examples lint spell
test-schema: gen-project
test-python:
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
$(RUN) pytest
lint:
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml
$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)
check-config:
@(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n - Remember to edit 'about.yaml'\n\n" || exit 0)
convert-examples-to-%:
$(patsubst %, $(RUN) linkml-convert % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell ${SHELL} find src/data/examples -name "*.yaml"))
examples/%.yaml: src/data/examples/%.yaml
$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
examples/%.json: src/data/examples/%.yaml
$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
examples/%.ttl: src/data/examples/%.yaml
$(RUN) linkml-convert -P EXAMPLE=http://example.org/ -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
test-examples: examples/output
examples/output: src/biolink_model/schema/biolink_model.yaml
mkdir -p $@
$(RUN) linkml-run-examples \
--output-formats json \
--output-formats yaml \
--counter-example-input-directory src/data/examples/invalid \
--input-directory src/data/examples/valid \
--output-directory $@ \
--schema $< > $@/README.md
# Test documentation locally
serve: mkd-serve
# Python datamodel
$(PYMODEL):
mkdir -p $@
$(DOCDIR):
mkdir -p $@
gen-viz:
$(RUN) generate_viz_json
gendoc: $(DOCDIR)
# put the model where it needs to go in order to generate the doc correctly
cp biolink-model.yaml src/biolink_model/schema/biolink_model.yaml ; \
# this generates the data structure required for the d3 visualizations
$(RUN) generate_viz_json ; \
# DO NOT REMOVE: these cp statements are crucial to maintain the w3 ids for the model artifacts
cp $(DEST)/owl/biolink_model.owl.ttl $(DOCDIR)/biolink-model.owl.ttl ; \
cp $(DEST)/jsonld/biolink_model.context.jsonld $(DOCDIR)/biolink-model.context.jsonld ; \
cp $(DEST)/jsonld/biolink_model.context.jsonld $(DOCDIR)/context.jsonld ; \
cp $(DEST)/jsonld/biolink_model.jsonld $(DOCDIR)/biolink-model.jsonld ; \
cp $(DEST)/jsonschema/biolink_model.schema.json $(DOCDIR)/biolink-model.json ; \
cp $(DEST)/graphql/biolink_model.graphql $(DOCDIR)/biolink-model.graphql ; \
cp $(DEST)/shex/biolink_model.shex $(DOCDIR)/biolink-modeln.shex ; \
cp $(DEST)/shacl/biolink_model.shacl.ttl $(DOCDIR)/biolink-model.shacl.ttl ; \
cp $(DEST)/prefixmap/* $(DOCDIR) ; \
cp semmed-exclude-list.yaml $(DOCDIR) ; \
cp semmed-exclude-list-model.yaml $(DOCDIR) ; \
cp predicate_mapping.yaml $(DOCDIR) ; \
cp biolink-model.yaml $(DOCDIR) ; \
cp $(SRC)/docs/*md $(DOCDIR) ; \
cp -r $(SRC)/docs/images $(DOCDIR)/images ; \
# the .json cp here is the data required for the d3 visualizations
cp $(SRC)/docs/*.json $(DOCDIR) ; \
cp $(SRC)/docs/*.html $(DOCDIR) ; \
cp $(SRC)/docs/*.js $(DOCDIR) ; \
# this supports the display of our d3 visualizations
cp $(SRC)/docs/*.css $(DOCDIR) ; \
$(RUN) gen-doc -d $(DOCDIR) --template-directory $(SRC)/$(TEMPLATEDIR) $(SOURCE_SCHEMA_PATH)
testdoc: gendoc serve
MKDOCS = $(RUN) mkdocs
mkd-%:
$(MKDOCS) $*
PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel
git-init-add: git-init git-add git-commit git-status
git-init:
git init
git-add: .cruft.json
git add .gitignore .github .cruft.json Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/biolink_model/schema/*yaml src/*/datamodel/*py src/data src/docs tests src/*/_version.py
git add $(patsubst %, project/%, $(PROJECT_FOLDERS))
git-commit:
git commit -m 'chore: initial commit' -a
git-status:
git status
# only necessary if setting up via cookiecutter
.cruft.json:
echo "creating a stub for .cruft.json. IMPORTANT: setup via cruft not cookiecutter recommended!" ; \
touch $@
clean:
rm -rf $(DEST)
rm -rf tmp
rm -fr docs/*
rm -fr $(PYMODEL)/*
include project.Makefile