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Makefile
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# All artifacts of the build should be preserved
.SECONDARY:
# ----------------------------------------
# Model documentation and schema directory
# ----------------------------------------
SRC_DIR = model
PKG_DIR = crdch_model
SCHEMA_DIR = $(SRC_DIR)/schema
MODEL_DOCS_DIR = $(SRC_DIR)/docs
SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml')
SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES))
SCHEMA_NAME = crdch_model
SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml
PKG_TGTS = graphql json_schema shex owl csv
TGTS = docs python $(PKG_TGTS)
# add csv to match established ccdhmodel repo
# MAM 20210806 does docs and python by default
# note json_schema vs jsonschema
# Targets by PKG_TGT
PKG_T_GRAPHQL = $(PKG_DIR)/graphql
PKG_T_JSON = $(PKG_DIR)/json
PKG_T_JSONLD_CONTEXT = $(PKG_DIR)/jsonld
PKG_T_JSON_SCHEMA = $(PKG_DIR)/json_schema
PKG_T_OWL = $(PKG_DIR)/owl
PKG_T_RDF = $(PKG_DIR)/rdf
PKG_T_SHEX = $(PKG_DIR)/shex
PKG_T_SQLDDL = $(PKG_DIR)/sqlddl
PKG_T_DOCS = $(MODEL_DOCS_DIR)
PKG_T_PYTHON = $(PKG_DIR)
PKG_T_MODEL = $(PKG_DIR)/model
PKG_T_SCHEMA = $(PKG_T_MODEL)/schema
# MAM 20210806
PKG_T_CSV = $(PKG_DIR)/csv
RUN = poetry run
GEN_OPTS = --log_level WARNING
CDM_GOOGLE_SHEET_ID=1oWS7cao-fgz2MKWtyr8h2dEL9unX__0bJrWKv6mQmM4
# ----------------------------------------
# TOP LEVEL TARGETS
# ----------------------------------------
all: install gen
# ---------------------------------------
# We don't want to pollute the python environment with linkml tool specific packages.
# For this reason, use Pipfile (which generates a Pipfile.lock file).
# ---------------------------------------
install:
poetry install
# To uninstall the virtual environment, we need to get the path from poetry.
# I'm nervous about passing that path directly to `rm -rf`, so instead let's just tell the users where it is for now.
uninstall:
echo Please delete the current environment: $(shell poetry env info --path)
# ---------------------------------------
# Test runner
# ---------------------------------------
test: install
PYTHONPATH=crdch_model poetry run python -m unittest
# ---------------------------------------
# Test runner with tox
# ---------------------------------------
test-tox:
$(RUN) tox
# ---------------------------------------
# GEN: run generator for each target
# ---------------------------------------
gen: $(patsubst %,gen-%,$(TGTS))
# ---------------------------------------
# CLEAN: clear out all of the targets
# ---------------------------------------
clean:
rm -rf target/
rm -rf docs/
poetry install --remove-untracked
.PHONY: clean
# ---------------------------------------
# SQUEAKY_CLEAN: remove all of the final targets to make sure we don't leave old artifacts around
# ---------------------------------------
squeaky-clean: uninstall clean $(patsubst %,squeaky-clean-%,$(PKG_TGTS))
# only depends on the existence of the $(PKG_DIR) directory
if [ -d $(PKG_DIR)/model/schema ] ;\
then echo '$(PKG_DIR)/model/schema present' ;\
find $(PKG_DIR)/model/schema ! -name 'README.*' -type f -exec rm -f {} + ;\
else echo 'no $(PKG_DIR)/model/schema to clean up' ;\
fi
# # this will fail if docs is totally empty including no README.*
# # oops it gets totally cleaned somewhere in make all
# find docs/* ! -name 'README.*' -exec rm -rf {} +
# just give up on a README or any placeholder in docs?
rm -rf docs/*
find $(PKG_DIR) -name "*.py" ! -name "__init__.py" ! -name "linkml_files.py" -exec rm -f {} +
# also uninstall the root virtual environment? how to check if one is present?
# have never seen .env, .venv or env.lock in the project root folder
@echo 'squeaky cleaning complete'
squeaky-clean-%: clean
echo $*
find $(PKG_DIR)/$* ! -name 'README.*' ! -name $* -type f -exec rm -f {} +
# ---------------------------------------
# T: List files to generate
# ---------------------------------------
t:
echo $(SCHEMA_NAMES)
# ---------------------------------------
# ECHO: List all targets
# ---------------------------------------
echo:
echo $(patsubst %,gen-%,$(TGTS))
tdir-%:
rm -rf target/$*
mkdir -p target/$*
# MAM 20210806 based on ccdhmodel main branch
### -- CSV --
# one file per module
gen-csv: $(patsubst %, $(PKG_T_CSV)/%.csv, $(SCHEMA_NAMES))
.PHONY: gen-csv
$(PKG_T_CSV)/%.csv: target/csv/%.csv
mkdir -p $(PKG_T_CSV)
cp $< $@
target/csv/%.csv: $(SCHEMA_DIR)/%.yaml tdir-csv install
${RUN} gen-csv $(GEN_OPTS) $< > $@
# --no-mergeimports?
# --mergeimports?
# ---------------------------------------
# MARKDOWN DOCS
# Generate documentation ready for mkdocs
# ---------------------------------------
gen-docs: docs/index.md
.PHONY: gen-docs
docs/index.md: target/docs/index.md install
mkdir -p $(PKG_T_DOCS)
cp -R $(MODEL_DOCS_DIR)/*.md target/docs
# mkdocs.yml moves from the target/docs to the docs directory
$(RUN) mkdocs build
# Note that we use our fork of markdowngen.py
# You can see the original markdowngen.py at https://github.com/linkml/linkml/blob/0f59fc520014d81e470dab6994561dbd0bb3d508/linkml/generators/markdowngen.py
# and its subsequent versions.
target/docs/index.md: $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml tdir-docs install
$(RUN) python generators/markdowngen.py $(GEN_OPTS) --mergeimports --notypesdir --warnonexist --dir target/docs $<
# ---------------------------------------
# YAML source
# ---------------------------------------
gen-model: $(patsubst %, $(PKG_T_SCHEMA)/%.yaml, $(SCHEMA_NAMES))
$(PKG_T_SCHEMA)/%.yaml: model/schema/%.yaml
mkdir -p $(PKG_T_SCHEMA)
cp $< $@
# ---------------------------------------
# PYTHON Source
# ---------------------------------------
gen-python: $(patsubst %, $(PKG_T_PYTHON)/%.py, $(SCHEMA_NAMES))
$(PKG_T_PYTHON)/%.py: target/python/%.py
mkdir -p $(PKG_T_PYTHON)
cp $< $@
target/python/%.py: $(SCHEMA_DIR)/%.yaml tdir-python install
$(RUN) gen-python $(GEN_OPTS) --no-slots --no-mergeimports $< > $@
# ---------------------------------------
# GRAPHQL Source
# ---------------------------------------
gen-graphql: $(PKG_T_GRAPHQL)/$(SCHEMA_NAME).graphql
.PHONY: gen-graphql
$(PKG_T_GRAPHQL)/%.graphql: target/graphql/%.graphql
mkdir -p $(PKG_T_GRAPHQL)
cp $< $@
target/graphql/%.graphql: $(SCHEMA_DIR)/%.yaml tdir-graphql install
$(RUN) gen-graphql $(GEN_OPTS) $< > $@
# ---------------------------------------
# JSON Schema
# ---------------------------------------
gen-json_schema: $(patsubst %, $(PKG_T_JSON_SCHEMA)/%.schema.json, $(SCHEMA_NAMES))
.PHONY: gen-json_schema
$(PKG_T_JSON_SCHEMA)/%.schema.json: target/json_schema/%.schema.json
mkdir -p $(PKG_T_JSON_SCHEMA)
cp $< $@
target/json_schema/%.schema.json: $(SCHEMA_DIR)/%.yaml tdir-json_schema install
$(RUN) gen-json-schema $(GEN_OPTS) -t transaction $< > $@
# ---------------------------------------
# ShEx
# ---------------------------------------
gen-shex: $(patsubst %, $(PKG_T_SHEX)/%.shex, $(SCHEMA_NAMES)) $(patsubst %, $(PKG_T_SHEX)/%.shexj, $(SCHEMA_NAMES))
.PHONY: gen-shex
$(PKG_T_SHEX)/%.shex: target/shex/%.shex
mkdir -p $(PKG_T_SHEX)
cp $< $@
$(PKG_T_SHEX)/%.shexj: target/shex/%.shexj
mkdir -p $(PKG_T_SHEX)
cp $< $@
target/shex/%.shex: $(SCHEMA_DIR)/%.yaml tdir-shex install
$(RUN) gen-shex --no-mergeimports $(GEN_OPTS) $< > $@
target/shex/%.shexj: $(SCHEMA_DIR)/%.yaml tdir-shex install
$(RUN) gen-shex --no-mergeimports $(GEN_OPTS) -f json $< > $@
# ---------------------------------------
# OWL
# ---------------------------------------
gen-owl: $(PKG_T_OWL)/$(SCHEMA_NAME).owl.ttl
.PHONY: gen-owl
$(PKG_T_OWL)/%.owl.ttl: target/owl/%.owl.ttl
mkdir -p $(PKG_T_OWL)
cp $< $@
target/owl/%.owl.ttl: $(SCHEMA_DIR)/%.yaml tdir-owl install
echo Deactivated because of https://github.com/cancerDHC/ccdhmodel/issues/64
echo $(RUN) gen-owl $(GEN_OPTS) $< > $@
# ---------------------------------------
# JSON-LD Context
# ---------------------------------------
gen-jsonld_context: $(patsubst %, $(PKG_T_JSONLD_CONTEXT)/%.context.jsonld, $(SCHEMA_NAMES)) $(patsubst %, $(PKG_T_JSONLD_CONTEXT)/%.model.context.jsonld, $(SCHEMA_NAMES))
.PHONY: gen-jsonld_context
$(PKG_T_JSONLD_CONTEXT)/%.context.jsonld: target/jsonld_context/%.context.jsonld
mkdir -p $(PKG_T_JSONLD_CONTEXT)
cp $< $@
$(PKG_T_JSONLD_CONTEXT)/%.model.context.jsonld: target/jsonld_context/%.model.context.jsonld
mkdir -p $(PKG_T_JSONLD_CONTEXT)
cp $< $@
target/jsonld_context/%.context.jsonld: $(SCHEMA_DIR)/%.yaml tdir-jsonld_context install
$(RUN) gen-jsonld-context $(GEN_OPTS) --no-mergeimports $< > $@
target/jsonld_context/%.model.context.jsonld: $(SCHEMA_DIR)/%.yaml tdir-jsonld_context install
$(RUN) gen-jsonld-context $(GEN_OPTS) --no-mergeimports $< > $@
# ---------------------------------------
# Plain Old (PO) JSON
# ---------------------------------------
gen-json: $(patsubst %, $(PKG_T_JSON)/%.json, $(SCHEMA_NAMES))
.PHONY: gen-json
$(PKG_T_JSON)/%.json: target/json/%.json
mkdir -p $(PKG_T_JSON)
cp $< $@
target/json/%.json: $(SCHEMA_DIR)/%.yaml tdir-json install
$(RUN) gen-jsonld $(GEN_OPTS) --no-mergeimports $< > $@
# ---------------------------------------
# RDF
# ---------------------------------------
gen-rdf: gen-jsonld $(patsubst %, $(PKG_T_RDF)/%.ttl, $(SCHEMA_NAMES)) $(patsubst %, $(PKG_T_RDF)/%.model.ttl, $(SCHEMA_NAMES))
.PHONY: gen-rdf
$(PKG_T_RDF)/%.ttl: target/rdf/%.ttl
mkdir -p $(PKG_T_RDF)
cp $< $@
$(PKG_T_RDF)/%.model.ttl: target/rdf/%.model.ttl
mkdir -p $(PKG_T_RDF)
cp $< $@
target/rdf/%.ttl: $(SCHEMA_DIR)/%.yaml $(PKG_DIR)/jsonld/%.context.jsonld tdir-rdf install
$(RUN) gen-rdf $(GEN_OPTS) --context $(realpath $(word 2,$^)) $< > $@
target/rdf/%.model.ttl: $(SCHEMA_DIR)/%.yaml $(PKG_DIR)/jsonld/%.model.context.jsonld tdir-rdf install
$(RUN) gen-rdf $(GEN_OPTS) --context $(realpath $(word 2,$^)) $< > $@
# ---------------------------------------
# SQLDDL
# ---------------------------------------
gen-sqlddl: $(PKG_T_SQLDDL)/$(SCHEMA_NAME).sql
.PHONY: gen-sqlddl
$(PKG_T_SQLDDL)/%.sql: target/sqlddl/%.sql
mkdir -p $(PKG_T_SQLDDL)
cp $< $@
target/sqlddl/%.sql: $(SCHEMA_DIR)/%.yaml tdir-sqlddl install
$(RUN) gen-sqlddl $(GEN_OPTS) $< > $@
####################
# MODEL GENERATION #
####################
# Generate the model. We use sheet2linkml to do this.
generate-model: install
CDM_GOOGLE_SHEET_ID=$(CDM_GOOGLE_SHEET_ID) $(RUN) sheet2linkml --output model/schema/crdch_model.yaml
#################
# DOCUMENTATION #
#################
# test docs locally.
docserve: gen-docs
$(RUN) mkdocs serve
# MAM 20210806 not sure how this fits into the linkml model template's doc building/publsihing approach
# Deploy changes to the `dev` version on the gh-pages branch.
# Note that this is not dependent on stage-docs, since you
# would generate the docs (usually as part of a `make all`)
# before you deploy it in a separate step.
gh-deploy: install
$(RUN) mike deploy dev -p
########
# PYPI #
########
# This target can be used to publish this package to PyPI.
pypi:
poetry build
poetry publish