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Makefile
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# Makefile for OBOFoundry.github.io
#
# This file contains commands for validating and generating
# configuration files for the OBO Foundry website.
# The `util/` directory contains additional scripts
# called from this Makefile.
# It is intended to be run on a Unix system (Linux, Mac OS X)
# **before** the site is built using
# [Jekyll](http://jekyllrb.com).
#
# Software requirements:
#
# - [GNU Make](http://www.gnu.org/software/make/)
# - [Apache Jena](https://jena.apache.org/download/)
# - [Python 3](https://www.python.org/downloads/)
# - [PyYAML](http://pyyaml.org/wiki/PyYAML)
# - [SPARQLWrapper](https://pypi.python.org/pypi/SPARQLWrapper)
#
# Run `make` in this directory to update all generated files
# (i.e. the default `all` task).
# Make does its best to detect changes and run only the required tasks,
# but sometimes it helps to delete the target files first by running `make clean`
#
# WARNING: Makefiles contain significant tab characters!
# Before editing this file, ensure that your editor is not set up to convert tabs
# to spaces, and then use tabs to indent recipe lines.
### Configuration
# All ontology .md files
ONTS := $(wildcard ontology/*.md)
# All principles .md files
PRINCIPLES := $(wildcard principles/*.md)
### Main Tasks
.PHONY: all pull_and_build test pull clean
all: _config.yml registry/ontologies.ttl registry/obo_context.jsonld registry/obo_prefixes.ttl
pull:
git pull
pull_and_build: pull all
test: reports/metadata-grid.html _config.yml tox
integration-test: test valid-purl-report.txt
# Remove and/or revert all targets to their repository versions:
clean:
rm -Rf registry/ontologies.nt registry/ontologies.ttl registry/ontologies.yml sparql-consistency-report.txt jenkins-output.txt valid-purl-report.txt valid-purl-report.txt.tmp _site/ tmp/ reports/
git checkout _config.yml registry/ontologies.jsonld registry/ontologies.ttl registry/ontologies.yml
### Directories:
tmp:
mkdir -p $@
reports:
mkdir -p $@
reports/robot:
mkdir -p $@
reports/principles:
mkdir -p $@
### Build Configuration Files
# Create the site-wide config file by combining all metadata on ontologies + principles
# and combining with site-wide metadata.
#
# Note that anything in _config.yml is accessible to any liquid template via the
# `sites` object - think of it like the global database
#
# (this is somewhat hacky, but concatenating these yamls is safe)
_config.yml: _config_header.yml registry/ontologies.yml principles/all.yml
cat $^ > [email protected] && mv [email protected] $@
# Sort ontologies based on the validation (metadata-grid)
registry/ontologies.yml: reports/metadata-grid.csv
./util/sort-ontologies.py tmp/unsorted-ontologies.yml $< $@ && rm -rf tmp
# Extract the metadata from each principle in the principles/ directory, and concatenate
# into a single yaml file in that directory
principles/all.yml: $(PRINCIPLES)
./util/extract-metadata.py concat-principles -o [email protected] $^ && mv [email protected] $@
# Use a generic yaml->json conversion, but adding a @content
registry/ontologies.jsonld: registry/ontologies.yml
./util/yaml2json.py $< > [email protected] && mv [email protected] $@
registry/obo_context.jsonld: registry/ontologies.yml
./util/processor.py -i $< extract-context > [email protected] && mv [email protected] $@
# generate triples mapping prefixes to their corresponding PURLs.
# we use the SHACL vocabulary for this
registry/obo_prefixes.ttl: registry/ontologies.yml
./util/make-shacl-prefixes.py $< > [email protected] && mv [email protected] $@
# Use Apache-Jena RIOT to convert jsonld to n-triples
# NOTE: UGLY HACK. If there is a problem then Jena will write WARN message (to stdout!!!), there appears to
# be no way to get it to flag this even with strict and check options, so we do a check with grep, ugh.
# see: http://stackoverflow.com/questions/20860222/why-do-i-have-these-warnings-with-jena-2-11-0
registry/ontologies.nt: registry/ontologies.jsonld
riot --base=http://purl.obolibrary.org/obo/ --strict --check -q registry/context.jsonld $< > [email protected] && mv [email protected] $@ && egrep '(WARN|ERROR)' $@ && exit 1 || echo ok
registry/ontologies.ttl: registry/ontologies.nt
riot --base=http://purl.obolibrary.org/obo/ --out=ttl $< > [email protected] && mv [email protected] $@
### Validate Configuration Files
# generate both a report of the violations and a grid of all results
# the grid is later used to sort the ontologies on the home page
RESULTS = reports/metadata-violations.tsv reports/metadata-grid.csv
reports/metadata-grid.csv: tmp/unsorted-ontologies.yml | extract-metadata reports
./util/validate-metadata.py $< $(RESULTS)
# generate an HTML output of the metadata grid
# TODO: determine where this output belongs
reports/metadata-grid.html: reports/metadata-grid.csv
./util/create-html-grid.py $< $@
# Extract metadata from each ontology .md file and combine into single yaml
tmp/unsorted-ontologies.yml: $(ONTS) | tmp
./util/extract-metadata.py concat -o [email protected] $^ && mv [email protected] $@
extract-metadata: $(ONTS)
./util/extract-metadata.py validate $^
prettify: $(ONTS)
./util/extract-metadata.py prettify $^
# Run tox tests (requires `pip install tox`)
tox:
tox -e py
##########################
## Metadata Maintenance ##
##########################
# Use SPARQL queries to Wikidata to enrich the
# OBO operations committee metadata file
.PHONY: update-operations-metadata
update-operations-metadata:
python -m obofoundry update-operations-metadata
### OBO Dashboard
# This is the Jenkins job
# The reports will be archived
dashboard: build/dashboard.zip
# Build directories
build:
mkdir -p $@
build/ontologies:
mkdir -p $@
# reboot the JVM for Py4J
reboot:
bash ./util/reboot.sh
# This version of ROBOT includes features for starting Py4J
# This will be changed to ROBOT release once feature is released
#.PHONY: build/robot.jar
build/robot.jar: | build
curl -o $@ -Lk \
https://build.obolibrary.io/job/ontodev/job/robot/job/py4j/lastSuccessfulBuild/artifact/bin/robot.jar
# This version of ROBOT includes features for removing external axioms to create 'base' artefacts
# This will be removed once this feature is released
#.PHONY: build/robot-foreign.jar
build/robot-foreign.jar: | build
curl -o $@ -Lk \
https://build.obolibrary.io/job/ontodev/job/robot/job/562-feature/lastSuccessfulBuild/artifact/bin/robot.jar
# Generate the initial dashboard results file
# ALWAYS make sure nothing is running on port 25333
# Then boot Py4J gateway to ROBOT on that port
reports/dashboard.csv: registry/ontologies.yml | \
reports/robot reports/principles build/ontologies build/robot.jar build/robot-foreign.jar
make reboot
./util/principles/dashboard.py $< $@ --big false
reports/big-dashboard.csv: reports/dashboard.csv
make reboot
./util/principles/dashboard.py registry/ontologies.yml $@ --big true
# Combine the dashboard files
reports/dashboard-full.csv: reports/dashboard.csv reports/big-dashboard.csv registry/ontologies.yml
./util/principles/sort_tables.py $^ $@
# Generate the HTML grid output for dashboard
reports/dashboard.html: reports/dashboard-full.csv
./util/create-html-grid.py $< $@
# Move all important results to a dashboard directory
build/dashboard: reports/dashboard.html
mkdir -p $@
mkdir -p $@/assets
mkdir -p $@/reports
cp $< $@
cp -r reports/robot $@/reports
cp -r reports/principles $@/reports
cp -r assets/svg $@/assets
rm -rf build/dashboard.zip
zip -r [email protected] $@
# Clean up, removing ontology files
# We don't want to keep them because we will download new ones each time to stay up-to-date
# Reports are all archived in build/dashboard.zip
clean-dashboard: build/dashboard
rm -rf build/ontologies
rm -rf reports/robot
rm -rf reports/principles
rm -rf build/dashboard
# Note this should *not* be run as part of general travis jobs, it is expensive
# and may be prone to false positives as it is inherently network-based
#
# TODO: Other non-travis CI job. Nightly?
# TODO: Integrate this with some kind of OCLC query check
#
# See: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/18
valid-purl-report.txt: registry/ontologies.yml
./util/processor.py -i $< check-urls > [email protected] && mv [email protected] $@
sparql-consistency-report.txt: registry/ontologies.yml
./util/processor.py -i $< sparql-compare > [email protected] && mv [email protected] $@
# output of central OBO build
# See FAQ for more details, and also README.md
jenkins-output.txt:
wget http://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull -O $@
reports/%.csv: registry/ontologies.ttl sparql/%.sparql
arq --data $< --query sparql/$*.sparql --results csv > [email protected] && mv [email protected] $@