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gulpfile.js
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gulpfile.js
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////
//// Usage: ./node_modules/.bin/gulp build, clean, test, etc.
////
var gulp = require('gulp');
//var jsdoc = require('gulp-jsdoc');
var mocha = require('gulp-mocha');
var uglify = require('gulp-uglify');
var rename = require("gulp-rename");
var git = require('gulp-git');
var bump = require('gulp-bump');
var del = require('del');
var shell = require('gulp-shell');
var runSequence = require('run-sequence');
var untar = require('gulp-untar');
var gunzip = require('gulp-gunzip');
var paths = {
'readme': ['./README.md'],
'tests': ['tests/*.test.js', 'tests/*.tests.js'],
'docable': ['lib/*.js', './README.md'],
'transients': ['./doc/*', '!./doc/README.md'],
// Heavier testing framework variables.
'tests-functional-data': ['tests-functional/*.test.js'],
'tests-functional': ['tests-functional/*.test.js'],
'ontologies-go': [
'_data/ontologies/go-gaf.owl',
'_data/ontologies/eco.owl',
'_data/ontologies/go-taxon-subsets.owl',
'_data/ontologies/neurogenesis.obo'
],
'gafs-go': [
// '_data/gafs/gene_association.fb.gz',
// '_data/gafs/goa_human.gaf.gz'
'_data/gafs/test_001_p53.gaf'
],
'metadata-go': '_data/metadata/ont-config.yaml'
};
// Browser runtime environment construction.
gulp.task('build', ['patch-bump', 'doc']);
gulp.task('patch-bump', function(cb) {
gulp.src('./package.json')
.pipe(bump({
type: 'patch'
}))
.pipe(gulp.dest('./'));
cb(null);
});
gulp.task('minor-bump', function(cb) {
gulp.src('./package.json')
.pipe(bump({
type: 'minor'
}))
.pipe(gulp.dest('./'));
cb(null);
});
gulp.task('major-bump', function(cb) {
gulp.src('./package.json')
.pipe(bump({
type: 'major'
}))
.pipe(gulp.dest('./'));
cb(null);
});
// Build docs directory with JSDoc.
//gulp.task('doc', ['md-to-org', 'jsdoc']);
gulp.task('doc', ['jsdoc']);
// Build docs directory with JSDoc.
// Completely dependent on clean before running doc.
// gulp.task('jsdoc', ['clean'], function(cb) {
// gulp.src(paths.docable, paths.readme)
// .pipe(jsdoc('./doc'));
// cb(null);
// });
// TODO: Ugh--do this manually until gulp-jsdoc gets its act together.
gulp.task('jsdoc', ['clean'], function(cb) {
gulp.src('')
.pipe(shell([
'./node_modules/.bin/jsdoc --verbose --template ./node_modules/jsdoc-baseline --readme ./README.md --destination ./doc/ ./lib/*.js'
]));
cb(null);
});
// Get rid of anything that is transient.
gulp.task('clean', function(cb) {
del(paths.transients);
cb(null);
});
// Testing with mocha/chai.
gulp.task('test', function() {
return gulp.src(paths.tests, {
read: false
}).pipe(mocha({
reporter: 'spec',
globals: {
// Use a different should.
should: require('chai').should()
}
}));
});
//gulp.task('release', ['build', 'publish-npm', 'git-commit', 'git-tag']);
gulp.task('release', ['build', 'publish-npm']);
// Needs to have ""
gulp.task('publish-npm', function() {
var npm = require("npm");
npm.load(function(er, npm) {
// NPM
npm.commands.publish();
});
});
gulp.task('git-commit', function() {
console.log('TODO: WORK IN PROGRESS');
// Make a note in the git repo.
var pkg = require('./package.json');
var pver = pkg.version;
gulp.src('./*')
.pipe(git.commit('Package/version tracking for go-exp/widget: ' + pver));
});
gulp.task('git-tag', function() {
console.log('TODO: WORK IN PROGRESS');
// Make a note in the git repo.
var pkg = require('./package.json');
var pver = pkg.version;
git.tag('go-exp-widget-' + pver, 'version message', function(err) {
if (err) {
throw err;
}
});
});
// Rerun doc build when a file changes.
gulp.task('watch-doc', function() {
gulp.watch(paths.docable, ['doc']);
gulp.watch(paths.readme, ['doc']);
});
// Rerun doc build when a file changes.
gulp.task('watch-test', function() {
gulp.watch(paths.docable, ['test']);
gulp.watch(paths.tests, ['test']);
});
// The default task (called when you run `gulp` from cli)
//gulp.task('default', ['watch', 'scripts', 'images']);
gulp.task('default', function() {
console.log("'allo 'allo!");
});
///
/// Experimental results-based testing.
///
// Local Solr settings.
var monarch_url = 'http://localhost:8983/solr/monarch';
var golr_url = 'http://localhost:8983/solr/amigo';
var golr_load_logfile = '/tmp/golr-load.log';
var owltools_max_memory = '4G';
var owltools_runner = 'java -Xms1024M -DentityExpansionLimit=4086000 -Djava.awt.headless=true -Xmx' + owltools_max_memory + ' -jar ./java/lib/owltools-runner-all.jar';
// The OWLTools options are a little harder, and variable with the
// load we're attempting.
// AmiGO's OWLTOOLS_USE_MERGE_IMPORT/
var otu_mrg_imp_p = false;
// AmiGO's OWLTOOLS_USE_REMOVE_DISJOINTS.
var otu_rm_dis_p = false;
var all_owltools_ops_flags_list = [
'--merge-support-ontologies',
(otu_mrg_imp_p ? '--merge-import http://purl.obolibrary.org/obo/go/extensions/go-plus.owl' : ''),
'--remove-subset-entities upperlevel',
(otu_rm_dis_p ? '--remove-disjoints' : ''),
'--silence-elk --reasoner elk',
'--solr-taxon-subset-name amigo_grouping_subset',
'--solr-eco-subset-name go_groupings'
];
var owltools_ops_flags =
all_owltools_ops_flags_list.join(' ').replace(/ +/g, ' ');
function _run_cmd(command_bits) {
var final_command = command_bits.join(' ');
return ['echo \'' + final_command + '\'', final_command];
}
gulp.task('golr-purge', shell.task(_run_cmd(
[owltools_runner,
'--solr-url ', golr_url,
'--solr-purge'
]
)));
gulp.task('load-ontology-go', shell.task(_run_cmd(
[owltools_runner,
paths['ontologies-go'].join(' '),
owltools_ops_flags,
'--solr-url', golr_url,
'--solr-config', paths['metadata-go'],
'--solr-log', golr_load_logfile,
'--solr-load-ontology',
'--solr-load-ontology-general'
]
)));
gulp.task('load-gafs-go', shell.task(_run_cmd(
[owltools_runner,
paths['ontologies-go'].join(' '),
owltools_ops_flags,
'--solr-url', golr_url,
'--solr-log', golr_load_logfile,
'--solr-load-gafs', paths['gafs-go'].join(' ')
]
)));
// Combined "safe" single step.
gulp.task('load-go-safe', shell.task(_run_cmd(
[owltools_runner,
paths['ontologies-go'].join(' '),
owltools_ops_flags,
//'--ontology-pre-check', // are local, no need to check
'--solr-url', golr_url,
'--solr-config', paths['metadata-go'],
'--solr-log', golr_load_logfile,
'--solr-purge',
//'--solr-load-ontology',
//'--solr-load-ontology-general'
'--solr-load-gafs', paths['gafs-go'].join(' ')
]
)));
// Functional tests for Amigo and Monarch.
gulp.task('test-functional', function(callback) {
runSequence(
'start-solr',
'load-go-safe',
'load-ontology-go',
'monarch-purge',
'extract-monarch-data',
'load-monarch',
'test-functional-run-test-only',
'stop-solr',
function(error) {
if (error) {
console.log(error.message);
} else {
console.log('Success!');
}
callback(error);
});
});
gulp.task('test-functional-run-test-only', function() {
return gulp.src(paths['tests-functional'], {
read: false
}).pipe(mocha({
reporter: 'spec',
globals: {
// Use a different should.
should: require('chai').should()
}
}));
});
// Starts solr server on port 8983
gulp.task('start-solr',
shell.task(_run_cmd(
['solr/bin/solr start -m 4g']
)));
// Stops solr server
gulp.task('stop-solr',
shell.task(_run_cmd(
['solr/bin/solr stop']
)));
// purge Monarch core
gulp.task('monarch-purge', shell.task(_run_cmd(
[owltools_runner,
'--solr-url ', monarch_url,
'--solr-purge'
]
)));
// load Monarch core
gulp.task('load-monarch', shell.task(_run_cmd(
['solr/bin/post -c monarch _data/monarch/monarch-data/_data/monarch/*.json']
)));
// extract Monarch data
// TODO it extracts to a weird path
gulp.task('extract-monarch-data', function () {
return gulp.src('./_data/monarch/*.tar.gz')
.pipe(gunzip())
.pipe(untar())
.pipe(gulp.dest('./_data/monarch/monarch-data'))
})