gulpfile.js

////
//// Usage: node ./node_modules/.bin/gulp doc|build|test|watch|clean
////

var gulp = require('gulp');
//var jsdoc = require("gulp-jsdoc");
var jshint = require('gulp-jshint');
var mocha = require('gulp-mocha');
var shell = require('gulp-shell');
var browserify = require('browserify');
var source = require('vinyl-source-stream');
var streamify = require('gulp-streamify');
var uglify = require('gulp-uglify');
var us = require('underscore');
var del = require('del');
var yaml = require('yamljs');
var fs = require('fs');
var url = require('url');
var tilde = require('expand-home-dir');
var bump = require('gulp-bump');
var flatten = require('gulp-flatten');
var request = require('request');
//var git = require('gulp-git');
//var watch = require('gulp-watch');
//var watchify = require('watchify');
//var concat = require('gulp-concat');
//var sourcemaps = require('gulp-sourcemaps');
///
/// Helpers.
///

// watch_mode is set by 'gulp watch' tasks to inhibit uglify (which is slow)
var watch_mode = false;
//var watch_mode = true;

function _die(str){
    console.error(str);
    process.exit(-1);
}

// Ping server; used during certain commands.
function _ping_count(){

    if( count_url && typeof(count_url) === 'string' && count_url !== '' ){

        request({
            url: count_url
        }, function(error, response, body){
            if( error || response.statusCode !== 200 ){
                console.log('Unable to ping: ' + count_url);
            }else{
                console.log('Pinged: ' + count_url);
            }
        });
    }else{
        console.log('Will not ping home.');
    }
}

function _tilde_expand(ufile){
    return tilde(ufile);
}

function _tilde_expand_list(list){
    return us.map(list, function(ufile){
        //console.log('ufile: ' + ufile);
        return tilde(ufile);
    });
}

function _run_cmd(command_bits){
    var final_command = command_bits.join(' ');
    return ['echo \'' + final_command + '\'', final_command];
}

function _run_cmd_list(commands){
    var final_list = [];

    us.each(commands, function(cmd){
        final_list.push('echo \'' + cmd + '\'');
        final_list.push(cmd);
    });

    return final_list;
}

///
///
///

var paths = {
    // WARNING: Cannot use glob for clients--I use the explicit listing
    // to generate a dynamic browserify set.
    'form_noctua_clients': [
	//'js/NoctuaBasic/NoctuaBasicApp.js'
    ],
    'core_noctua_clients': [
    	'js/NoctuaEditor.js',
    	'js/NoctuaLanding.js'
    ],
    // 'core_workbench_clients': [
    //     // A temporary place for internal workspaces.
    //     //'workbenches/copy_in_model/CopyInModel.js',
    //     'workbenches/mmcc/MMCC.js',
    //     'workbenches/bioentity_companion/BioentityCompanion.js',
    //     'workbenches/companion/Companion.js',
    //     'workbenches/cytoview/CytoView.js'
    // ],
    support: ['js/connectors-sugiyama.js'],
    scripts: ['scripts/*'],
    tests: ['tests/*.test.js'],
    lint_targets: [
	'js/NoctuaEditor.js',
	'js/NoctuaLanding.js'
    ]
};

// var paths = {
//     // WARNING: Cannot use glob for clients--I use the explicit listing
//     // to generate a dynamic browserify set.
//     'core_noctua_clients': [
// 	'js/NoctuaEditor.js',
// 	'js/NoctuaLanding.js'
//      //'js/NoctuaBasic/NoctuaBasicApp.js'
//     ],
//     support: ['js/connectors-sugiyama.js'],
//     scripts: ['scripts/*'],
//     tests: ['tests/*.test.js']
// };

///
/// Build tasks.
///

// // Build docs directory with JSDoc.
// gulp.task('doc', function() {
//   gulp.src(paths.clients, paths.scripts)
//     .pipe(jsdoc('./doc'));
// });

// Testing with mocha/chai.
// NOTE: I'm using chai here.
gulp.task('unit-tests', function() {
  return gulp.src(paths.tests, {
    read: false
  }).pipe(mocha({
    reporter: 'spec',
    globals: {
      // Use a different should.
      should: require('chai').should()
    }
  }));
});

gulp.task('lint-tests', function(){
    return gulp.src(paths.lint_targets)
	.pipe(jshint('./config/jshintrc'))
	.pipe(jshint.reporter('fail'));
});

gulp.task('test', ['unit-tests', 'lint-tests']);

//
gulp.task('ready-non-commonjs-libs', function() {
  var pkg = require('./package.json');
  us.each(pkg.browser, function(val, key) {
    console.log('copy: ' + key);
    gulp.src(val)
      .pipe(gulp.dest('./deploy/'));
  });
});

gulp.task('copy-css-from-npm-deps', function() {
  gulp.src('./node_modules/**/*.css', {
      base: './node_modules'
    })
    .pipe(flatten())
    .pipe(gulp.dest('./deploy/css'));
});

// See what browserify-shim is up to.
//process.env.BROWSERIFYSHIM_DIAGNOSTICS = 1;
// Browser runtime environment construction.
function _client_compile_task(file) {
  console.log('client_compile_task', file);
  var b = browserify(file);

  if (file === 'js/NoctuaBasic/NoctuaBasicApp.js') {
    // Need to manually apply global=true transform here
    // Setting this in package.json FAILS for jquery when require()-ed via
    // another file that has been require()-ed...no idea why
    // See: https://github.com/thlorenz/browserify-shim/issues/143
    b.transform('browserify-shim', {
        global: true
    });
  }

  var result = b
                // not in npm, don't need in browser
                .exclude('ringo/httpclient')
                .bundle()
                // desired output filename to vinyl-source-stream
                .pipe(source(file));

  if( ! watch_mode ){    // Only uglify when building, not when watching.
      result = result.pipe(streamify(uglify()));
  }

  result = result.pipe(gulp.dest('./deploy/'));
  return result;
}

// Build the clients as best we can.
var base_build_tasks = [
  'ready-non-commonjs-libs',
  'copy-css-from-npm-deps'
];

// Dynamically define tasks.
var form_build_tasks = us.clone(base_build_tasks);
us.each(paths.form_noctua_clients, function(file, index) {
    var taskname = 'build-client_' + file;
    form_build_tasks.push(taskname);
    gulp.task(taskname, function(cb){
       return _client_compile_task(file);
    });
});

var noctua_build_tasks = us.clone(base_build_tasks);
us.each(paths.core_noctua_clients, function(file, index) {
    var taskname = 'build-client_' + file;
    noctua_build_tasks.push(taskname);
    gulp.task(taskname, function(cb){
       return _client_compile_task(file);
    });
});

// var workbench_build_tasks = us.clone(base_build_tasks);
// us.each(paths.core_workbench_clients, function(file, index) {
//     var taskname = 'build-client_' + file;
//     workbench_build_tasks.push(taskname);
//     gulp.task(taskname, function(cb){
//         _client_compile_task(file);
//         cb(null);
//     });
// });

gulp.task('build', noctua_build_tasks.concat(
    form_build_tasks));
// workbench_build_tasks));

gulp.task('watch', ['watch-noctua', 'watch-form']);

// Rerun tasks when a file changes.
gulp.task('watch-noctua', function(cb) {
    watch_mode = true;
    var basic_client_files = paths.core_noctua_clients;
    gulp.watch(basic_client_files, noctua_build_tasks);
    //gulp.watch(paths.core_workbench_clients, workbench_build_tasks);
    cb(null);
});

// Rerun tasks when a file changes.
gulp.task('watch-form', function(cb) {
    watch_mode = true;
    var basic_client_files = paths.form_noctua_clients.concat(
                                'js/NoctuaBasic/NoctuaBasicController.js',
                                'node_modules/selectize/dist/js/standalone/selectize.js');
    gulp.watch(basic_client_files, form_build_tasks);
    cb(null);
});

//
gulp.task('clean', function(cb) {
  del(['./deploy/*', './deploy/js/*', '!./deploy/README.org',
    './doc/*', '!./doc/README.org'
  ]);
  cb(null);
});

// Release tools for patch release.
gulp.task('release', ['patch-bump', 'publish-npm']);

gulp.task('patch-bump', function() {
  gulp.src('./package.json')
    .pipe(bump({
      type: 'patch'
    }))
    .pipe(gulp.dest('./'));
});

//
gulp.task('publish-npm', function(cb) {
  var npm = require("npm");
  npm.load(function(er, npm) {
    // NPM
    npm.commands.publish();
  });
  cb(null);
});

///
/// Runtime tasks/coordination.
///

var conf_file = './startup.yaml';

// Pull in our configuration.
var config = null;
try {
    config = yaml.load(conf_file);
}catch(e){
    _die('Could not find "' + conf_file + '", look in ./config for examples.');
}

function ensure_noslash(s) {
  return s.replace(/\/$/, '');
}

// Lookup/public locations.
var golr_lookup_url_noslash = ensure_noslash(config['GOLR_LOOKUP_URL'].value);
var golr_lookup_url = golr_lookup_url_noslash + '/';
var golr_neo_lookup_url_noslash = ensure_noslash(config['GOLR_NEO_LOOKUP_URL'].value);
var golr_neo_lookup_url = golr_neo_lookup_url_noslash + '/';
var noctua_lookup_url = config['NOCTUA_LOOKUP_URL'].value;
var barista_lookup_url = config['BARISTA_LOOKUP_URL'].value;

// Real/self/internal locations.
var golr_location = config['GOLR_LOCATION'].value;
var noctua_location = config['NOCTUA_LOCATION'].value;
var barista_location = config['BARISTA_LOCATION'].value;
var minerva_location = config['MINERVA_LOCATION'].value;

// Minerva.
var minerva_port = url.parse(minerva_location).port || 80;
var minerva_max_mem = parseInt(config['MINERVA_MAX_MEMORY'].value);
var minerva_reasoner = config['MINERVA_REASONER'].value;
var minerva_ontology_journal = config['MINERVA_ONTOLOGY_JOURNAL'].value;

// External tools.
var external_browser_location = null;
if( config['EXTERNAL_BROWSER_LOCATION'] ){
    external_browser_location =
	config['EXTERNAL_BROWSER_LOCATION'].value || null;
}

// Now necessary.
var barista_default_namespace = config['BARISTA_DEFAULT_NAMESPACE'].value;

// Optional.
var barista_repl_port = config['BARISTA_REPL_PORT'].value;

// Optional external.
var use_github_p = false;
var github_api = null;
var github_org = null;
var github_repo = null;
if( config['GITHUB_API'] ){
    github_api = config['GITHUB_API'].value || null;
}
if( config['GITHUB_ORG'] ){
    github_org = config['GITHUB_ORG'].value || null;
}
if( config['GITHUB_REPO'] ){
    github_repo = config['GITHUB_REPO'].value || null;
}
if( github_api && github_org && github_repo ){
    use_github_p = true;
}

//
var noctua_context = config['NOCTUA_CONTEXT'] ? config['NOCTUA_CONTEXT'].value : 'go';
var noctua_models = config['NOCTUA_MODELS'].value;
var noctua_store = config['NOCTUA_STORE'].value;
var user_data = config['USER_DATA'].value;
var group_data = config['GROUP_DATA'].value;
var login_secrets_dir = config['BARISTA_LOGIN_SECRETS'].value;
var ontology_list = _tilde_expand_list(config['ONTOLOGY_LIST'].value);
//var ontology_catalog = config['ONTOLOGY_CATALOG'] ? config['ONTOLOGY_CATALOG'].value : null;
var workbench_dirs = config['WORKBENCHES'].value;
var workbench_dirs_str = workbench_dirs.join(' ');
var collapsible_relations = config['COLLAPSIBLE_RELATIONS'].value;
var collapsible_relations_str = collapsible_relations.join(' ');
var collapsible_reverse_relations =
        config['COLLAPSIBLE_REVERSE_RELATIONS'].value;
var collapsible_reverse_relations_str =
        collapsible_reverse_relations.join(' ');
var def_app_def = config['DEFAULT_APP_DEFINITION'].value;
// NOTE: Allowing barista to slurp up startup.yaml itself to get the
// application definitions.

// Execute by default; variable must be present and empty to stop.
var count_url =
        'https://s3-us-west-1.amazonaws.com/go-noctua-usage-master/ping.json';
if( config['NOCTUA_COUNTER_URL'] && config['NOCTUA_COUNTER_URL'].value ){
    count_url = config['NOCTUA_COUNTER_URL'].value;
}

// Execute counter.
_ping_count();

///
/// Runner assembly.
///

// Select minerva jar to use.
function _select_minerva(){

    // Default reasoner is still legacy.
    var ret = null;
    if( config['MINERVA_JAR'] && config['MINERVA_JAR'].value ){
	ret = config['MINERVA_JAR'].value;
    }else{
	_die('External MINERVA_JAR path must be defined'+
	     ' explicitly in startup.yaml.');
    }

    return ret;
}

// Add reasoner, or not, depending on external cues.
function _select_reasoner(){

    // Default reasoner is still legacy.
    var ret = '--slme-elk';

    if( minerva_reasoner === 'none' ){
	// Apparently no reasoner--should only be used for debugging or
	// madness.
    }else if( minerva_reasoner === 'arachne' ){
	ret = '--arachne';
    }else if( minerva_reasoner === 'slme-elk' ){
	// Legacy reasoner.
	ret = '--slme-elk';
    }

    return ret;
}

// TODO: All of the listed options should be pushed into the config
// file like the ontology catalog--no more secrets in the gulpfiles.
var minerva_opts_base = [
    'java',
    '-Xmx' + minerva_max_mem + 'G',
    '-cp', _select_minerva(),
    'org.geneontology.minerva.server.StartUpTool',
    '--use-golr-url-logging', // possibly unnecessary in non-lookup cases
    '--use-request-logging',
    _select_reasoner(),
    '-g', ontology_list,
    '--set-important-relation-parent', 'http://purl.obolibrary.org/obo/LEGOREL_0000000',
    '--port', minerva_port,
    '--ontojournal', minerva_ontology_journal, // ontology journal file
    '-f', noctua_store, // blazegraph journal file
    '--export-folder', noctua_models
];

var minerva_opts_lookup = [
    '--golr-labels', golr_neo_lookup_url_noslash,
    '--golr-seed', golr_lookup_url_noslash
];

// Using validation is the default setting.
var minerva_opts_no_validation = [
    '--skip-class-id-validation'
];

// // Optional catalog, depending on startup config environment.
// if (us.isString(ontology_catalog) && ontology_catalog !== '') {
//     minerva_opts_base.push('-c');
//     minerva_opts_base.push(ontology_catalog);
// }

// Minerva runner: +lookup +validation
gulp.task('run-minerva', shell.task(_run_cmd(
    minerva_opts_base.concat(minerva_opts_lookup)
)));

// Minerva runner: -lookup +validation
gulp.task('run-minerva-no-lookup', shell.task(_run_cmd(
    minerva_opts_base.concat([])
)));

// Minerva runner: +lookup -validation
gulp.task('run-minerva-no-validation', shell.task(_run_cmd(
    minerva_opts_base.concat(minerva_opts_lookup, minerva_opts_no_validation)
)));

// Minerva runner: -lookup -validation
gulp.task('run-minerva-no-lookup-no-validation', shell.task(_run_cmd(
    minerva_opts_base.concat(minerva_opts_no_validation)
)));

// Minerva batch: create a new journal from the files directory.
gulp.task('batch-minerva-create-journal', shell.task(_run_cmd([
    'java',
    '-Xmx' + minerva_max_mem + 'G',
    '-jar', _select_minerva(),
    '--import-owl-models',
    '-j', noctua_store,
    ' -f', noctua_models
])));

// Minerva batch: destroy the current journal.
gulp.task('batch-minerva-destroy-journal', shell.task(_run_cmd([
    'rm', '-f', noctua_store
])));

// Minerva batch: destroy the current ontology journal.
gulp.task('batch-minerva-destroy-ontology-journal', shell.task(_run_cmd([
  'rm', '-f',  minerva_ontology_journal
])));

// Minerva batch: get used minerva version.
gulp.task('batch-minerva-version', shell.task(_run_cmd([
    'java',
    '-jar', _select_minerva(),
    '--version'
])));

// Minerva batch: dump models in offline journal to directory.
gulp.task('batch-minerva-dump-from-journal', shell.task(_run_cmd([
    'java',
    '-Xmx' + minerva_max_mem + 'G',
    '-jar', _select_minerva(),
    '--dump-owl-models',
    '-j', noctua_store,
    ' -f', noctua_models
])));

// Minerva batch: apply 'update.rq' to offline journal.
gulp.task('batch-minerva-apply-sparql-update', shell.task(_run_cmd([
    'java',
    '-Xmx' + minerva_max_mem + 'G',
    '-jar', _select_minerva(),
    '--sparql-update',
    '-j', noctua_store,
    ' -f', 'update.rq'
])));

//node barista.js --self http://localhost:3400
gulp.task('run-barista', shell.task(_run_cmd(
    ['node', 'barista.js',
     '--debug', 0,
     '--users', user_data,
     '--groups', group_data,
     // '--public', barista_lookup_url,
     '--self', barista_location,
     '--secrets', login_secrets_dir,
     '--context', noctua_context,
     '--default-namespace', barista_default_namespace,
     '--repl', barista_repl_port
    ]
)));

//node noctua.js -c "RO:0002333 BFO:0000066 RO:0002233 RO:0002488" -g http://golr.geneontology.org/solr/ -b http://localhost:3400 -m minerva_local
var noctua_run_list = [
    'node', 'noctua.js',
    '--golr', golr_lookup_url,
    '--golr-neo', golr_neo_lookup_url,
    '--barista', barista_lookup_url,
    '--noctua-context', noctua_context,
    '--noctua-public', noctua_lookup_url,
    '--noctua-self', noctua_location,
    '--minerva-definition', def_app_def,
    // Lists need to be quoted.
    '--workbenches', '"' + workbench_dirs_str + '"'
];
// The relations are variable.
if( collapsible_relations_str ){
    noctua_run_list.push('--collapsible-relations');
    noctua_run_list.push('"' + collapsible_relations_str + '"');
}
if( collapsible_reverse_relations_str ){
    noctua_run_list.push('--collapsible-reverse-relations');
    noctua_run_list.push('"' + collapsible_reverse_relations_str + '"');
}
// See if we have an external browser.
if( external_browser_location ){
    noctua_run_list.push('--external-browser-location');
    noctua_run_list.push('"' + external_browser_location + '"');
}
// See if we will be using github.
if( use_github_p ){
    noctua_run_list.push('--github-api');
    noctua_run_list.push(github_api);
    noctua_run_list.push('--github-org');
    noctua_run_list.push(github_org);
    noctua_run_list.push('--github-repo');
    noctua_run_list.push(github_repo);
}
gulp.task('run-noctua', shell.task(_run_cmd(
    noctua_run_list
)));

///
/// Default.
///

// The default task (called when you run `gulp` from cli)
//gulp.task('default', ['doc', 'build', 'test']);