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Merge to dev

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This commit is contained in:
Carl Eberhard
2015-03-17 10:56:40 -04:00
parent ff34ef0ed7 ba20f5f6e1
commit 2632738584
542 changed files with 738 additions and 116566 deletions
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client/GruntFile.js
+169 -159
View File
@@ -1,171 +1,181 @@
module.exports = function(grunt) {
var DEV_PATH = './galaxy/scripts',
DIST_PATH = '../static/scripts',
MAPS_PATH = '../static/maps',
// this symlink allows us to serve uncompressed scripts in DEV_PATH for use with sourcemaps
SRC_SYMLINK = '../static/src';
// Project configuration.
grunt.initConfig({
pkg: grunt.file.readJSON( 'package.json' ),
// Project configuration.
grunt.initConfig({
pkg: grunt.file.readJSON( 'package.json' ),
// default task
// use 'grunt copy' to copy the entire <galaxy>/client/galaxy/scripts dir into <galaxy>/static/scripts
copy: {
main: {
files: [
{
uglify: {
target : {
files: [{
expand : true,
cwd : SRC_SYMLINK,
src : '**/*.js',
dest : DIST_PATH
}],
options : {
sourceMap : true,
sourceMapName : function( path ){
// rewrite name to have all source maps in 'static/maps'
return path.replace( DIST_PATH, MAPS_PATH ) + '.map';
}
}
},
options : {
mangle : {
screw_ie8 : true
},
compress : {
// high compression options
screw_ie8 : true,
sequences: true,
dead_code : true,
drop_debugger : true,
comparisons : true,
conditionals : true,
evaluate : true,
booleans : true,
loops : true,
unused : true,
hoist_funs : true,
if_return : true,
join_vars : true,
cascade : true,
drop_console : true
}
}
},
// use 'grunt watch' (from a new tab in your terminal) to have grunt re-copy changed files automatically
watch: {
// watch for changes in the src dir
files: [ SRC_SYMLINK + '/**' ],
tasks: [ 'uglify' ],
// tasks: [ 'copy', 'pack' ],
options: {
spawn: false
}
},
// call bower to install libraries and other external resources
"bower-install-simple" : {
options: {
color: true
},
"prod": {
options: {
production: true
}
},
"dev": {
options: {
production: false
}
}
},
// where to move fetched bower components into the build structure (libName: [ bower-location, libs-location ])
libraryLocations : {
"jquery": [ "dist/jquery.js", "jquery/jquery.js" ],
"jquery-migrate": [ "jquery-migrate.js", "jquery/jquery.migrate.js" ],
"traceKit": [ "tracekit.js", "tracekit.js" ],
"ravenjs": [ "dist/raven.js", "raven.js" ],
"underscore": [ "underscore.js", "underscore.js" ],
"handlebars": [ "handlebars.runtime.js", "handlebars.runtime.js" ],
"lunr.js": [ "lunr.js", "lunr.js" ],
"backbone": [ "backbone.js", "backbone/backbone.js" ],
// these need to be updated and tested
//"require": [ "build/require.js", "require.js" ],
//"d3": [ "d3.js", "d3.js" ],
//"farbtastic": [ "src/farbtastic.js", "farbtastic.js" ],
//"jQTouch": [ "src/reference/jqtouch.js", "jquery/jqtouch.js" ],
//"bib2json": [ "Parser.js", "bibtex.js" ],
//"jquery-form": [ "jquery.form.js", "jquery/jquery.form.js" ],
//"jquery-autocomplete": [ "src/jquery.autocomplete.js", "jquery/jquery.autocomplete.js" ],
//"select2": [ "select2.js", "jquery/select2.js" ],
//"jStorage": [ "jstorage.js", "jquery/jstorage.js" ],
//"jquery.cookie": [ "", "jquery/jquery.cookie.js" ],
//"dynatree": [ "dist/jquery.dynatree.js", "jquery/jquery.dynatree.js" ],
//"jquery-mousewheel": [ "jquery.mousewheel.js", "jquery/jquery.mousewheel.js" ],
//"jquery.event.drag-drop": [
// [ "event.drag/jquery.event.drag.js", "jquery/jquery.event.drag.js" ],
// [ "event.drag/jquery.event.drop.js", "jquery/jquery.event.drop.js" ]
//],
// these are complicated by additional css/less
//"toastr": [ "toastr.js", "toastr.js" ],
//"wymeditor": [ "dist/wymeditor/jquery.wymeditor.js", "jquery/jquery.wymeditor.js" ],
//"jstree": [ "jstree.js", "jquery/jstree.js" ],
// these have been customized by Galaxy
//"bootstrap": [ "dist/js/bootstrap.js", "bootstrap.js" ],
//"jquery-ui": [
// // multiple components now
// [ "", "jquery/jquery-ui.js" ]
//],
}
});
grunt.loadNpmTasks( 'grunt-contrib-watch' );
grunt.loadNpmTasks( 'grunt-contrib-uglify' );
grunt.loadNpmTasks( 'grunt-bower-install-simple');
grunt.registerTask( 'default', [ 'uglify' ] );
// -------------------------------------------------------------------------- copy,pack only those changed
// adapted from grunt-contrib-watch jslint example
//TODO: a bit hacky and there's prob. a better way
//NOTE: copy will fail silently if a file isn't found
// outer scope variable for the event handler and onChange fn - begin with empty hash
var changedFiles = Object.create(null);
// when files are changed, set the copy src and packScripts target to the filenames of the updated files
var onChange = grunt.util._.debounce(function() {
grunt.log.writeln( 'onChange, changedFiles:', Object.keys( changedFiles ) );
grunt.config( 'uglify.target.files', [{
expand : true,
cwd : 'galaxy/scripts/',
src : '**',
dest : '../static/scripts'
}
]
}
},
cwd : SRC_SYMLINK,
src : Object.keys( changedFiles ),
dest : DIST_PATH
}]);
changedFiles = Object.create(null);
}, 200);
// use 'grunt pack' to call pack_scripts.py to pack all or selected files in static/scripts
exec: {
packScripts: {
cwd: '../static/scripts',
target: [],
cmd: function(){
var targets = grunt.config( 'exec.packScripts.target' );
// if nothing was passed in pack all scripts
if( !targets.length ){
return './pack_scripts.py';
}
grunt.event.on( 'watch', function( action, filepath ) {
// store each filepath in a Files obj, the debounced fn above will use it as an aggregate list for copying
// we need to take galaxy/scripts out of the filepath or it will be copied to the wrong loc
filepath = filepath.replace( SRC_SYMLINK + '/', '' );
grunt.log.writeln( 'on.watch, filepath:', filepath );
changedFiles[filepath] = action;
onChange();
});
grunt.log.write( 'packing: ' + targets + '\n' );
return targets.map( function( target ){
return './pack_scripts.py ' + target;
}).join( '; ' );
// -------------------------------------------------------------------------- fetch/update external libraries
/** copy external libraries from bower components to scripts/libs */
function copyLibs(){
var LIB_PATH = DEV_PATH + '/libs/',
libraryLocations = grunt.config( 'libraryLocations' );
for( var libName in libraryLocations ){
if( libraryLocations.hasOwnProperty( libName ) ){
var BOWER_DIR = 'bower_components',
location = libraryLocations[ libName ],
source = [ BOWER_DIR, libName, location[0] ].join( '/' ),
destination = LIB_PATH + location[1];
grunt.log.writeln( source + ' -> ' + destination );
grunt.file.copy( source, destination );
}
}
}
},
// use 'grunt watch' (from a new tab in your terminal) to have grunt re-copy changed files automatically
watch: {
// watch for changes in the src dir
files: [ 'galaxy/scripts/**' ],
tasks: [ 'copy', 'pack' ],
options: {
spawn: false
}
},
// call bower to install libraries and other external resources
"bower-install-simple" : {
options: {
color: true
},
"prod": {
options: {
production: true
}
},
"dev": {
options: {
production: false
}
}
},
// where to move fetched bower components into the build structure (libName: [ bower-location, libs-location ])
libraryLocations : {
"jquery": [ "dist/jquery.js", "jquery/jquery.js" ],
"jquery-migrate": [ "jquery-migrate.js", "jquery/jquery.migrate.js" ],
"traceKit": [ "tracekit.js", "tracekit.js" ],
"ravenjs": [ "dist/raven.js", "raven.js" ],
"underscore": [ "underscore.js", "underscore.js" ],
"handlebars": [ "handlebars.runtime.js", "handlebars.runtime.js" ],
"lunr.js": [ "lunr.js", "lunr.js" ],
"backbone": [ "backbone.js", "backbone/backbone.js" ],
// these need to be updated and tested
//"require": [ "build/require.js", "require.js" ],
//"d3": [ "d3.js", "d3.js" ],
//"farbtastic": [ "src/farbtastic.js", "farbtastic.js" ],
//"jQTouch": [ "src/reference/jqtouch.js", "jquery/jqtouch.js" ],
//"bib2json": [ "Parser.js", "bibtex.js" ],
//"jquery-form": [ "jquery.form.js", "jquery/jquery.form.js" ],
//"jquery-autocomplete": [ "src/jquery.autocomplete.js", "jquery/jquery.autocomplete.js" ],
//"select2": [ "select2.js", "jquery/select2.js" ],
//"jStorage": [ "jstorage.js", "jquery/jstorage.js" ],
//"jquery.cookie": [ "", "jquery/jquery.cookie.js" ],
//"dynatree": [ "dist/jquery.dynatree.js", "jquery/jquery.dynatree.js" ],
//"jquery-mousewheel": [ "jquery.mousewheel.js", "jquery/jquery.mousewheel.js" ],
//"jquery.event.drag-drop": [
// [ "event.drag/jquery.event.drag.js", "jquery/jquery.event.drag.js" ],
// [ "event.drag/jquery.event.drop.js", "jquery/jquery.event.drop.js" ]
//],
// these are complicated by additional css/less
//"toastr": [ "toastr.js", "toastr.js" ],
//"wymeditor": [ "dist/wymeditor/jquery.wymeditor.js", "jquery/jquery.wymeditor.js" ],
//"jstree": [ "jstree.js", "jquery/jstree.js" ],
// these have been customized by Galaxy
//"bootstrap": [ "dist/js/bootstrap.js", "bootstrap.js" ],
//"jquery-ui": [
// // multiple components now
// [ "", "jquery/jquery-ui.js" ]
//],
}
});
grunt.loadNpmTasks( 'grunt-contrib-watch' );
grunt.loadNpmTasks( 'grunt-contrib-copy');
grunt.loadNpmTasks( 'grunt-bower-install-simple');
grunt.loadNpmTasks( 'grunt-exec' );
grunt.registerTask( 'pack', [ 'exec' ] );
grunt.registerTask( 'default', [ 'copy:main', 'pack' ] );
// -------------------------------------------------------------------------- copy,pack only those changed
// adapted from grunt-contrib-watch jslint example
//TODO: a bit hacky and there's prob. a better way
//NOTE: copy will fail silently if a file isn't found
// outer scope variable for the event handler and onChange fn - begin with empty hash
var changedFiles = Object.create(null);
// when files are changed, set the copy src and packScripts target to the filenames of the updated files
var onChange = grunt.util._.debounce(function() {
grunt.config( 'copy.main.files', [{
expand: true,
cwd: 'galaxy/scripts',
src: Object.keys( changedFiles ),
dest: '../static/scripts/'
}]);
grunt.config( 'exec.packScripts.target', Object.keys( changedFiles ) );
changedFiles = Object.create(null);
}, 200);
grunt.event.on('watch', function(action, filepath) {
// store each filepath in a Files obj, the debounced fn above will use it as an aggregate list for copying
// we need to take galaxy/scripts out of the filepath or it will be copied to the wrong loc
filepath = filepath.replace( /galaxy\/scripts\//, '' );
changedFiles[filepath] = action;
onChange();
});
// -------------------------------------------------------------------------- fetch/update external libraries
/** copy external libraries from bower components to scripts/libs */
function copyLibs(){
var libraryLocations = grunt.config( 'libraryLocations' );
for( var libName in libraryLocations ){
if( libraryLocations.hasOwnProperty( libName ) ){
var BOWER_DIR = 'bower_components',
location = libraryLocations[ libName ],
source = [ BOWER_DIR, libName, location[0] ].join( '/' ),
destination = 'galaxy/scripts/libs/' + location[1];
grunt.log.writeln( source + ' -> ' + destination );
grunt.file.copy( source, destination );
}
}
}
grunt.registerTask( 'copy-libs', 'copy external libraries to src', copyLibs );
grunt.registerTask( 'install-libs', 'fetch external libraries and copy to src',
grunt.registerTask( 'copy-libs', 'copy external libraries to src', copyLibs );
grunt.registerTask( 'install-libs', 'fetch external libraries and copy to src',
[ 'bower-install-simple:prod', 'copy-libs' ] );
};
client/package.json
+1
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@@ -9,6 +9,7 @@
"grunt": "^0.4.5",
"grunt-bower-install-simple": "^1.1.0",
"grunt-contrib-copy": "^0.5.0",
"grunt-contrib-uglify": "^0.8.0",
"grunt-contrib-watch": "^0.6.1",
"grunt-exec": "^0.4.6",
"grunt-webpack": "^1.0.8",
config/galaxy.ini.sample
+1 -7
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@@ -523,12 +523,6 @@ nglims_config_file = tool-data/nglims.yaml
#static_style_dir = static/june_2007_style/blue
#static_robots_txt = static/robots.txt
# Pack javascript at launch (/static/scripts/*.js)
# This only happens if the modified timestamp of the source .js is newer
# than the version (if it exists) in /static/scripts/packed/
# Note that this requires java > 1.4 for executing yuicompressor.jar
#pack_scripts = False
# Cloud Launch
#enable_cloud_launch = False
@@ -813,7 +807,7 @@ use_interactive = True
# Expose user list. Setting this to true will expose the user list to authenticated users. This
# makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and
# have the correct user show up. This makes less sense on large public galaxy instances where
# have the correct user show up. This makes less sense on large public galaxy instances where
# that data shouldn't be exposed. For semi-public galaxies, it may make sense to expose just the
# username and not email, or vice versa.
#expose_user_name = False
lib/galaxy/webapps/galaxy/buildapp.py
-18
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@@ -101,9 +101,6 @@ def app_factory( global_conf, **kwargs ):
log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.")
else:
webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs )
if asbool(kwargs.get('pack_scripts', False)):
log.warn( "The 'pack_scripts' option is deprecated" )
pack_scripts()
# Close any pooled database connections before forking
try:
galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose()
@@ -536,21 +533,6 @@ def populate_api_routes( webapp, app ):
webapp.mapper.connect( "create", "/api/metrics", controller="metrics",
action="create", conditions=dict( method=["POST"] ) )
def pack_scripts():
from glob import glob
from subprocess import call
cmd = "java -jar scripts/yuicompressor.jar --type js static/scripts/%(fname)s -o static/scripts/packed/%(fname)s"
raw_js = [os.path.basename(g) for g in glob( "static/scripts/*.js" )]
for fname in raw_js:
if os.path.exists('static/scripts/packed/%s' % fname):
if os.path.getmtime('static/scripts/packed/%s' % fname) > os.path.getmtime('static/scripts/%s' % fname):
continue # Skip, packed is newer than source.
d = dict( fname=fname )
log.info("%(fname)s --> packed/%(fname)s" % d)
call( cmd % d, shell=True )
def _add_item_tags_controller( webapp, name_prefix, path_prefix, **kwd ):
# Not just using map.resources because actions should be based on name not id
controller = "%stags" % name_prefix
scripts/yuicompressor.jar
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static/maps/base.js.map
+1
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@@ -0,0 +1 @@
{"version":3,"file":"base.js","sources":["../src/base.js"],"names":["define","Backbone","Base","this","initialize","apply","arguments","extend","Model"],"mappings":"AAAAA,QAAS,0BAA2B,SAAUC,GAE7C,GAAIC,GAAO,WACNC,KAAKC,YACRD,KAAKC,WAAWC,MAAMF,KAAMG,WAK9B,OAFAJ,GAAKK,OAASN,EAASO,MAAMD,QAG5BL,KAAMA,EACND,SAAUA"}
static/maps/galaxy-app-base.js.map
+1
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@@ -0,0 +1 @@
{"version":3,"file":"galaxy-app-base.js","sources":["../src/galaxy-app-base.js"],"names":["define","userModel","metricsLogger","addLogging","localize","bootstrapped","GalaxyApp","options","self","this","_init","prototype","defaultOptions","patchExisting","root","_","extend","Backbone","Events","_processOptions","debug","_patchGalaxy","window","Galaxy","_initLogger","loggerOptions","logger","_initLocale","config","_initUser","user","trigger","_setUpListeners","defaults","k","hasOwnProperty","patchWith","MetricsLogger","_l","userJSON","User","currUser","lastAjax","$","document","bind","ev","xhr","data","JSON","parse","err","url","location","href","slice","toString","userEmail","get"],"mappings":"AAAAA,QACI,sBACA,uBACA,oBACA,qBACA,qBACD,SAAUC,EAAWC,EAAeC,EAAYC,EAAUC,GAU7D,QAASC,GAAWC,GAChB,GAAIC,GAAOC,IACX,OAAOD,GAAKE,MAAOH,OA0InB,MAtIJJ,GAAYG,EAAW,aAGvBA,EAAUK,UAAUC,gBAEhBC,eAAkB,EAGlBC,KAAkB,KAItBR,EAAUK,UAAUD,MAAQ,SAAeH,GACvC,GAAIC,GAAOC,IA4BX,OA3BAM,GAAEC,OAAQR,EAAMS,SAASC,QAEzBV,EAAKW,gBAAiBZ,GACtBC,EAAKY,MAAO,sBAAuBZ,EAAKD,SAExCC,EAAKa,aAAcC,OAAOC,QAE1Bf,EAAKgB,YAAajB,EAAQkB,mBAC1BjB,EAAKY,MAAO,qBAAsBZ,EAAKkB,QAEvClB,EAAKmB,cACLnB,EAAKY,MAAO,uBAAwBZ,EAAKJ,UAEzCI,EAAKoB,OAASrB,EAAQqB,QAAUvB,EAAauB,WAC7CpB,EAAKY,MAAO,qBAAsBZ,EAAKoB,QAEvCpB,EAAKqB,UAAWtB,EAAQuB,MAAQzB,EAAayB,UAC7CtB,EAAKY,MAAO,mBAAoBZ,EAAKsB,MAGrCtB,EAAKuB,QAAS,QAASvB,GAKvBA,EAAKwB,kBAEExB,GAIXF,EAAUK,UAAUQ,gBAAkB,SAA0BZ,GAC5D,GAAIC,GAAOC,KACPwB,EAAWzB,EAAKI,cACpBJ,GAAKY,MAAO,oBAAqBb,GAEjCC,EAAKD,UACL,KAAK,GAAI2B,KAAKD,GACNA,EAASE,eAAgBD,KACzB1B,EAAKD,QAAS2B,GAAQ3B,EAAQ4B,eAAgBD,GAAQ3B,EAAS2B,GAAQD,EAAUC,GAGzF,OAAO1B,IAIXF,EAAUK,UAAUU,aAAe,SAA0Be,GACzD,GAAI5B,GAAOC,IAEX,IAAID,EAAKD,QAAQM,eAAiBuB,EAAW,CACzC5B,EAAKY,MAAO,gCAAiCgB,EAG7C,KAAK,GAAIF,KAAKE,GACNA,EAAUD,eAAgBD,KAC1B1B,EAAKY,MAAO,iBAAoBc,EAAI,cACpC1B,EAAM0B,GAAME,EAAWF,MAOvC5B,EAAUK,UAAUa,YAAc,SAAsBC,GACpD,GAAIjB,GAAOC,IAGX,OAFAD,GAAKY,MAAO,eAAgBK,GAC5BjB,EAAKkB,OAAS,GAAIxB,GAAcmC,cAAeZ,GACxCjB,GAIXF,EAAUK,UAAUgB,YAAc,SAAsBpB,GACpD,GAAIC,GAAOC,IAKX,OAJAD,GAAKY,MAAO,eAAgBb,GAC5BC,EAAKJ,SAAWA,EAEhBkB,OAAOgB,GAAK9B,EAAKJ,SACVI,GAIXF,EAAUK,UAAUkB,UAAY,SAAoBU,GAChD,GAAI/B,GAAOC,IAKX,OAJAD,GAAKY,MAAO,aAAcmB,GAC1B/B,EAAKsB,KAAO,GAAI7B,GAAUuC,KAAMD,GAEhC/B,EAAKiC,SAAWjC,EAAKsB,KACdtB,GAIXF,EAAUK,UAAUqB,gBAAkB,WAClC,GAAIxB,GAAOC,IAIXD,GAAKkC,YACLC,EAAGC,UAAWC,KAAM,WAAY,SAAUC,EAAIC,EAAKxC,GAC/C,GAAIyC,GAAOzC,EAAQyC,IACnB,KACIA,EAAOC,KAAKC,MAAOF,GACrB,MAAOG,IAET3C,EAAKkC,UACDU,IAAUC,SAASC,KAAKC,MAAO,EAAG,IAAOhD,EAAQ6C,IACjDJ,KAAUA,MAQtB1C,EAAUK,UAAU6C,SAAW,WAC3B,GAAIC,GAAYhD,KAAKqB,KAAK4B,IAAK,UAAa,aAC5C,OAAO,aAAeD,EAAY,MAM9BnD,UAAYA"}
static/maps/galaxy.autocom_tagging.js.map
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static/maps/galaxy.base.js.map
+1
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static/maps/galaxy.frame.js.map
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