diff --git a/.hgignore b/.hgignore index b1cb3ca9553..beab290cf6b 100644 --- a/.hgignore +++ b/.hgignore @@ -30,9 +30,9 @@ database/openid_consumer_cache *.pyc # Galaxy Runtime Files -paster.lock -paster.log -paster.pid +*.lock +*.log +*.pid # Tool Shed Runtime Files tool_shed_webapp.lock @@ -108,12 +108,9 @@ tool-data/shared/jars/ # CSS build artifacts. sprite-*.less -# Local node_modules directories +# Local node_modules and bower_components directories node_modules - -# Testing -selenium-server.jar -selenium_results.html +bower_components # Documentation build files. doc/build diff --git a/.hgtags b/.hgtags index 22ac92bb8d0..68d98974a64 100644 --- a/.hgtags +++ b/.hgtags @@ -8,16 +8,18 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -7a4d321c0e38fa263ea83d29a35a608c3181fcba latest_2014.06.02 -9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 -6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 -3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 -425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 -9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 -9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 -81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 -2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 +9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 +8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 +b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 +dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 +19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 +cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 +7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 +0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 +f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 +9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 +4039bfd5584aac053f686197a76ac176253e6f3d latest_2015.01.13 diff --git a/client/GruntFile.js b/client/GruntFile.js index 9d42d7dcb33..c8e08c11938 100644 --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -47,15 +47,77 @@ module.exports = function(grunt) { 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-exec'); + grunt.loadNpmTasks( 'grunt-bower-install-simple'); + grunt.loadNpmTasks( 'grunt-exec' ); grunt.registerTask( 'pack', [ 'exec' ] ); - grunt.registerTask( 'default', [ 'copy', 'pack' ] ); + grunt.registerTask( 'default', [ 'copy:main', 'pack' ] ); + // -------------------------------------------------------------------------- copy,pack only those changed // adapted from grunt-contrib-watch jslint example @@ -85,4 +147,25 @@ module.exports = function(grunt) { 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', + [ 'bower-install-simple:prod', 'copy-libs' ] ); + }; diff --git a/client/bower.json b/client/bower.json new file mode 100644 index 00000000000..173a855d922 --- /dev/null +++ b/client/bower.json @@ -0,0 +1,41 @@ +{ + "name": "galaxy-client-libs", + "version": "0.0.0", + "description": "External client-side libraries used by Galaxy", + "keywords": [ + "galaxy", + "galaxyproject" + ], + "homepage": "usegalaxy.org", + "dependencies": { + "jquery": "~1.11.1", + "traceKit": "*", + "ravenjs": "~1.1.16", + "require": "*", + "underscore": "~1.7.0", + "backbone": "~1.1.2", + "bootstrap": "~3.3.2", + "d3": "~3.5.3", + "farbtastic": "~2.0.0-alpha.1", + "toastr": "~2.1.0", + "jQTouch": "git://github.com/senchalabs/jQTouch#~1.0.0", + "bib2json": "git://github.com/mayanklahiri/bib2json", + "jquery-form": "~3.46.0", + "jquery-autocomplete": "git://github.com/dyve/jquery-autocomplete", + "select2": "~3.5.2", + "jStorage": "~0.4.12", + "jquery.cookie": "~1.4.1", + "dynatree": "~1.2.5", + "jquery-mousewheel": "~3.1.12", + "wymeditor": "~1.0.0-rc.1", + "jstree": "~3.0.9", + "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2", + "jquery.event.drag-drop": "~2.2.1", + "handlebars": "~2.0.0", + "jquery-migrate": "~1.2.1", + "lunr.js": "git://github.com/olivernn/lunr.js.git#~0.5.7" + }, + "resolutions": { + "jquery": "~1.11.1" + } +} diff --git a/client/galaxy/scripts/galaxy.masthead.js b/client/galaxy/scripts/galaxy.masthead.js index 66be6dfabf5..bf488a0de99 100644 --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -364,7 +364,7 @@ var GalaxyMastheadTab = Backbone.View.extend({ var $popover_element = $(this.el).find('.head'); $popover_element.popover({ html: true, - content: 'Please log in or register to use this feature.', + content: 'Please log in or register to use this feature.', placement: 'bottom' }).on('shown.bs.popover', function() { // hooking on bootstrap event to automatically hide popovers after delay setTimeout(function() { diff --git a/client/galaxy/scripts/galaxy.workflow_editor.canvas.js b/client/galaxy/scripts/galaxy.workflow_editor.canvas.js index b22dc903c69..2ec9f9543e0 100644 --- a/client/galaxy/scripts/galaxy.workflow_editor.canvas.js +++ b/client/galaxy/scripts/galaxy.workflow_editor.canvas.js @@ -805,7 +805,7 @@ var Node = Backbone.Model.extend({ nodeView.addDataOutput( output ); } ); nodeView.render(); - workflow.node_changed( this ); + workflow.node_changed( this, true); }, update_field_data : function( data ) { var node = this; @@ -1089,17 +1089,25 @@ $.extend( Workflow.prototype, { if ( this.active_node != node ) { this.check_changes_in_active_form(); this.clear_active_node(); - parent.show_form_for_tool( node.form_html + node.tooltip, node ); + if (parent.__NEWTOOLFORM__) { + parent.show_form_for_tool( node.form_html, node ); + } else { + parent.show_form_for_tool( node.form_html + node.tooltip, node ); + } node.make_active(); this.active_node = node; } }, - node_changed : function ( node ) { + node_changed : function ( node, force ) { this.has_changes = true; - if ( this.active_node == node ) { + if ( this.active_node == node && (!parent.__NEWTOOLFORM__ || force)) { // Reactive with new form_html this.check_changes_in_active_form(); //Force changes to be saved even on new connection (previously dumped) - parent.show_form_for_tool( node.form_html + node.tooltip, node ); + if (parent.__NEWTOOLFORM__) { + parent.show_form_for_tool( node.form_html, node ); + } else { + parent.show_form_for_tool( node.form_html + node.tooltip, node ); + } } }, layout : function () { @@ -1305,7 +1313,6 @@ function add_node( type, title_text, tool_id ) { return node; } - var ext_to_type = null; var type_to_type = null; @@ -1863,6 +1870,9 @@ $.extend( CanvasManager.prototype, { left: x, top: y }); + self.cv.css( { "background-position-x": x, + "background-position-y": y + }); self.update_viewport_overlay(); }; // Dragging within canvas background diff --git a/client/galaxy/scripts/libs/handlebars.runtime.js b/client/galaxy/scripts/libs/handlebars.runtime.js index b9f4e492055..932fb7aea01 100644 --- a/client/galaxy/scripts/libs/handlebars.runtime.js +++ b/client/galaxy/scripts/libs/handlebars.runtime.js @@ -1,6 +1,8 @@ -/* +/*! -Copyright (C) 2011 by Yehuda Katz + handlebars v2.0.0 + +Copyright (C) 2011-2014 by Yehuda Katz Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -20,343 +22,639 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +@license */ - -// lib/handlebars/browser-prefix.js -var Handlebars = {}; - -(function(Handlebars, undefined) { -; -// lib/handlebars/base.js - -Handlebars.VERSION = "1.0.0"; -Handlebars.COMPILER_REVISION = 4; - -Handlebars.REVISION_CHANGES = { - 1: '<= 1.0.rc.2', // 1.0.rc.2 is actually rev2 but doesn't report it - 2: '== 1.0.0-rc.3', - 3: '== 1.0.0-rc.4', - 4: '>= 1.0.0' -}; - -Handlebars.helpers = {}; -Handlebars.partials = {}; - -var toString = Object.prototype.toString, - functionType = '[object Function]', - objectType = '[object Object]'; - -Handlebars.registerHelper = function(name, fn, inverse) { - if (toString.call(name) === objectType) { - if (inverse || fn) { throw new Handlebars.Exception('Arg not supported with multiple helpers'); } - Handlebars.Utils.extend(this.helpers, name); +/* exported Handlebars */ +(function (root, factory) { + if (typeof define === 'function' && define.amd) { + define([], factory); + } else if (typeof exports === 'object') { + module.exports = factory(); } else { - if (inverse) { fn.not = inverse; } - this.helpers[name] = fn; + root.Handlebars = root.Handlebars || factory(); } -}; - -Handlebars.registerPartial = function(name, str) { - if (toString.call(name) === objectType) { - Handlebars.Utils.extend(this.partials, name); - } else { - this.partials[name] = str; - } -}; - -Handlebars.registerHelper('helperMissing', function(arg) { - if(arguments.length === 2) { - return undefined; - } else { - throw new Error("Missing helper: '" + arg + "'"); - } -}); - -Handlebars.registerHelper('blockHelperMissing', function(context, options) { - var inverse = options.inverse || function() {}, fn = options.fn; - - var type = toString.call(context); - - if(type === functionType) { context = context.call(this); } - - if(context === true) { - return fn(this); - } else if(context === false || context == null) { - return inverse(this); - } else if(type === "[object Array]") { - if(context.length > 0) { - return Handlebars.helpers.each(context, options); - } else { - return inverse(this); - } - } else { - return fn(context); - } -}); - -Handlebars.K = function() {}; - -Handlebars.createFrame = Object.create || function(object) { - Handlebars.K.prototype = object; - var obj = new Handlebars.K(); - Handlebars.K.prototype = null; - return obj; -}; - -Handlebars.logger = { - DEBUG: 0, INFO: 1, WARN: 2, ERROR: 3, level: 3, - - methodMap: {0: 'debug', 1: 'info', 2: 'warn', 3: 'error'}, - - // can be overridden in the host environment - log: function(level, obj) { - if (Handlebars.logger.level <= level) { - var method = Handlebars.logger.methodMap[level]; - if (typeof console !== 'undefined' && console[method]) { - console[method].call(console, obj); - } - } - } -}; - -Handlebars.log = function(level, obj) { Handlebars.logger.log(level, obj); }; - -Handlebars.registerHelper('each', function(context, options) { - var fn = options.fn, inverse = options.inverse; - var i = 0, ret = "", data; - - var type = toString.call(context); - if(type === functionType) { context = context.call(this); } - - if (options.data) { - data = Handlebars.createFrame(options.data); +}(this, function () { +// handlebars/safe-string.js +var __module3__ = (function() { + "use strict"; + var __exports__; + // Build out our basic SafeString type + function SafeString(string) { + this.string = string; } - if(context && typeof context === 'object') { - if(context instanceof Array){ - for(var j = context.length; i": ">", + '"': """, + "'": "'", + "`": "`" + }; + + var badChars = /[&<>"'`]/g; + var possible = /[&<>"'`]/; + + function escapeChar(chr) { + return escape[chr]; + } + + function extend(obj /* , ...source */) { + for (var i = 1; i < arguments.length; i++) { + for (var key in arguments[i]) { + if (Object.prototype.hasOwnProperty.call(arguments[i], key)) { + obj[key] = arguments[i][key]; } } } + + return obj; } - if(i === 0){ - ret = inverse(this); + __exports__.extend = extend;var toString = Object.prototype.toString; + __exports__.toString = toString; + // Sourced from lodash + // https://github.com/bestiejs/lodash/blob/master/LICENSE.txt + var isFunction = function(value) { + return typeof value === 'function'; + }; + // fallback for older versions of Chrome and Safari + /* istanbul ignore next */ + if (isFunction(/x/)) { + isFunction = function(value) { + return typeof value === 'function' && toString.call(value) === '[object Function]'; + }; } + var isFunction; + __exports__.isFunction = isFunction; + /* istanbul ignore next */ + var isArray = Array.isArray || function(value) { + return (value && typeof value === 'object') ? toString.call(value) === '[object Array]' : false; + }; + __exports__.isArray = isArray; - return ret; -}); - -Handlebars.registerHelper('if', function(conditional, options) { - var type = toString.call(conditional); - if(type === functionType) { conditional = conditional.call(this); } - - if(!conditional || Handlebars.Utils.isEmpty(conditional)) { - return options.inverse(this); - } else { - return options.fn(this); - } -}); - -Handlebars.registerHelper('unless', function(conditional, options) { - return Handlebars.helpers['if'].call(this, conditional, {fn: options.inverse, inverse: options.fn}); -}); - -Handlebars.registerHelper('with', function(context, options) { - var type = toString.call(context); - if(type === functionType) { context = context.call(this); } - - if (!Handlebars.Utils.isEmpty(context)) return options.fn(context); -}); - -Handlebars.registerHelper('log', function(context, options) { - var level = options.data && options.data.level != null ? parseInt(options.data.level, 10) : 1; - Handlebars.log(level, context); -}); -; -// lib/handlebars/utils.js - -var errorProps = ['description', 'fileName', 'lineNumber', 'message', 'name', 'number', 'stack']; - -Handlebars.Exception = function(message) { - var tmp = Error.prototype.constructor.apply(this, arguments); - - // Unfortunately errors are not enumerable in Chrome (at least), so `for prop in tmp` doesn't work. - for (var idx = 0; idx < errorProps.length; idx++) { - this[errorProps[idx]] = tmp[errorProps[idx]]; - } -}; -Handlebars.Exception.prototype = new Error(); - -// Build out our basic SafeString type -Handlebars.SafeString = function(string) { - this.string = string; -}; -Handlebars.SafeString.prototype.toString = function() { - return this.string.toString(); -}; - -var escape = { - "&": "&", - "<": "<", - ">": ">", - '"': """, - "'": "'", - "`": "`" -}; - -var badChars = /[&<>"'`]/g; -var possible = /[&<>"'`]/; - -var escapeChar = function(chr) { - return escape[chr] || "&"; -}; - -Handlebars.Utils = { - extend: function(obj, value) { - for(var key in value) { - if(value.hasOwnProperty(key)) { - obj[key] = value[key]; - } - } - }, - - escapeExpression: function(string) { + function escapeExpression(string) { // don't escape SafeStrings, since they're already safe - if (string instanceof Handlebars.SafeString) { + if (string instanceof SafeString) { return string.toString(); - } else if (string == null || string === false) { + } else if (string == null) { return ""; + } else if (!string) { + return string + ''; } // Force a string conversion as this will be done by the append regardless and // the regex test will do this transparently behind the scenes, causing issues if // an object's to string has escaped characters in it. - string = string.toString(); + string = "" + string; if(!possible.test(string)) { return string; } return string.replace(badChars, escapeChar); - }, + } - isEmpty: function(value) { + __exports__.escapeExpression = escapeExpression;function isEmpty(value) { if (!value && value !== 0) { return true; - } else if(toString.call(value) === "[object Array]" && value.length === 0) { + } else if (isArray(value) && value.length === 0) { return true; } else { return false; } } -}; -; -// lib/handlebars/runtime.js -Handlebars.VM = { - template: function(templateSpec) { + __exports__.isEmpty = isEmpty;function appendContextPath(contextPath, id) { + return (contextPath ? contextPath + '.' : '') + id; + } + + __exports__.appendContextPath = appendContextPath; + return __exports__; +})(__module3__); + +// handlebars/exception.js +var __module4__ = (function() { + "use strict"; + var __exports__; + + var errorProps = ['description', 'fileName', 'lineNumber', 'message', 'name', 'number', 'stack']; + + function Exception(message, node) { + var line; + if (node && node.firstLine) { + line = node.firstLine; + + message += ' - ' + line + ':' + node.firstColumn; + } + + var tmp = Error.prototype.constructor.call(this, message); + + // Unfortunately errors are not enumerable in Chrome (at least), so `for prop in tmp` doesn't work. + for (var idx = 0; idx < errorProps.length; idx++) { + this[errorProps[idx]] = tmp[errorProps[idx]]; + } + + if (line) { + this.lineNumber = line; + this.column = node.firstColumn; + } + } + + Exception.prototype = new Error(); + + __exports__ = Exception; + return __exports__; +})(); + +// handlebars/base.js +var __module1__ = (function(__dependency1__, __dependency2__) { + "use strict"; + var __exports__ = {}; + var Utils = __dependency1__; + var Exception = __dependency2__; + + var VERSION = "2.0.0"; + __exports__.VERSION = VERSION;var COMPILER_REVISION = 6; + __exports__.COMPILER_REVISION = COMPILER_REVISION; + var REVISION_CHANGES = { + 1: '<= 1.0.rc.2', // 1.0.rc.2 is actually rev2 but doesn't report it + 2: '== 1.0.0-rc.3', + 3: '== 1.0.0-rc.4', + 4: '== 1.x.x', + 5: '== 2.0.0-alpha.x', + 6: '>= 2.0.0-beta.1' + }; + __exports__.REVISION_CHANGES = REVISION_CHANGES; + var isArray = Utils.isArray, + isFunction = Utils.isFunction, + toString = Utils.toString, + objectType = '[object Object]'; + + function HandlebarsEnvironment(helpers, partials) { + this.helpers = helpers || {}; + this.partials = partials || {}; + + registerDefaultHelpers(this); + } + + __exports__.HandlebarsEnvironment = HandlebarsEnvironment;HandlebarsEnvironment.prototype = { + constructor: HandlebarsEnvironment, + + logger: logger, + log: log, + + registerHelper: function(name, fn) { + if (toString.call(name) === objectType) { + if (fn) { throw new Exception('Arg not supported with multiple helpers'); } + Utils.extend(this.helpers, name); + } else { + this.helpers[name] = fn; + } + }, + unregisterHelper: function(name) { + delete this.helpers[name]; + }, + + registerPartial: function(name, partial) { + if (toString.call(name) === objectType) { + Utils.extend(this.partials, name); + } else { + this.partials[name] = partial; + } + }, + unregisterPartial: function(name) { + delete this.partials[name]; + } + }; + + function registerDefaultHelpers(instance) { + instance.registerHelper('helperMissing', function(/* [args, ]options */) { + if(arguments.length === 1) { + // A missing field in a {{foo}} constuct. + return undefined; + } else { + // Someone is actually trying to call something, blow up. + throw new Exception("Missing helper: '" + arguments[arguments.length-1].name + "'"); + } + }); + + instance.registerHelper('blockHelperMissing', function(context, options) { + var inverse = options.inverse, + fn = options.fn; + + if(context === true) { + return fn(this); + } else if(context === false || context == null) { + return inverse(this); + } else if (isArray(context)) { + if(context.length > 0) { + if (options.ids) { + options.ids = [options.name]; + } + + return instance.helpers.each(context, options); + } else { + return inverse(this); + } + } else { + if (options.data && options.ids) { + var data = createFrame(options.data); + data.contextPath = Utils.appendContextPath(options.data.contextPath, options.name); + options = {data: data}; + } + + return fn(context, options); + } + }); + + instance.registerHelper('each', function(context, options) { + if (!options) { + throw new Exception('Must pass iterator to #each'); + } + + var fn = options.fn, inverse = options.inverse; + var i = 0, ret = "", data; + + var contextPath; + if (options.data && options.ids) { + contextPath = Utils.appendContextPath(options.data.contextPath, options.ids[0]) + '.'; + } + + if (isFunction(context)) { context = context.call(this); } + + if (options.data) { + data = createFrame(options.data); + } + + if(context && typeof context === 'object') { + if (isArray(context)) { + for(var j = context.length; i= 0; + // adding 1 corrects loss of precision from parseFloat (#15100) + return !jQuery.isArray( obj ) && (obj - parseFloat( obj ) + 1) >= 0; }, isEmptyObject: function( obj ) { @@ -584,14 +585,14 @@ function isArraylike( obj ) { } var Sizzle = /*! - * Sizzle CSS Selector Engine v1.10.19 + * Sizzle CSS Selector Engine v2.2.0-pre * http://sizzlejs.com/ * - * Copyright 2013 jQuery Foundation, Inc. and other contributors + * Copyright 2008, 2014 jQuery Foundation, Inc. and other contributors * Released under the MIT license * http://jquery.org/license * - * Date: 2014-04-18 + * Date: 2014-12-16 */ (function( window ) { @@ -618,7 +619,7 @@ var i, contains, // Instance-specific data - expando = "sizzle" + -(new Date()), + expando = "sizzle" + 1 * new Date(), preferredDoc = window.document, dirruns = 0, done = 0, @@ -633,7 +634,6 @@ var i, }, // General-purpose constants - strundefined = typeof undefined, MAX_NEGATIVE = 1 << 31, // Instance methods @@ -643,12 +643,13 @@ var i, push_native = arr.push, push = arr.push, slice = arr.slice, - // Use a stripped-down indexOf if we can't use a native one - indexOf = arr.indexOf || function( elem ) { + // Use a stripped-down indexOf as it's faster than native + // http://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { var i = 0, - len = this.length; + len = list.length; for ( ; i < len; i++ ) { - if ( this[i] === elem ) { + if ( list[i] === elem ) { return i; } } @@ -688,6 +689,7 @@ var i, ")\\)|)", // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ), rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), @@ -739,6 +741,14 @@ var i, String.fromCharCode( high + 0x10000 ) : // Supplemental Plane codepoint (surrogate pair) String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); }; // Optimize for push.apply( _, NodeList ) @@ -781,19 +791,18 @@ function Sizzle( selector, context, results, seed ) { context = context || document; results = results || []; + nodeType = context.nodeType; + + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { - if ( !selector || typeof selector !== "string" ) { return results; } - if ( (nodeType = context.nodeType) !== 1 && nodeType !== 9 ) { - return []; - } + if ( !seed && documentIsHTML ) { - if ( documentIsHTML && !seed ) { - - // Shortcuts - if ( (match = rquickExpr.exec( selector )) ) { + // Try to shortcut find operations when possible (e.g., not under DocumentFragment) + if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) { // Speed-up: Sizzle("#ID") if ( (m = match[1]) ) { if ( nodeType === 9 ) { @@ -825,7 +834,7 @@ function Sizzle( selector, context, results, seed ) { return results; // Speed-up: Sizzle(".CLASS") - } else if ( (m = match[3]) && support.getElementsByClassName && context.getElementsByClassName ) { + } else if ( (m = match[3]) && support.getElementsByClassName ) { push.apply( results, context.getElementsByClassName( m ) ); return results; } @@ -835,7 +844,7 @@ function Sizzle( selector, context, results, seed ) { if ( support.qsa && (!rbuggyQSA || !rbuggyQSA.test( selector )) ) { nid = old = expando; newContext = context; - newSelector = nodeType === 9 && selector; + newSelector = nodeType !== 1 && selector; // qSA works strangely on Element-rooted queries // We can work around this by specifying an extra ID on the root @@ -1022,7 +1031,7 @@ function createPositionalPseudo( fn ) { * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value */ function testContext( context ) { - return context && typeof context.getElementsByTagName !== strundefined && context; + return context && typeof context.getElementsByTagName !== "undefined" && context; } // Expose support vars for convenience @@ -1046,9 +1055,8 @@ isXML = Sizzle.isXML = function( elem ) { * @returns {Object} Returns the current document */ setDocument = Sizzle.setDocument = function( node ) { - var hasCompare, - doc = node ? node.ownerDocument || node : preferredDoc, - parent = doc.defaultView; + var hasCompare, parent, + doc = node ? node.ownerDocument || node : preferredDoc; // If no document and documentElement is available, return if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) { @@ -1058,9 +1066,7 @@ setDocument = Sizzle.setDocument = function( node ) { // Set our document document = doc; docElem = doc.documentElement; - - // Support tests - documentIsHTML = !isXML( doc ); + parent = doc.defaultView; // Support: IE>8 // If iframe document is assigned to "document" variable and if iframe has been reloaded, @@ -1069,21 +1075,22 @@ setDocument = Sizzle.setDocument = function( node ) { if ( parent && parent !== parent.top ) { // IE11 does not have attachEvent, so all must suffer if ( parent.addEventListener ) { - parent.addEventListener( "unload", function() { - setDocument(); - }, false ); + parent.addEventListener( "unload", unloadHandler, false ); } else if ( parent.attachEvent ) { - parent.attachEvent( "onunload", function() { - setDocument(); - }); + parent.attachEvent( "onunload", unloadHandler ); } } + /* Support tests + ---------------------------------------------------------------------- */ + documentIsHTML = !isXML( doc ); + /* Attributes ---------------------------------------------------------------------- */ // Support: IE<8 - // Verify that getAttribute really returns attributes and not properties (excepting IE8 booleans) + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) support.attributes = assert(function( div ) { div.className = "i"; return !div.getAttribute("className"); @@ -1098,17 +1105,8 @@ setDocument = Sizzle.setDocument = function( node ) { return !div.getElementsByTagName("*").length; }); - // Check if getElementsByClassName can be trusted - support.getElementsByClassName = rnative.test( doc.getElementsByClassName ) && assert(function( div ) { - div.innerHTML = "
"; - - // Support: Safari<4 - // Catch class over-caching - div.firstChild.className = "i"; - // Support: Opera<10 - // Catch gEBCN failure to find non-leading classes - return div.getElementsByClassName("i").length === 2; - }); + // Support: IE<9 + support.getElementsByClassName = rnative.test( doc.getElementsByClassName ); // Support: IE<10 // Check if getElementById returns elements by name @@ -1122,7 +1120,7 @@ setDocument = Sizzle.setDocument = function( node ) { // ID find and filter if ( support.getById ) { Expr.find["ID"] = function( id, context ) { - if ( typeof context.getElementById !== strundefined && documentIsHTML ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { var m = context.getElementById( id ); // Check parentNode to catch when Blackberry 4.6 returns // nodes that are no longer in the document #6963 @@ -1143,7 +1141,7 @@ setDocument = Sizzle.setDocument = function( node ) { Expr.filter["ID"] = function( id ) { var attrId = id.replace( runescape, funescape ); return function( elem ) { - var node = typeof elem.getAttributeNode !== strundefined && elem.getAttributeNode("id"); + var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id"); return node && node.value === attrId; }; }; @@ -1152,14 +1150,20 @@ setDocument = Sizzle.setDocument = function( node ) { // Tag Expr.find["TAG"] = support.getElementsByTagName ? function( tag, context ) { - if ( typeof context.getElementsByTagName !== strundefined ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); } } : + function( tag, context ) { var elem, tmp = [], i = 0, + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too results = context.getElementsByTagName( tag ); // Filter out possible comments @@ -1177,7 +1181,7 @@ setDocument = Sizzle.setDocument = function( node ) { // Class Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) { - if ( typeof context.getElementsByClassName !== strundefined && documentIsHTML ) { + if ( documentIsHTML ) { return context.getElementsByClassName( className ); } }; @@ -1206,13 +1210,15 @@ setDocument = Sizzle.setDocument = function( node ) { // setting a boolean content attribute, // since its presence should be enough // http://bugs.jquery.com/ticket/12359 - div.innerHTML = ""; + docElem.appendChild( div ).innerHTML = "" + + ""; // Support: IE8, Opera 11-12.16 // Nothing should be selected when empty strings follow ^= or $= or *= // The test attribute must be unknown in Opera but "safe" for WinRT // http://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section - if ( div.querySelectorAll("[msallowclip^='']").length ) { + if ( div.querySelectorAll("[msallowcapture^='']").length ) { rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); } @@ -1222,12 +1228,24 @@ setDocument = Sizzle.setDocument = function( node ) { rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); } + // Support: Chrome<29, Android<4.2+, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.7+ + if ( !div.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push("~="); + } + // Webkit/Opera - :checked should return selected option elements // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked // IE8 throws error here and will not see later tests if ( !div.querySelectorAll(":checked").length ) { rbuggyQSA.push(":checked"); } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibing-combinator selector` fails + if ( !div.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push(".#.+[+~]"); + } }); assert(function( div ) { @@ -1344,7 +1362,7 @@ setDocument = Sizzle.setDocument = function( node ) { // Maintain original order return sortInput ? - ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : 0; } @@ -1371,7 +1389,7 @@ setDocument = Sizzle.setDocument = function( node ) { aup ? -1 : bup ? 1 : sortInput ? - ( indexOf.call( sortInput, a ) - indexOf.call( sortInput, b ) ) : + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : 0; // If the nodes are siblings, we can do a quick check @@ -1434,7 +1452,7 @@ Sizzle.matchesSelector = function( elem, expr ) { elem.document && elem.document.nodeType !== 11 ) { return ret; } - } catch(e) {} + } catch (e) {} } return Sizzle( expr, document, null, [ elem ] ).length > 0; @@ -1653,7 +1671,7 @@ Expr = Sizzle.selectors = { return pattern || (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) && classCache( className, function( elem ) { - return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== strundefined && elem.getAttribute("class") || "" ); + return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" ); }); }, @@ -1675,7 +1693,7 @@ Expr = Sizzle.selectors = { operator === "^=" ? check && result.indexOf( check ) === 0 : operator === "*=" ? check && result.indexOf( check ) > -1 : operator === "$=" ? check && result.slice( -check.length ) === check : - operator === "~=" ? ( " " + result + " " ).indexOf( check ) > -1 : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : false; }; @@ -1795,7 +1813,7 @@ Expr = Sizzle.selectors = { matched = fn( seed, argument ), i = matched.length; while ( i-- ) { - idx = indexOf.call( seed, matched[i] ); + idx = indexOf( seed, matched[i] ); seed[ idx ] = !( matches[ idx ] = matched[i] ); } }) : @@ -1834,6 +1852,8 @@ Expr = Sizzle.selectors = { function( elem, context, xml ) { input[0] = elem; matcher( input, null, xml, results ); + // Don't keep the element (issue #299) + input[0] = null; return !results.pop(); }; }), @@ -1845,6 +1865,7 @@ Expr = Sizzle.selectors = { }), "contains": markFunction(function( text ) { + text = text.replace( runescape, funescape ); return function( elem ) { return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1; }; @@ -2266,7 +2287,7 @@ function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postS i = matcherOut.length; while ( i-- ) { if ( (elem = matcherOut[i]) && - (temp = postFinder ? indexOf.call( seed, elem ) : preMap[i]) > -1 ) { + (temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) { seed[temp] = !(results[temp] = elem); } @@ -2301,13 +2322,16 @@ function matcherFromTokens( tokens ) { return elem === checkContext; }, implicitRelative, true ), matchAnyContext = addCombinator( function( elem ) { - return indexOf.call( checkContext, elem ) > -1; + return indexOf( checkContext, elem ) > -1; }, implicitRelative, true ), matchers = [ function( elem, context, xml ) { - return ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( (checkContext = context).nodeType ? matchContext( elem, context, xml ) : matchAnyContext( elem, context, xml ) ); + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; } ]; for ( ; i < len; i++ ) { @@ -2557,7 +2581,7 @@ select = Sizzle.select = function( selector, context, results, seed ) { // Sort stability support.sortStable = expando.split("").sort( sortOrder ).join("") === expando; -// Support: Chrome<14 +// Support: Chrome 14-35+ // Always assume duplicates if they aren't passed to the comparison function support.detectDuplicates = !!hasDuplicate; @@ -6115,7 +6139,14 @@ var getStyles, curCSS, if ( window.getComputedStyle ) { getStyles = function( elem ) { - return elem.ownerDocument.defaultView.getComputedStyle( elem, null ); + // Support: IE<=11+, Firefox<=30+ (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + if ( elem.ownerDocument.defaultView.opener ) { + return elem.ownerDocument.defaultView.getComputedStyle( elem, null ); + } + + return window.getComputedStyle( elem, null ); }; curCSS = function( elem, name, computed ) { @@ -6363,6 +6394,8 @@ function addGetHookIf( conditionFn, hookFn ) { reliableMarginRightVal = !parseFloat( ( window.getComputedStyle( contents, null ) || {} ).marginRight ); + + div.removeChild( contents ); } // Support: IE8 @@ -9070,7 +9103,8 @@ jQuery.extend({ } // We can fire global events as of now if asked to - fireGlobals = s.global; + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; // Watch for a new set of requests if ( fireGlobals && jQuery.active++ === 0 ) { @@ -9329,13 +9363,6 @@ jQuery.each( [ "get", "post" ], function( i, method ) { }; }); -// Attach a bunch of functions for handling common AJAX events -jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) { - jQuery.fn[ type ] = function( fn ) { - return this.on( type, fn ); - }; -}); - jQuery._evalUrl = function( url ) { return jQuery.ajax({ @@ -9561,8 +9588,9 @@ var xhrId = 0, // Support: IE<10 // Open requests must be manually aborted on unload (#5280) -if ( window.ActiveXObject ) { - jQuery( window ).on( "unload", function() { +// See https://support.microsoft.com/kb/2856746 for more info +if ( window.attachEvent ) { + window.attachEvent( "onunload", function() { for ( var key in xhrCallbacks ) { xhrCallbacks[ key ]( undefined, true ); } @@ -9996,6 +10024,16 @@ jQuery.fn.load = function( url, params, callback ) { +// Attach a bunch of functions for handling common AJAX events +jQuery.each( [ "ajaxStart", "ajaxStop", "ajaxComplete", "ajaxError", "ajaxSuccess", "ajaxSend" ], function( i, type ) { + jQuery.fn[ type ] = function( fn ) { + return this.on( type, fn ); + }; +}); + + + + jQuery.expr.filters.animated = function( elem ) { return jQuery.grep(jQuery.timers, function( fn ) { return elem === fn.elem; diff --git a/client/galaxy/scripts/libs/lunr.js b/client/galaxy/scripts/libs/lunr.js new file mode 100644 index 00000000000..b5bacd97960 --- /dev/null +++ b/client/galaxy/scripts/libs/lunr.js @@ -0,0 +1,1910 @@ +/** + * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 0.5.7 + * Copyright (C) 2014 Oliver Nightingale + * MIT Licensed + * @license + */ + +(function(){ + +/** + * Convenience function for instantiating a new lunr index and configuring it + * with the default pipeline functions and the passed config function. + * + * When using this convenience function a new index will be created with the + * following functions already in the pipeline: + * + * lunr.StopWordFilter - filters out any stop words before they enter the + * index + * + * lunr.stemmer - stems the tokens before entering the index. + * + * Example: + * + * var idx = lunr(function () { + * this.field('title', 10) + * this.field('tags', 100) + * this.field('body') + * + * this.ref('cid') + * + * this.pipeline.add(function () { + * // some custom pipeline function + * }) + * + * }) + * + * @param {Function} config A function that will be called with the new instance + * of the lunr.Index as both its context and first parameter. It can be used to + * customize the instance of new lunr.Index. + * @namespace + * @module + * @returns {lunr.Index} + * + */ +var lunr = function (config) { + var idx = new lunr.Index + + idx.pipeline.add( + lunr.trimmer, + lunr.stopWordFilter, + lunr.stemmer + ) + + if (config) config.call(idx, idx) + + return idx +} + +lunr.version = "0.5.7" +/*! + * lunr.utils + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * A namespace containing utils for the rest of the lunr library + */ +lunr.utils = {} + +/** + * Print a warning message to the console. + * + * @param {String} message The message to be printed. + * @memberOf Utils + */ +lunr.utils.warn = (function (global) { + return function (message) { + if (global.console && console.warn) { + console.warn(message) + } + } +})(this) + +/*! + * lunr.EventEmitter + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.EventEmitter is an event emitter for lunr. It manages adding and removing event handlers and triggering events and their handlers. + * + * @constructor + */ +lunr.EventEmitter = function () { + this.events = {} +} + +/** + * Binds a handler function to a specific event(s). + * + * Can bind a single function to many different events in one call. + * + * @param {String} [eventName] The name(s) of events to bind this function to. + * @param {Function} handler The function to call when an event is fired. + * @memberOf EventEmitter + */ +lunr.EventEmitter.prototype.addListener = function () { + var args = Array.prototype.slice.call(arguments), + fn = args.pop(), + names = args + + if (typeof fn !== "function") throw new TypeError ("last argument must be a function") + + names.forEach(function (name) { + if (!this.hasHandler(name)) this.events[name] = [] + this.events[name].push(fn) + }, this) +} + +/** + * Removes a handler function from a specific event. + * + * @param {String} eventName The name of the event to remove this function from. + * @param {Function} handler The function to remove from an event. + * @memberOf EventEmitter + */ +lunr.EventEmitter.prototype.removeListener = function (name, fn) { + if (!this.hasHandler(name)) return + + var fnIndex = this.events[name].indexOf(fn) + this.events[name].splice(fnIndex, 1) + + if (!this.events[name].length) delete this.events[name] +} + +/** + * Calls all functions bound to the given event. + * + * Additional data can be passed to the event handler as arguments to `emit` + * after the event name. + * + * @param {String} eventName The name of the event to emit. + * @memberOf EventEmitter + */ +lunr.EventEmitter.prototype.emit = function (name) { + if (!this.hasHandler(name)) return + + var args = Array.prototype.slice.call(arguments, 1) + + this.events[name].forEach(function (fn) { + fn.apply(undefined, args) + }) +} + +/** + * Checks whether a handler has ever been stored against an event. + * + * @param {String} eventName The name of the event to check. + * @private + * @memberOf EventEmitter + */ +lunr.EventEmitter.prototype.hasHandler = function (name) { + return name in this.events +} + +/*! + * lunr.tokenizer + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * A function for splitting a string into tokens ready to be inserted into + * the search index. + * + * @module + * @param {String} obj The string to convert into tokens + * @returns {Array} + */ +lunr.tokenizer = function (obj) { + if (!arguments.length || obj == null || obj == undefined) return [] + if (Array.isArray(obj)) return obj.map(function (t) { return t.toLowerCase() }) + + var str = obj.toString().replace(/^\s+/, '') + + for (var i = str.length - 1; i >= 0; i--) { + if (/\S/.test(str.charAt(i))) { + str = str.substring(0, i + 1) + break + } + } + + return str + .split(/(?:\s+|\-)/) + .filter(function (token) { + return !!token + }) + .map(function (token) { + return token.toLowerCase() + }) +} +/*! + * lunr.Pipeline + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.Pipelines maintain an ordered list of functions to be applied to all + * tokens in documents entering the search index and queries being ran against + * the index. + * + * An instance of lunr.Index created with the lunr shortcut will contain a + * pipeline with a stop word filter and an English language stemmer. Extra + * functions can be added before or after either of these functions or these + * default functions can be removed. + * + * When run the pipeline will call each function in turn, passing a token, the + * index of that token in the original list of all tokens and finally a list of + * all the original tokens. + * + * The output of functions in the pipeline will be passed to the next function + * in the pipeline. To exclude a token from entering the index the function + * should return undefined, the rest of the pipeline will not be called with + * this token. + * + * For serialisation of pipelines to work, all functions used in an instance of + * a pipeline should be registered with lunr.Pipeline. Registered functions can + * then be loaded. If trying to load a serialised pipeline that uses functions + * that are not registered an error will be thrown. + * + * If not planning on serialising the pipeline then registering pipeline functions + * is not necessary. + * + * @constructor + */ +lunr.Pipeline = function () { + this._stack = [] +} + +lunr.Pipeline.registeredFunctions = {} + +/** + * Register a function with the pipeline. + * + * Functions that are used in the pipeline should be registered if the pipeline + * needs to be serialised, or a serialised pipeline needs to be loaded. + * + * Registering a function does not add it to a pipeline, functions must still be + * added to instances of the pipeline for them to be used when running a pipeline. + * + * @param {Function} fn The function to check for. + * @param {String} label The label to register this function with + * @memberOf Pipeline + */ +lunr.Pipeline.registerFunction = function (fn, label) { + if (label in this.registeredFunctions) { + lunr.utils.warn('Overwriting existing registered function: ' + label) + } + + fn.label = label + lunr.Pipeline.registeredFunctions[fn.label] = fn +} + +/** + * Warns if the function is not registered as a Pipeline function. + * + * @param {Function} fn The function to check for. + * @private + * @memberOf Pipeline + */ +lunr.Pipeline.warnIfFunctionNotRegistered = function (fn) { + var isRegistered = fn.label && (fn.label in this.registeredFunctions) + + if (!isRegistered) { + lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\n', fn) + } +} + +/** + * Loads a previously serialised pipeline. + * + * All functions to be loaded must already be registered with lunr.Pipeline. + * If any function from the serialised data has not been registered then an + * error will be thrown. + * + * @param {Object} serialised The serialised pipeline to load. + * @returns {lunr.Pipeline} + * @memberOf Pipeline + */ +lunr.Pipeline.load = function (serialised) { + var pipeline = new lunr.Pipeline + + serialised.forEach(function (fnName) { + var fn = lunr.Pipeline.registeredFunctions[fnName] + + if (fn) { + pipeline.add(fn) + } else { + throw new Error ('Cannot load un-registered function: ' + fnName) + } + }) + + return pipeline +} + +/** + * Adds new functions to the end of the pipeline. + * + * Logs a warning if the function has not been registered. + * + * @param {Function} functions Any number of functions to add to the pipeline. + * @memberOf Pipeline + */ +lunr.Pipeline.prototype.add = function () { + var fns = Array.prototype.slice.call(arguments) + + fns.forEach(function (fn) { + lunr.Pipeline.warnIfFunctionNotRegistered(fn) + this._stack.push(fn) + }, this) +} + +/** + * Adds a single function after a function that already exists in the + * pipeline. + * + * Logs a warning if the function has not been registered. + * + * @param {Function} existingFn A function that already exists in the pipeline. + * @param {Function} newFn The new function to add to the pipeline. + * @memberOf Pipeline + */ +lunr.Pipeline.prototype.after = function (existingFn, newFn) { + lunr.Pipeline.warnIfFunctionNotRegistered(newFn) + + var pos = this._stack.indexOf(existingFn) + 1 + this._stack.splice(pos, 0, newFn) +} + +/** + * Adds a single function before a function that already exists in the + * pipeline. + * + * Logs a warning if the function has not been registered. + * + * @param {Function} existingFn A function that already exists in the pipeline. + * @param {Function} newFn The new function to add to the pipeline. + * @memberOf Pipeline + */ +lunr.Pipeline.prototype.before = function (existingFn, newFn) { + lunr.Pipeline.warnIfFunctionNotRegistered(newFn) + + var pos = this._stack.indexOf(existingFn) + this._stack.splice(pos, 0, newFn) +} + +/** + * Removes a function from the pipeline. + * + * @param {Function} fn The function to remove from the pipeline. + * @memberOf Pipeline + */ +lunr.Pipeline.prototype.remove = function (fn) { + var pos = this._stack.indexOf(fn) + this._stack.splice(pos, 1) +} + +/** + * Runs the current list of functions that make up the pipeline against the + * passed tokens. + * + * @param {Array} tokens The tokens to run through the pipeline. + * @returns {Array} + * @memberOf Pipeline + */ +lunr.Pipeline.prototype.run = function (tokens) { + var out = [], + tokenLength = tokens.length, + stackLength = this._stack.length + + for (var i = 0; i < tokenLength; i++) { + var token = tokens[i] + + for (var j = 0; j < stackLength; j++) { + token = this._stack[j](token, i, tokens) + if (token === void 0) break + }; + + if (token !== void 0) out.push(token) + }; + + return out +} + +/** + * Resets the pipeline by removing any existing processors. + * + * @memberOf Pipeline + */ +lunr.Pipeline.prototype.reset = function () { + this._stack = [] +} + +/** + * Returns a representation of the pipeline ready for serialisation. + * + * Logs a warning if the function has not been registered. + * + * @returns {Array} + * @memberOf Pipeline + */ +lunr.Pipeline.prototype.toJSON = function () { + return this._stack.map(function (fn) { + lunr.Pipeline.warnIfFunctionNotRegistered(fn) + + return fn.label + }) +} +/*! + * lunr.Vector + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.Vectors implement vector related operations for + * a series of elements. + * + * @constructor + */ +lunr.Vector = function () { + this._magnitude = null + this.list = undefined + this.length = 0 +} + +/** + * lunr.Vector.Node is a simple struct for each node + * in a lunr.Vector. + * + * @private + * @param {Number} The index of the node in the vector. + * @param {Object} The data at this node in the vector. + * @param {lunr.Vector.Node} The node directly after this node in the vector. + * @constructor + * @memberOf Vector + */ +lunr.Vector.Node = function (idx, val, next) { + this.idx = idx + this.val = val + this.next = next +} + +/** + * Inserts a new value at a position in a vector. + * + * @param {Number} The index at which to insert a value. + * @param {Object} The object to insert in the vector. + * @memberOf Vector. + */ +lunr.Vector.prototype.insert = function (idx, val) { + var list = this.list + + if (!list) { + this.list = new lunr.Vector.Node (idx, val, list) + return this.length++ + } + + var prev = list, + next = list.next + + while (next != undefined) { + if (idx < next.idx) { + prev.next = new lunr.Vector.Node (idx, val, next) + return this.length++ + } + + prev = next, next = next.next + } + + prev.next = new lunr.Vector.Node (idx, val, next) + return this.length++ +} + +/** + * Calculates the magnitude of this vector. + * + * @returns {Number} + * @memberOf Vector + */ +lunr.Vector.prototype.magnitude = function () { + if (this._magniture) return this._magnitude + var node = this.list, + sumOfSquares = 0, + val + + while (node) { + val = node.val + sumOfSquares += val * val + node = node.next + } + + return this._magnitude = Math.sqrt(sumOfSquares) +} + +/** + * Calculates the dot product of this vector and another vector. + * + * @param {lunr.Vector} otherVector The vector to compute the dot product with. + * @returns {Number} + * @memberOf Vector + */ +lunr.Vector.prototype.dot = function (otherVector) { + var node = this.list, + otherNode = otherVector.list, + dotProduct = 0 + + while (node && otherNode) { + if (node.idx < otherNode.idx) { + node = node.next + } else if (node.idx > otherNode.idx) { + otherNode = otherNode.next + } else { + dotProduct += node.val * otherNode.val + node = node.next + otherNode = otherNode.next + } + } + + return dotProduct +} + +/** + * Calculates the cosine similarity between this vector and another + * vector. + * + * @param {lunr.Vector} otherVector The other vector to calculate the + * similarity with. + * @returns {Number} + * @memberOf Vector + */ +lunr.Vector.prototype.similarity = function (otherVector) { + return this.dot(otherVector) / (this.magnitude() * otherVector.magnitude()) +} +/*! + * lunr.SortedSet + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.SortedSets are used to maintain an array of uniq values in a sorted + * order. + * + * @constructor + */ +lunr.SortedSet = function () { + this.length = 0 + this.elements = [] +} + +/** + * Loads a previously serialised sorted set. + * + * @param {Array} serialisedData The serialised set to load. + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.load = function (serialisedData) { + var set = new this + + set.elements = serialisedData + set.length = serialisedData.length + + return set +} + +/** + * Inserts new items into the set in the correct position to maintain the + * order. + * + * @param {Object} The objects to add to this set. + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.add = function () { + Array.prototype.slice.call(arguments).forEach(function (element) { + if (~this.indexOf(element)) return + this.elements.splice(this.locationFor(element), 0, element) + }, this) + + this.length = this.elements.length +} + +/** + * Converts this sorted set into an array. + * + * @returns {Array} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.toArray = function () { + return this.elements.slice() +} + +/** + * Creates a new array with the results of calling a provided function on every + * element in this sorted set. + * + * Delegates to Array.prototype.map and has the same signature. + * + * @param {Function} fn The function that is called on each element of the + * set. + * @param {Object} ctx An optional object that can be used as the context + * for the function fn. + * @returns {Array} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.map = function (fn, ctx) { + return this.elements.map(fn, ctx) +} + +/** + * Executes a provided function once per sorted set element. + * + * Delegates to Array.prototype.forEach and has the same signature. + * + * @param {Function} fn The function that is called on each element of the + * set. + * @param {Object} ctx An optional object that can be used as the context + * @memberOf SortedSet + * for the function fn. + */ +lunr.SortedSet.prototype.forEach = function (fn, ctx) { + return this.elements.forEach(fn, ctx) +} + +/** + * Returns the index at which a given element can be found in the + * sorted set, or -1 if it is not present. + * + * @param {Object} elem The object to locate in the sorted set. + * @param {Number} start An optional index at which to start searching from + * within the set. + * @param {Number} end An optional index at which to stop search from within + * the set. + * @returns {Number} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.indexOf = function (elem, start, end) { + var start = start || 0, + end = end || this.elements.length, + sectionLength = end - start, + pivot = start + Math.floor(sectionLength / 2), + pivotElem = this.elements[pivot] + + if (sectionLength <= 1) { + if (pivotElem === elem) { + return pivot + } else { + return -1 + } + } + + if (pivotElem < elem) return this.indexOf(elem, pivot, end) + if (pivotElem > elem) return this.indexOf(elem, start, pivot) + if (pivotElem === elem) return pivot +} + +/** + * Returns the position within the sorted set that an element should be + * inserted at to maintain the current order of the set. + * + * This function assumes that the element to search for does not already exist + * in the sorted set. + * + * @param {Object} elem The elem to find the position for in the set + * @param {Number} start An optional index at which to start searching from + * within the set. + * @param {Number} end An optional index at which to stop search from within + * the set. + * @returns {Number} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.locationFor = function (elem, start, end) { + var start = start || 0, + end = end || this.elements.length, + sectionLength = end - start, + pivot = start + Math.floor(sectionLength / 2), + pivotElem = this.elements[pivot] + + if (sectionLength <= 1) { + if (pivotElem > elem) return pivot + if (pivotElem < elem) return pivot + 1 + } + + if (pivotElem < elem) return this.locationFor(elem, pivot, end) + if (pivotElem > elem) return this.locationFor(elem, start, pivot) +} + +/** + * Creates a new lunr.SortedSet that contains the elements in the intersection + * of this set and the passed set. + * + * @param {lunr.SortedSet} otherSet The set to intersect with this set. + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.intersect = function (otherSet) { + var intersectSet = new lunr.SortedSet, + i = 0, j = 0, + a_len = this.length, b_len = otherSet.length, + a = this.elements, b = otherSet.elements + + while (true) { + if (i > a_len - 1 || j > b_len - 1) break + + if (a[i] === b[j]) { + intersectSet.add(a[i]) + i++, j++ + continue + } + + if (a[i] < b[j]) { + i++ + continue + } + + if (a[i] > b[j]) { + j++ + continue + } + }; + + return intersectSet +} + +/** + * Makes a copy of this set + * + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.clone = function () { + var clone = new lunr.SortedSet + + clone.elements = this.toArray() + clone.length = clone.elements.length + + return clone +} + +/** + * Creates a new lunr.SortedSet that contains the elements in the union + * of this set and the passed set. + * + * @param {lunr.SortedSet} otherSet The set to union with this set. + * @returns {lunr.SortedSet} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.union = function (otherSet) { + var longSet, shortSet, unionSet + + if (this.length >= otherSet.length) { + longSet = this, shortSet = otherSet + } else { + longSet = otherSet, shortSet = this + } + + unionSet = longSet.clone() + + unionSet.add.apply(unionSet, shortSet.toArray()) + + return unionSet +} + +/** + * Returns a representation of the sorted set ready for serialisation. + * + * @returns {Array} + * @memberOf SortedSet + */ +lunr.SortedSet.prototype.toJSON = function () { + return this.toArray() +} +/*! + * lunr.Index + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.Index is object that manages a search index. It contains the indexes + * and stores all the tokens and document lookups. It also provides the main + * user facing API for the library. + * + * @constructor + */ +lunr.Index = function () { + this._fields = [] + this._ref = 'id' + this.pipeline = new lunr.Pipeline + this.documentStore = new lunr.Store + this.tokenStore = new lunr.TokenStore + this.corpusTokens = new lunr.SortedSet + this.eventEmitter = new lunr.EventEmitter + + this._idfCache = {} + + this.on('add', 'remove', 'update', (function () { + this._idfCache = {} + }).bind(this)) +} + +/** + * Bind a handler to events being emitted by the index. + * + * The handler can be bound to many events at the same time. + * + * @param {String} [eventName] The name(s) of events to bind the function to. + * @param {Function} handler The serialised set to load. + * @memberOf Index + */ +lunr.Index.prototype.on = function () { + var args = Array.prototype.slice.call(arguments) + return this.eventEmitter.addListener.apply(this.eventEmitter, args) +} + +/** + * Removes a handler from an event being emitted by the index. + * + * @param {String} eventName The name of events to remove the function from. + * @param {Function} handler The serialised set to load. + * @memberOf Index + */ +lunr.Index.prototype.off = function (name, fn) { + return this.eventEmitter.removeListener(name, fn) +} + +/** + * Loads a previously serialised index. + * + * Issues a warning if the index being imported was serialised + * by a different version of lunr. + * + * @param {Object} serialisedData The serialised set to load. + * @returns {lunr.Index} + * @memberOf Index + */ +lunr.Index.load = function (serialisedData) { + if (serialisedData.version !== lunr.version) { + lunr.utils.warn('version mismatch: current ' + lunr.version + ' importing ' + serialisedData.version) + } + + var idx = new this + + idx._fields = serialisedData.fields + idx._ref = serialisedData.ref + + idx.documentStore = lunr.Store.load(serialisedData.documentStore) + idx.tokenStore = lunr.TokenStore.load(serialisedData.tokenStore) + idx.corpusTokens = lunr.SortedSet.load(serialisedData.corpusTokens) + idx.pipeline = lunr.Pipeline.load(serialisedData.pipeline) + + return idx +} + +/** + * Adds a field to the list of fields that will be searchable within documents + * in the index. + * + * An optional boost param can be passed to affect how much tokens in this field + * rank in search results, by default the boost value is 1. + * + * Fields should be added before any documents are added to the index, fields + * that are added after documents are added to the index will only apply to new + * documents added to the index. + * + * @param {String} fieldName The name of the field within the document that + * should be indexed + * @param {Number} boost An optional boost that can be applied to terms in this + * field. + * @returns {lunr.Index} + * @memberOf Index + */ +lunr.Index.prototype.field = function (fieldName, opts) { + var opts = opts || {}, + field = { name: fieldName, boost: opts.boost || 1 } + + this._fields.push(field) + return this +} + +/** + * Sets the property used to uniquely identify documents added to the index, + * by default this property is 'id'. + * + * This should only be changed before adding documents to the index, changing + * the ref property without resetting the index can lead to unexpected results. + * + * @param {String} refName The property to use to uniquely identify the + * documents in the index. + * @param {Boolean} emitEvent Whether to emit add events, defaults to true + * @returns {lunr.Index} + * @memberOf Index + */ +lunr.Index.prototype.ref = function (refName) { + this._ref = refName + return this +} + +/** + * Add a document to the index. + * + * This is the way new documents enter the index, this function will run the + * fields from the document through the index's pipeline and then add it to + * the index, it will then show up in search results. + * + * An 'add' event is emitted with the document that has been added and the index + * the document has been added to. This event can be silenced by passing false + * as the second argument to add. + * + * @param {Object} doc The document to add to the index. + * @param {Boolean} emitEvent Whether or not to emit events, default true. + * @memberOf Index + */ +lunr.Index.prototype.add = function (doc, emitEvent) { + var docTokens = {}, + allDocumentTokens = new lunr.SortedSet, + docRef = doc[this._ref], + emitEvent = emitEvent === undefined ? true : emitEvent + + this._fields.forEach(function (field) { + var fieldTokens = this.pipeline.run(lunr.tokenizer(doc[field.name])) + + docTokens[field.name] = fieldTokens + lunr.SortedSet.prototype.add.apply(allDocumentTokens, fieldTokens) + }, this) + + this.documentStore.set(docRef, allDocumentTokens) + lunr.SortedSet.prototype.add.apply(this.corpusTokens, allDocumentTokens.toArray()) + + for (var i = 0; i < allDocumentTokens.length; i++) { + var token = allDocumentTokens.elements[i] + var tf = this._fields.reduce(function (memo, field) { + var fieldLength = docTokens[field.name].length + + if (!fieldLength) return memo + + var tokenCount = docTokens[field.name].filter(function (t) { return t === token }).length + + return memo + (tokenCount / fieldLength * field.boost) + }, 0) + + this.tokenStore.add(token, { ref: docRef, tf: tf }) + }; + + if (emitEvent) this.eventEmitter.emit('add', doc, this) +} + +/** + * Removes a document from the index. + * + * To make sure documents no longer show up in search results they can be + * removed from the index using this method. + * + * The document passed only needs to have the same ref property value as the + * document that was added to the index, they could be completely different + * objects. + * + * A 'remove' event is emitted with the document that has been removed and the index + * the document has been removed from. This event can be silenced by passing false + * as the second argument to remove. + * + * @param {Object} doc The document to remove from the index. + * @param {Boolean} emitEvent Whether to emit remove events, defaults to true + * @memberOf Index + */ +lunr.Index.prototype.remove = function (doc, emitEvent) { + var docRef = doc[this._ref], + emitEvent = emitEvent === undefined ? true : emitEvent + + if (!this.documentStore.has(docRef)) return + + var docTokens = this.documentStore.get(docRef) + + this.documentStore.remove(docRef) + + docTokens.forEach(function (token) { + this.tokenStore.remove(token, docRef) + }, this) + + if (emitEvent) this.eventEmitter.emit('remove', doc, this) +} + +/** + * Updates a document in the index. + * + * When a document contained within the index gets updated, fields changed, + * added or removed, to make sure it correctly matched against search queries, + * it should be updated in the index. + * + * This method is just a wrapper around `remove` and `add` + * + * An 'update' event is emitted with the document that has been updated and the index. + * This event can be silenced by passing false as the second argument to update. Only + * an update event will be fired, the 'add' and 'remove' events of the underlying calls + * are silenced. + * + * @param {Object} doc The document to update in the index. + * @param {Boolean} emitEvent Whether to emit update events, defaults to true + * @see Index.prototype.remove + * @see Index.prototype.add + * @memberOf Index + */ +lunr.Index.prototype.update = function (doc, emitEvent) { + var emitEvent = emitEvent === undefined ? true : emitEvent + + this.remove(doc, false) + this.add(doc, false) + + if (emitEvent) this.eventEmitter.emit('update', doc, this) +} + +/** + * Calculates the inverse document frequency for a token within the index. + * + * @param {String} token The token to calculate the idf of. + * @see Index.prototype.idf + * @private + * @memberOf Index + */ +lunr.Index.prototype.idf = function (term) { + var cacheKey = "@" + term + if (Object.prototype.hasOwnProperty.call(this._idfCache, cacheKey)) return this._idfCache[cacheKey] + + var documentFrequency = this.tokenStore.count(term), + idf = 1 + + if (documentFrequency > 0) { + idf = 1 + Math.log(this.tokenStore.length / documentFrequency) + } + + return this._idfCache[cacheKey] = idf +} + +/** + * Searches the index using the passed query. + * + * Queries should be a string, multiple words are allowed and will lead to an + * AND based query, e.g. `idx.search('foo bar')` will run a search for + * documents containing both 'foo' and 'bar'. + * + * All query tokens are passed through the same pipeline that document tokens + * are passed through, so any language processing involved will be run on every + * query term. + * + * Each query term is expanded, so that the term 'he' might be expanded to + * 'hello' and 'help' if those terms were already included in the index. + * + * Matching documents are returned as an array of objects, each object contains + * the matching document ref, as set for this index, and the similarity score + * for this document against the query. + * + * @param {String} query The query to search the index with. + * @returns {Object} + * @see Index.prototype.idf + * @see Index.prototype.documentVector + * @memberOf Index + */ +lunr.Index.prototype.search = function (query) { + var queryTokens = this.pipeline.run(lunr.tokenizer(query)), + queryVector = new lunr.Vector, + documentSets = [], + fieldBoosts = this._fields.reduce(function (memo, f) { return memo + f.boost }, 0) + + var hasSomeToken = queryTokens.some(function (token) { + return this.tokenStore.has(token) + }, this) + + if (!hasSomeToken) return [] + + queryTokens + .forEach(function (token, i, tokens) { + var tf = 1 / tokens.length * this._fields.length * fieldBoosts, + self = this + + var set = this.tokenStore.expand(token).reduce(function (memo, key) { + var pos = self.corpusTokens.indexOf(key), + idf = self.idf(key), + similarityBoost = 1, + set = new lunr.SortedSet + + // if the expanded key is not an exact match to the token then + // penalise the score for this key by how different the key is + // to the token. + if (key !== token) { + var diff = Math.max(3, key.length - token.length) + similarityBoost = 1 / Math.log(diff) + } + + // calculate the query tf-idf score for this token + // applying an similarityBoost to ensure exact matches + // these rank higher than expanded terms + if (pos > -1) queryVector.insert(pos, tf * idf * similarityBoost) + + // add all the documents that have this key into a set + Object.keys(self.tokenStore.get(key)).forEach(function (ref) { set.add(ref) }) + + return memo.union(set) + }, new lunr.SortedSet) + + documentSets.push(set) + }, this) + + var documentSet = documentSets.reduce(function (memo, set) { + return memo.intersect(set) + }) + + return documentSet + .map(function (ref) { + return { ref: ref, score: queryVector.similarity(this.documentVector(ref)) } + }, this) + .sort(function (a, b) { + return b.score - a.score + }) +} + +/** + * Generates a vector containing all the tokens in the document matching the + * passed documentRef. + * + * The vector contains the tf-idf score for each token contained in the + * document with the passed documentRef. The vector will contain an element + * for every token in the indexes corpus, if the document does not contain that + * token the element will be 0. + * + * @param {Object} documentRef The ref to find the document with. + * @returns {lunr.Vector} + * @private + * @memberOf Index + */ +lunr.Index.prototype.documentVector = function (documentRef) { + var documentTokens = this.documentStore.get(documentRef), + documentTokensLength = documentTokens.length, + documentVector = new lunr.Vector + + for (var i = 0; i < documentTokensLength; i++) { + var token = documentTokens.elements[i], + tf = this.tokenStore.get(token)[documentRef].tf, + idf = this.idf(token) + + documentVector.insert(this.corpusTokens.indexOf(token), tf * idf) + }; + + return documentVector +} + +/** + * Returns a representation of the index ready for serialisation. + * + * @returns {Object} + * @memberOf Index + */ +lunr.Index.prototype.toJSON = function () { + return { + version: lunr.version, + fields: this._fields, + ref: this._ref, + documentStore: this.documentStore.toJSON(), + tokenStore: this.tokenStore.toJSON(), + corpusTokens: this.corpusTokens.toJSON(), + pipeline: this.pipeline.toJSON() + } +} + +/** + * Applies a plugin to the current index. + * + * A plugin is a function that is called with the index as its context. + * Plugins can be used to customise or extend the behaviour the index + * in some way. A plugin is just a function, that encapsulated the custom + * behaviour that should be applied to the index. + * + * The plugin function will be called with the index as its argument, additional + * arguments can also be passed when calling use. The function will be called + * with the index as its context. + * + * Example: + * + * var myPlugin = function (idx, arg1, arg2) { + * // `this` is the index to be extended + * // apply any extensions etc here. + * } + * + * var idx = lunr(function () { + * this.use(myPlugin, 'arg1', 'arg2') + * }) + * + * @param {Function} plugin The plugin to apply. + * @memberOf Index + */ +lunr.Index.prototype.use = function (plugin) { + var args = Array.prototype.slice.call(arguments, 1) + args.unshift(this) + plugin.apply(this, args) +} +/*! + * lunr.Store + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.Store is a simple key-value store used for storing sets of tokens for + * documents stored in index. + * + * @constructor + * @module + */ +lunr.Store = function () { + this.store = {} + this.length = 0 +} + +/** + * Loads a previously serialised store + * + * @param {Object} serialisedData The serialised store to load. + * @returns {lunr.Store} + * @memberOf Store + */ +lunr.Store.load = function (serialisedData) { + var store = new this + + store.length = serialisedData.length + store.store = Object.keys(serialisedData.store).reduce(function (memo, key) { + memo[key] = lunr.SortedSet.load(serialisedData.store[key]) + return memo + }, {}) + + return store +} + +/** + * Stores the given tokens in the store against the given id. + * + * @param {Object} id The key used to store the tokens against. + * @param {Object} tokens The tokens to store against the key. + * @memberOf Store + */ +lunr.Store.prototype.set = function (id, tokens) { + if (!this.has(id)) this.length++ + this.store[id] = tokens +} + +/** + * Retrieves the tokens from the store for a given key. + * + * @param {Object} id The key to lookup and retrieve from the store. + * @returns {Object} + * @memberOf Store + */ +lunr.Store.prototype.get = function (id) { + return this.store[id] +} + +/** + * Checks whether the store contains a key. + * + * @param {Object} id The id to look up in the store. + * @returns {Boolean} + * @memberOf Store + */ +lunr.Store.prototype.has = function (id) { + return id in this.store +} + +/** + * Removes the value for a key in the store. + * + * @param {Object} id The id to remove from the store. + * @memberOf Store + */ +lunr.Store.prototype.remove = function (id) { + if (!this.has(id)) return + + delete this.store[id] + this.length-- +} + +/** + * Returns a representation of the store ready for serialisation. + * + * @returns {Object} + * @memberOf Store + */ +lunr.Store.prototype.toJSON = function () { + return { + store: this.store, + length: this.length + } +} + +/*! + * lunr.stemmer + * Copyright (C) 2014 Oliver Nightingale + * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt + */ + +/** + * lunr.stemmer is an english language stemmer, this is a JavaScript + * implementation of the PorterStemmer taken from http://tartaurs.org/~martin + * + * @module + * @param {String} str The string to stem + * @returns {String} + * @see lunr.Pipeline + */ +lunr.stemmer = (function(){ + var step2list = { + "ational" : "ate", + "tional" : "tion", + "enci" : "ence", + "anci" : "ance", + "izer" : "ize", + "bli" : "ble", + "alli" : "al", + "entli" : "ent", + "eli" : "e", + "ousli" : "ous", + "ization" : "ize", + "ation" : "ate", + "ator" : "ate", + "alism" : "al", + "iveness" : "ive", + "fulness" : "ful", + "ousness" : "ous", + "aliti" : "al", + "iviti" : "ive", + "biliti" : "ble", + "logi" : "log" + }, + + step3list = { + "icate" : "ic", + "ative" : "", + "alize" : "al", + "iciti" : "ic", + "ical" : "ic", + "ful" : "", + "ness" : "" + }, + + c = "[^aeiou]", // consonant + v = "[aeiouy]", // vowel + C = c + "[^aeiouy]*", // consonant sequence + V = v + "[aeiou]*", // vowel sequence + + mgr0 = "^(" + C + ")?" + V + C, // [C]VC... is m>0 + meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$", // [C]VC[V] is m=1 + mgr1 = "^(" + C + ")?" + V + C + V + C, // [C]VCVC... is m>1 + s_v = "^(" + C + ")?" + v; // vowel in stem + + var re_mgr0 = new RegExp(mgr0); + var re_mgr1 = new RegExp(mgr1); + var re_meq1 = new RegExp(meq1); + var re_s_v = new RegExp(s_v); + + var re_1a = /^(.+?)(ss|i)es$/; + var re2_1a = /^(.+?)([^s])s$/; + var re_1b = /^(.+?)eed$/; + var re2_1b = /^(.+?)(ed|ing)$/; + var re_1b_2 = /.$/; + var re2_1b_2 = /(at|bl|iz)$/; + var re3_1b_2 = new RegExp("([^aeiouylsz])\\1$"); + var re4_1b_2 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + + var re_1c = /^(.+?[^aeiou])y$/; + var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + + var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + + var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + var re2_4 = /^(.+?)(s|t)(ion)$/; + + var re_5 = /^(.+?)e$/; + var re_5_1 = /ll$/; + var re3_5 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + + var porterStemmer = function porterStemmer(w) { + var stem, + suffix, + firstch, + re, + re2, + re3, + re4; + + if (w.length < 3) { return w; } + + firstch = w.substr(0,1); + if (firstch == "y") { + w = firstch.toUpperCase() + w.substr(1); + } + + // Step 1a + re = re_1a + re2 = re2_1a; + + if (re.test(w)) { w = w.replace(re,"$1$2"); } + else if (re2.test(w)) { w = w.replace(re2,"$1$2"); } + + // Step 1b + re = re_1b; + re2 = re2_1b; + if (re.test(w)) { + var fp = re.exec(w); + re = re_mgr0; + if (re.test(fp[1])) { + re = re_1b_2; + w = w.replace(re,""); + } + } else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = re_s_v; + if (re2.test(stem)) { + w = stem; + re2 = re2_1b_2; + re3 = re3_1b_2; + re4 = re4_1b_2; + if (re2.test(w)) { w = w + "e"; } + else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,""); } + else if (re4.test(w)) { w = w + "e"; } + } + } + + // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say) + re = re_1c; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + w = stem + "i"; + } + + // Step 2 + re = re_2; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = re_mgr0; + if (re.test(stem)) { + w = stem + step2list[suffix]; + } + } + + // Step 3 + re = re_3; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = re_mgr0; + if (re.test(stem)) { + w = stem + step3list[suffix]; + } + } + + // Step 4 + re = re_4; + re2 = re2_4; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = re_mgr1; + if (re.test(stem)) { + w = stem; + } + } else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = re_mgr1; + if (re2.test(stem)) { + w = stem; + } + } + + // Step 5 + re = re_5; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = re_mgr1; + re2 = re_meq1; + re3 = re3_5; + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) { + w = stem; + } + } + + re = re_5_1; + re2 = re_mgr1; + if (re.test(w) && re2.test(w)) { + re = re_1b_2; + w = w.replace(re,""); + } + + // and turn initial Y back to y + + if (firstch == "y") { + w = firstch.toLowerCase() + w.substr(1); + } + + return w; + }; + + return porterStemmer; +})(); + +lunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer') +/*! + * lunr.stopWordFilter + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.stopWordFilter is an English language stop word list filter, any words + * contained in the list will not be passed through the filter. + * + * This is intended to be used in the Pipeline. If the token does not pass the + * filter then undefined will be returned. + * + * @module + * @param {String} token The token to pass through the filter + * @returns {String} + * @see lunr.Pipeline + */ +lunr.stopWordFilter = function (token) { + if (lunr.stopWordFilter.stopWords.indexOf(token) === -1) return token +} + +lunr.stopWordFilter.stopWords = new lunr.SortedSet +lunr.stopWordFilter.stopWords.length = 119 +lunr.stopWordFilter.stopWords.elements = [ + "", + "a", + "able", + "about", + "across", + "after", + "all", + "almost", + "also", + "am", + "among", + "an", + "and", + "any", + "are", + "as", + "at", + "be", + "because", + "been", + "but", + "by", + "can", + "cannot", + "could", + "dear", + "did", + "do", + "does", + "either", + "else", + "ever", + "every", + "for", + "from", + "get", + "got", + "had", + "has", + "have", + "he", + "her", + "hers", + "him", + "his", + "how", + "however", + "i", + "if", + "in", + "into", + "is", + "it", + "its", + "just", + "least", + "let", + "like", + "likely", + "may", + "me", + "might", + "most", + "must", + "my", + "neither", + "no", + "nor", + "not", + "of", + "off", + "often", + "on", + "only", + "or", + "other", + "our", + "own", + "rather", + "said", + "say", + "says", + "she", + "should", + "since", + "so", + "some", + "than", + "that", + "the", + "their", + "them", + "then", + "there", + "these", + "they", + "this", + "tis", + "to", + "too", + "twas", + "us", + "wants", + "was", + "we", + "were", + "what", + "when", + "where", + "which", + "while", + "who", + "whom", + "why", + "will", + "with", + "would", + "yet", + "you", + "your" +] + +lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter') +/*! + * lunr.trimmer + * Copyright (C) 2014 Oliver Nightingale + */ + +/** + * lunr.trimmer is a pipeline function for trimming non word + * characters from the begining and end of tokens before they + * enter the index. + * + * This implementation may not work correctly for non latin + * characters and should either be removed or adapted for use + * with languages with non-latin characters. + * + * @module + * @param {String} token The token to pass through the filter + * @returns {String} + * @see lunr.Pipeline + */ +lunr.trimmer = function (token) { + return token + .replace(/^\W+/, '') + .replace(/\W+$/, '') +} + +lunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer') +/*! + * lunr.stemmer + * Copyright (C) 2014 Oliver Nightingale + * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt + */ + +/** + * lunr.TokenStore is used for efficient storing and lookup of the reverse + * index of token to document ref. + * + * @constructor + */ +lunr.TokenStore = function () { + this.root = { docs: {} } + this.length = 0 +} + +/** + * Loads a previously serialised token store + * + * @param {Object} serialisedData The serialised token store to load. + * @returns {lunr.TokenStore} + * @memberOf TokenStore + */ +lunr.TokenStore.load = function (serialisedData) { + var store = new this + + store.root = serialisedData.root + store.length = serialisedData.length + + return store +} + +/** + * Adds a new token doc pair to the store. + * + * By default this function starts at the root of the current store, however + * it can start at any node of any token store if required. + * + * @param {String} token The token to store the doc under + * @param {Object} doc The doc to store against the token + * @param {Object} root An optional node at which to start looking for the + * correct place to enter the doc, by default the root of this lunr.TokenStore + * is used. + * @memberOf TokenStore + */ +lunr.TokenStore.prototype.add = function (token, doc, root) { + var root = root || this.root, + key = token[0], + rest = token.slice(1) + + if (!(key in root)) root[key] = {docs: {}} + + if (rest.length === 0) { + root[key].docs[doc.ref] = doc + this.length += 1 + return + } else { + return this.add(rest, doc, root[key]) + } +} + +/** + * Checks whether this key is contained within this lunr.TokenStore. + * + * By default this function starts at the root of the current store, however + * it can start at any node of any token store if required. + * + * @param {String} token The token to check for + * @param {Object} root An optional node at which to start + * @memberOf TokenStore + */ +lunr.TokenStore.prototype.has = function (token) { + if (!token) return false + + var node = this.root + + for (var i = 0; i < token.length; i++) { + if (!node[token[i]]) return false + + node = node[token[i]] + } + + return true +} + +/** + * Retrieve a node from the token store for a given token. + * + * By default this function starts at the root of the current store, however + * it can start at any node of any token store if required. + * + * @param {String} token The token to get the node for. + * @param {Object} root An optional node at which to start. + * @returns {Object} + * @see TokenStore.prototype.get + * @memberOf TokenStore + */ +lunr.TokenStore.prototype.getNode = function (token) { + if (!token) return {} + + var node = this.root + + for (var i = 0; i < token.length; i++) { + if (!node[token[i]]) return {} + + node = node[token[i]] + } + + return node +} + +/** + * Retrieve the documents for a node for the given token. + * + * By default this function starts at the root of the current store, however + * it can start at any node of any token store if required. + * + * @param {String} token The token to get the documents for. + * @param {Object} root An optional node at which to start. + * @returns {Object} + * @memberOf TokenStore + */ +lunr.TokenStore.prototype.get = function (token, root) { + return this.getNode(token, root).docs || {} +} + +lunr.TokenStore.prototype.count = function (token, root) { + return Object.keys(this.get(token, root)).length +} + +/** + * Remove the document identified by ref from the token in the store. + * + * By default this function starts at the root of the current store, however + * it can start at any node of any token store if required. + * + * @param {String} token The token to get the documents for. + * @param {String} ref The ref of the document to remove from this token. + * @param {Object} root An optional node at which to start. + * @returns {Object} + * @memberOf TokenStore + */ +lunr.TokenStore.prototype.remove = function (token, ref) { + if (!token) return + var node = this.root + + for (var i = 0; i < token.length; i++) { + if (!(token[i] in node)) return + node = node[token[i]] + } + + delete node.docs[ref] +} + +/** + * Find all the possible suffixes of the passed token using tokens + * currently in the store. + * + * @param {String} token The token to expand. + * @returns {Array} + * @memberOf TokenStore + */ +lunr.TokenStore.prototype.expand = function (token, memo) { + var root = this.getNode(token), + docs = root.docs || {}, + memo = memo || [] + + if (Object.keys(docs).length) memo.push(token) + + Object.keys(root) + .forEach(function (key) { + if (key === 'docs') return + + memo.concat(this.expand(token + key, memo)) + }, this) + + return memo +} + +/** + * Returns a representation of the token store ready for serialisation. + * + * @returns {Object} + * @memberOf TokenStore + */ +lunr.TokenStore.prototype.toJSON = function () { + return { + root: this.root, + length: this.length + } +} + + + /** + * export the module via AMD, CommonJS or as a browser global + * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js + */ + ;(function (root, factory) { + if (typeof define === 'function' && define.amd) { + // AMD. Register as an anonymous module. + define(factory) + } else if (typeof exports === 'object') { + /** + * Node. Does not work with strict CommonJS, but + * only CommonJS-like enviroments that support module.exports, + * like Node. + */ + module.exports = factory() + } else { + // Browser globals (root is window) + root.lunr = factory() + } + }(this, function () { + /** + * Just return a value to define the module export. + * This example returns an object, but the module + * can return a function as the exported value. + */ + return lunr + })) +})() diff --git a/client/galaxy/scripts/libs/raven.js b/client/galaxy/scripts/libs/raven.js index f8e45d7e50e..37896c4018a 100644 --- a/client/galaxy/scripts/libs/raven.js +++ b/client/galaxy/scripts/libs/raven.js @@ -1,11 +1,1089 @@ -(function(){ +/*! Raven.js 1.1.16 (463f68f) | github.com/getsentry/raven-js */ -// Raven.js -// -// Originally based on the Arecibo JavaScript client. -// -// Requires: -// * TraceKit (included in the full and minified distribution files) +/* + * Includes TraceKit + * https://github.com/getsentry/TraceKit + * + * Copyright 2014 Matt Robenolt and other contributors + * Released under the BSD license + * https://github.com/getsentry/raven-js/blob/master/LICENSE + * + */ +;(function(window, undefined){ +'use strict'; + +/* + TraceKit - Cross brower stack traces - github.com/occ/TraceKit + MIT license +*/ + +var TraceKit = { + remoteFetching: false, + collectWindowErrors: true, + // 3 lines before, the offending line, 3 lines after + linesOfContext: 7 +}; + +// global reference to slice +var _slice = [].slice; +var UNKNOWN_FUNCTION = '?'; + + +/** + * TraceKit.wrap: Wrap any function in a TraceKit reporter + * Example: func = TraceKit.wrap(func); + * + * @param {Function} func Function to be wrapped + * @return {Function} The wrapped func + */ +TraceKit.wrap = function traceKitWrapper(func) { + function wrapped() { + try { + return func.apply(this, arguments); + } catch (e) { + TraceKit.report(e); + throw e; + } + } + return wrapped; +}; + +/** + * TraceKit.report: cross-browser processing of unhandled exceptions + * + * Syntax: + * TraceKit.report.subscribe(function(stackInfo) { ... }) + * TraceKit.report.unsubscribe(function(stackInfo) { ... }) + * TraceKit.report(exception) + * try { ...code... } catch(ex) { TraceKit.report(ex); } + * + * Supports: + * - Firefox: full stack trace with line numbers, plus column number + * on top frame; column number is not guaranteed + * - Opera: full stack trace with line and column numbers + * - Chrome: full stack trace with line and column numbers + * - Safari: line and column number for the top frame only; some frames + * may be missing, and column number is not guaranteed + * - IE: line and column number for the top frame only; some frames + * may be missing, and column number is not guaranteed + * + * In theory, TraceKit should work on all of the following versions: + * - IE5.5+ (only 8.0 tested) + * - Firefox 0.9+ (only 3.5+ tested) + * - Opera 7+ (only 10.50 tested; versions 9 and earlier may require + * Exceptions Have Stacktrace to be enabled in opera:config) + * - Safari 3+ (only 4+ tested) + * - Chrome 1+ (only 5+ tested) + * - Konqueror 3.5+ (untested) + * + * Requires TraceKit.computeStackTrace. + * + * Tries to catch all unhandled exceptions and report them to the + * subscribed handlers. Please note that TraceKit.report will rethrow the + * exception. This is REQUIRED in order to get a useful stack trace in IE. + * If the exception does not reach the top of the browser, you will only + * get a stack trace from the point where TraceKit.report was called. + * + * Handlers receive a stackInfo object as described in the + * TraceKit.computeStackTrace docs. + */ +TraceKit.report = (function reportModuleWrapper() { + var handlers = [], + lastArgs = null, + lastException = null, + lastExceptionStack = null; + + /** + * Add a crash handler. + * @param {Function} handler + */ + function subscribe(handler) { + installGlobalHandler(); + handlers.push(handler); + } + + /** + * Remove a crash handler. + * @param {Function} handler + */ + function unsubscribe(handler) { + for (var i = handlers.length - 1; i >= 0; --i) { + if (handlers[i] === handler) { + handlers.splice(i, 1); + } + } + } + + /** + * Remove all crash handlers. + */ + function unsubscribeAll() { + uninstallGlobalHandler(); + handlers = []; + } + + /** + * Dispatch stack information to all handlers. + * @param {Object.} stack + */ + function notifyHandlers(stack, isWindowError) { + var exception = null; + if (isWindowError && !TraceKit.collectWindowErrors) { + return; + } + for (var i in handlers) { + if (hasKey(handlers, i)) { + try { + handlers[i].apply(null, [stack].concat(_slice.call(arguments, 2))); + } catch (inner) { + exception = inner; + } + } + } + + if (exception) { + throw exception; + } + } + + var _oldOnerrorHandler, _onErrorHandlerInstalled; + + /** + * Ensures all global unhandled exceptions are recorded. + * Supported by Gecko and IE. + * @param {string} message Error message. + * @param {string} url URL of script that generated the exception. + * @param {(number|string)} lineNo The line number at which the error + * occurred. + * @param {?(number|string)} colNo The column number at which the error + * occurred. + * @param {?Error} ex The actual Error object. + */ + function traceKitWindowOnError(message, url, lineNo, colNo, ex) { + var stack = null; + + if (lastExceptionStack) { + TraceKit.computeStackTrace.augmentStackTraceWithInitialElement(lastExceptionStack, url, lineNo, message); + processLastException(); + } else if (ex) { + // New chrome and blink send along a real error object + // Let's just report that like a normal error. + // See: https://mikewest.org/2013/08/debugging-runtime-errors-with-window-onerror + stack = TraceKit.computeStackTrace(ex); + notifyHandlers(stack, true); + } else { + var location = { + 'url': url, + 'line': lineNo, + 'column': colNo + }; + location.func = TraceKit.computeStackTrace.guessFunctionName(location.url, location.line); + location.context = TraceKit.computeStackTrace.gatherContext(location.url, location.line); + stack = { + 'message': message, + 'url': document.location.href, + 'stack': [location] + }; + notifyHandlers(stack, true); + } + + if (_oldOnerrorHandler) { + return _oldOnerrorHandler.apply(this, arguments); + } + + return false; + } + + function installGlobalHandler () + { + if (_onErrorHandlerInstalled) { + return; + } + _oldOnerrorHandler = window.onerror; + window.onerror = traceKitWindowOnError; + _onErrorHandlerInstalled = true; + } + + function uninstallGlobalHandler () + { + if (!_onErrorHandlerInstalled) { + return; + } + window.onerror = _oldOnerrorHandler; + _onErrorHandlerInstalled = false; + _oldOnerrorHandler = undefined; + } + + function processLastException() { + var _lastExceptionStack = lastExceptionStack, + _lastArgs = lastArgs; + lastArgs = null; + lastExceptionStack = null; + lastException = null; + notifyHandlers.apply(null, [_lastExceptionStack, false].concat(_lastArgs)); + } + + /** + * Reports an unhandled Error to TraceKit. + * @param {Error} ex + * @param {?boolean} rethrow If false, do not re-throw the exception. + * Only used for window.onerror to not cause an infinite loop of + * rethrowing. + */ + function report(ex, rethrow) { + var args = _slice.call(arguments, 1); + if (lastExceptionStack) { + if (lastException === ex) { + return; // already caught by an inner catch block, ignore + } else { + processLastException(); + } + } + + var stack = TraceKit.computeStackTrace(ex); + lastExceptionStack = stack; + lastException = ex; + lastArgs = args; + + // If the stack trace is incomplete, wait for 2 seconds for + // slow slow IE to see if onerror occurs or not before reporting + // this exception; otherwise, we will end up with an incomplete + // stack trace + window.setTimeout(function () { + if (lastException === ex) { + processLastException(); + } + }, (stack.incomplete ? 2000 : 0)); + + if (rethrow !== false) { + throw ex; // re-throw to propagate to the top level (and cause window.onerror) + } + } + + report.subscribe = subscribe; + report.unsubscribe = unsubscribe; + report.uninstall = unsubscribeAll; + return report; +}()); + +/** + * TraceKit.computeStackTrace: cross-browser stack traces in JavaScript + * + * Syntax: + * s = TraceKit.computeStackTrace.ofCaller([depth]) + * s = TraceKit.computeStackTrace(exception) // consider using TraceKit.report instead (see below) + * Returns: + * s.name - exception name + * s.message - exception message + * s.stack[i].url - JavaScript or HTML file URL + * s.stack[i].func - function name, or empty for anonymous functions (if guessing did not work) + * s.stack[i].args - arguments passed to the function, if known + * s.stack[i].line - line number, if known + * s.stack[i].column - column number, if known + * s.stack[i].context - an array of source code lines; the middle element corresponds to the correct line# + * + * Supports: + * - Firefox: full stack trace with line numbers and unreliable column + * number on top frame + * - Opera 10: full stack trace with line and column numbers + * - Opera 9-: full stack trace with line numbers + * - Chrome: full stack trace with line and column numbers + * - Safari: line and column number for the topmost stacktrace element + * only + * - IE: no line numbers whatsoever + * + * Tries to guess names of anonymous functions by looking for assignments + * in the source code. In IE and Safari, we have to guess source file names + * by searching for function bodies inside all page scripts. This will not + * work for scripts that are loaded cross-domain. + * Here be dragons: some function names may be guessed incorrectly, and + * duplicate functions may be mismatched. + * + * TraceKit.computeStackTrace should only be used for tracing purposes. + * Logging of unhandled exceptions should be done with TraceKit.report, + * which builds on top of TraceKit.computeStackTrace and provides better + * IE support by utilizing the window.onerror event to retrieve information + * about the top of the stack. + * + * Note: In IE and Safari, no stack trace is recorded on the Error object, + * so computeStackTrace instead walks its *own* chain of callers. + * This means that: + * * in Safari, some methods may be missing from the stack trace; + * * in IE, the topmost function in the stack trace will always be the + * caller of computeStackTrace. + * + * This is okay for tracing (because you are likely to be calling + * computeStackTrace from the function you want to be the topmost element + * of the stack trace anyway), but not okay for logging unhandled + * exceptions (because your catch block will likely be far away from the + * inner function that actually caused the exception). + * + * Tracing example: + * function trace(message) { + * var stackInfo = TraceKit.computeStackTrace.ofCaller(); + * var data = message + "\n"; + * for(var i in stackInfo.stack) { + * var item = stackInfo.stack[i]; + * data += (item.func || '[anonymous]') + "() in " + item.url + ":" + (item.line || '0') + "\n"; + * } + * if (window.console) + * console.info(data); + * else + * alert(data); + * } + */ +TraceKit.computeStackTrace = (function computeStackTraceWrapper() { + var debug = false, + sourceCache = {}; + + /** + * Attempts to retrieve source code via XMLHttpRequest, which is used + * to look up anonymous function names. + * @param {string} url URL of source code. + * @return {string} Source contents. + */ + function loadSource(url) { + if (!TraceKit.remoteFetching) { //Only attempt request if remoteFetching is on. + return ''; + } + try { + var getXHR = function() { + try { + return new window.XMLHttpRequest(); + } catch (e) { + // explicitly bubble up the exception if not found + return new window.ActiveXObject('Microsoft.XMLHTTP'); + } + }; + + var request = getXHR(); + request.open('GET', url, false); + request.send(''); + return request.responseText; + } catch (e) { + return ''; + } + } + + /** + * Retrieves source code from the source code cache. + * @param {string} url URL of source code. + * @return {Array.} Source contents. + */ + function getSource(url) { + if (!isString(url)) return []; + if (!hasKey(sourceCache, url)) { + // URL needs to be able to fetched within the acceptable domain. Otherwise, + // cross-domain errors will be triggered. + var source = ''; + if (url.indexOf(document.domain) !== -1) { + source = loadSource(url); + } + sourceCache[url] = source ? source.split('\n') : []; + } + + return sourceCache[url]; + } + + /** + * Tries to use an externally loaded copy of source code to determine + * the name of a function by looking at the name of the variable it was + * assigned to, if any. + * @param {string} url URL of source code. + * @param {(string|number)} lineNo Line number in source code. + * @return {string} The function name, if discoverable. + */ + function guessFunctionName(url, lineNo) { + var reFunctionArgNames = /function ([^(]*)\(([^)]*)\)/, + reGuessFunction = /['"]?([0-9A-Za-z$_]+)['"]?\s*[:=]\s*(function|eval|new Function)/, + line = '', + maxLines = 10, + source = getSource(url), + m; + + if (!source.length) { + return UNKNOWN_FUNCTION; + } + + // Walk backwards from the first line in the function until we find the line which + // matches the pattern above, which is the function definition + for (var i = 0; i < maxLines; ++i) { + line = source[lineNo - i] + line; + + if (!isUndefined(line)) { + if ((m = reGuessFunction.exec(line))) { + return m[1]; + } else if ((m = reFunctionArgNames.exec(line))) { + return m[1]; + } + } + } + + return UNKNOWN_FUNCTION; + } + + /** + * Retrieves the surrounding lines from where an exception occurred. + * @param {string} url URL of source code. + * @param {(string|number)} line Line number in source code to centre + * around for context. + * @return {?Array.} Lines of source code. + */ + function gatherContext(url, line) { + var source = getSource(url); + + if (!source.length) { + return null; + } + + var context = [], + // linesBefore & linesAfter are inclusive with the offending line. + // if linesOfContext is even, there will be one extra line + // *before* the offending line. + linesBefore = Math.floor(TraceKit.linesOfContext / 2), + // Add one extra line if linesOfContext is odd + linesAfter = linesBefore + (TraceKit.linesOfContext % 2), + start = Math.max(0, line - linesBefore - 1), + end = Math.min(source.length, line + linesAfter - 1); + + line -= 1; // convert to 0-based index + + for (var i = start; i < end; ++i) { + if (!isUndefined(source[i])) { + context.push(source[i]); + } + } + + return context.length > 0 ? context : null; + } + + /** + * Escapes special characters, except for whitespace, in a string to be + * used inside a regular expression as a string literal. + * @param {string} text The string. + * @return {string} The escaped string literal. + */ + function escapeRegExp(text) { + return text.replace(/[\-\[\]{}()*+?.,\\\^$|#]/g, '\\$&'); + } + + /** + * Escapes special characters in a string to be used inside a regular + * expression as a string literal. Also ensures that HTML entities will + * be matched the same as their literal friends. + * @param {string} body The string. + * @return {string} The escaped string. + */ + function escapeCodeAsRegExpForMatchingInsideHTML(body) { + return escapeRegExp(body).replace('<', '(?:<|<)').replace('>', '(?:>|>)').replace('&', '(?:&|&)').replace('"', '(?:"|")').replace(/\s+/g, '\\s+'); + } + + /** + * Determines where a code fragment occurs in the source code. + * @param {RegExp} re The function definition. + * @param {Array.} urls A list of URLs to search. + * @return {?Object.} An object containing + * the url, line, and column number of the defined function. + */ + function findSourceInUrls(re, urls) { + var source, m; + for (var i = 0, j = urls.length; i < j; ++i) { + // console.log('searching', urls[i]); + if ((source = getSource(urls[i])).length) { + source = source.join('\n'); + if ((m = re.exec(source))) { + // console.log('Found function in ' + urls[i]); + + return { + 'url': urls[i], + 'line': source.substring(0, m.index).split('\n').length, + 'column': m.index - source.lastIndexOf('\n', m.index) - 1 + }; + } + } + } + + // console.log('no match'); + + return null; + } + + /** + * Determines at which column a code fragment occurs on a line of the + * source code. + * @param {string} fragment The code fragment. + * @param {string} url The URL to search. + * @param {(string|number)} line The line number to examine. + * @return {?number} The column number. + */ + function findSourceInLine(fragment, url, line) { + var source = getSource(url), + re = new RegExp('\\b' + escapeRegExp(fragment) + '\\b'), + m; + + line -= 1; + + if (source && source.length > line && (m = re.exec(source[line]))) { + return m.index; + } + + return null; + } + + /** + * Determines where a function was defined within the source code. + * @param {(Function|string)} func A function reference or serialized + * function definition. + * @return {?Object.} An object containing + * the url, line, and column number of the defined function. + */ + function findSourceByFunctionBody(func) { + var urls = [window.location.href], + scripts = document.getElementsByTagName('script'), + body, + code = '' + func, + codeRE = /^function(?:\s+([\w$]+))?\s*\(([\w\s,]*)\)\s*\{\s*(\S[\s\S]*\S)\s*\}\s*$/, + eventRE = /^function on([\w$]+)\s*\(event\)\s*\{\s*(\S[\s\S]*\S)\s*\}\s*$/, + re, + parts, + result; + + for (var i = 0; i < scripts.length; ++i) { + var script = scripts[i]; + if (script.src) { + urls.push(script.src); + } + } + + if (!(parts = codeRE.exec(code))) { + re = new RegExp(escapeRegExp(code).replace(/\s+/g, '\\s+')); + } + + // not sure if this is really necessary, but I don’t have a test + // corpus large enough to confirm that and it was in the original. + else { + var name = parts[1] ? '\\s+' + parts[1] : '', + args = parts[2].split(',').join('\\s*,\\s*'); + + body = escapeRegExp(parts[3]).replace(/;$/, ';?'); // semicolon is inserted if the function ends with a comment.replace(/\s+/g, '\\s+'); + re = new RegExp('function' + name + '\\s*\\(\\s*' + args + '\\s*\\)\\s*{\\s*' + body + '\\s*}'); + } + + // look for a normal function definition + if ((result = findSourceInUrls(re, urls))) { + return result; + } + + // look for an old-school event handler function + if ((parts = eventRE.exec(code))) { + var event = parts[1]; + body = escapeCodeAsRegExpForMatchingInsideHTML(parts[2]); + + // look for a function defined in HTML as an onXXX handler + re = new RegExp('on' + event + '=[\\\'"]\\s*' + body + '\\s*[\\\'"]', 'i'); + + if ((result = findSourceInUrls(re, urls[0]))) { + return result; + } + + // look for ??? + re = new RegExp(body); + + if ((result = findSourceInUrls(re, urls))) { + return result; + } + } + + return null; + } + + // Contents of Exception in various browsers. + // + // SAFARI: + // ex.message = Can't find variable: qq + // ex.line = 59 + // ex.sourceId = 580238192 + // ex.sourceURL = http://... + // ex.expressionBeginOffset = 96 + // ex.expressionCaretOffset = 98 + // ex.expressionEndOffset = 98 + // ex.name = ReferenceError + // + // FIREFOX: + // ex.message = qq is not defined + // ex.fileName = http://... + // ex.lineNumber = 59 + // ex.columnNumber = 69 + // ex.stack = ...stack trace... (see the example below) + // ex.name = ReferenceError + // + // CHROME: + // ex.message = qq is not defined + // ex.name = ReferenceError + // ex.type = not_defined + // ex.arguments = ['aa'] + // ex.stack = ...stack trace... + // + // INTERNET EXPLORER: + // ex.message = ... + // ex.name = ReferenceError + // + // OPERA: + // ex.message = ...message... (see the example below) + // ex.name = ReferenceError + // ex.opera#sourceloc = 11 (pretty much useless, duplicates the info in ex.message) + // ex.stacktrace = n/a; see 'opera:config#UserPrefs|Exceptions Have Stacktrace' + + /** + * Computes stack trace information from the stack property. + * Chrome and Gecko use this property. + * @param {Error} ex + * @return {?Object.} Stack trace information. + */ + function computeStackTraceFromStackProp(ex) { + if (!ex.stack) { + return null; + } + + var chrome = /^\s*at (?:((?:\[object object\])?\S+(?: \[as \S+\])?) )?\(?((?:file|https?|chrome-extension):.*?):(\d+)(?::(\d+))?\)?\s*$/i, + gecko = /^\s*(\S*)(?:\((.*?)\))?@((?:file|https?|chrome).*?):(\d+)(?::(\d+))?\s*$/i, + lines = ex.stack.split('\n'), + stack = [], + parts, + element, + reference = /^(.*) is undefined$/.exec(ex.message); + + for (var i = 0, j = lines.length; i < j; ++i) { + if ((parts = gecko.exec(lines[i]))) { + element = { + 'url': parts[3], + 'func': parts[1] || UNKNOWN_FUNCTION, + 'args': parts[2] ? parts[2].split(',') : '', + 'line': +parts[4], + 'column': parts[5] ? +parts[5] : null + }; + } else if ((parts = chrome.exec(lines[i]))) { + element = { + 'url': parts[2], + 'func': parts[1] || UNKNOWN_FUNCTION, + 'line': +parts[3], + 'column': parts[4] ? +parts[4] : null + }; + } else { + continue; + } + + if (!element.func && element.line) { + element.func = guessFunctionName(element.url, element.line); + } + + if (element.line) { + element.context = gatherContext(element.url, element.line); + } + + stack.push(element); + } + + if (!stack.length) { + return null; + } + + if (stack[0].line && !stack[0].column && reference) { + stack[0].column = findSourceInLine(reference[1], stack[0].url, stack[0].line); + } else if (!stack[0].column && !isUndefined(ex.columnNumber)) { + // FireFox uses this awesome columnNumber property for its top frame + // Also note, Firefox's column number is 0-based and everything else expects 1-based, + // so adding 1 + stack[0].column = ex.columnNumber + 1; + } + + return { + 'name': ex.name, + 'message': ex.message, + 'url': document.location.href, + 'stack': stack + }; + } + + /** + * Computes stack trace information from the stacktrace property. + * Opera 10 uses this property. + * @param {Error} ex + * @return {?Object.} Stack trace information. + */ + function computeStackTraceFromStacktraceProp(ex) { + // Access and store the stacktrace property before doing ANYTHING + // else to it because Opera is not very good at providing it + // reliably in other circumstances. + var stacktrace = ex.stacktrace; + + var testRE = / line (\d+), column (\d+) in (?:]+)>|([^\)]+))\((.*)\) in (.*):\s*$/i, + lines = stacktrace.split('\n'), + stack = [], + parts; + + for (var i = 0, j = lines.length; i < j; i += 2) { + if ((parts = testRE.exec(lines[i]))) { + var element = { + 'line': +parts[1], + 'column': +parts[2], + 'func': parts[3] || parts[4], + 'args': parts[5] ? parts[5].split(',') : [], + 'url': parts[6] + }; + + if (!element.func && element.line) { + element.func = guessFunctionName(element.url, element.line); + } + if (element.line) { + try { + element.context = gatherContext(element.url, element.line); + } catch (exc) {} + } + + if (!element.context) { + element.context = [lines[i + 1]]; + } + + stack.push(element); + } + } + + if (!stack.length) { + return null; + } + + return { + 'name': ex.name, + 'message': ex.message, + 'url': document.location.href, + 'stack': stack + }; + } + + /** + * NOT TESTED. + * Computes stack trace information from an error message that includes + * the stack trace. + * Opera 9 and earlier use this method if the option to show stack + * traces is turned on in opera:config. + * @param {Error} ex + * @return {?Object.} Stack information. + */ + function computeStackTraceFromOperaMultiLineMessage(ex) { + // Opera includes a stack trace into the exception message. An example is: + // + // Statement on line 3: Undefined variable: undefinedFunc + // Backtrace: + // Line 3 of linked script file://localhost/Users/andreyvit/Projects/TraceKit/javascript-client/sample.js: In function zzz + // undefinedFunc(a); + // Line 7 of inline#1 script in file://localhost/Users/andreyvit/Projects/TraceKit/javascript-client/sample.html: In function yyy + // zzz(x, y, z); + // Line 3 of inline#1 script in file://localhost/Users/andreyvit/Projects/TraceKit/javascript-client/sample.html: In function xxx + // yyy(a, a, a); + // Line 1 of function script + // try { xxx('hi'); return false; } catch(ex) { TraceKit.report(ex); } + // ... + + var lines = ex.message.split('\n'); + if (lines.length < 4) { + return null; + } + + var lineRE1 = /^\s*Line (\d+) of linked script ((?:file|https?)\S+)(?:: in function (\S+))?\s*$/i, + lineRE2 = /^\s*Line (\d+) of inline#(\d+) script in ((?:file|https?)\S+)(?:: in function (\S+))?\s*$/i, + lineRE3 = /^\s*Line (\d+) of function script\s*$/i, + stack = [], + scripts = document.getElementsByTagName('script'), + inlineScriptBlocks = [], + parts, + i, + len, + source; + + for (i in scripts) { + if (hasKey(scripts, i) && !scripts[i].src) { + inlineScriptBlocks.push(scripts[i]); + } + } + + for (i = 2, len = lines.length; i < len; i += 2) { + var item = null; + if ((parts = lineRE1.exec(lines[i]))) { + item = { + 'url': parts[2], + 'func': parts[3], + 'line': +parts[1] + }; + } else if ((parts = lineRE2.exec(lines[i]))) { + item = { + 'url': parts[3], + 'func': parts[4] + }; + var relativeLine = (+parts[1]); // relative to the start of the @@ -317,9 +314,6 @@ }); tool_shed_repository_status_updater( repository_status_list ); }, - error: function() { - alert( "tool_shed_repository_status_updater_callback failed..." ); - } }); }; diff --git a/templates/admin/tool_shed_repository/initiate_repository_installation.mako b/templates/admin/tool_shed_repository/initiate_repository_installation.mako index 35743d5c00d..87957f99e92 100644 --- a/templates/admin/tool_shed_repository/initiate_repository_installation.mako +++ b/templates/admin/tool_shed_repository/initiate_repository_installation.mako @@ -23,9 +23,6 @@ success : function ( data ) { //alert( "Initializing repository installation succeeded" ); }, - error: function() { - alert( "Initializing repository installation failed" ); - }, }); }; diff --git a/templates/galaxy_client_app.mako b/templates/galaxy_client_app.mako index c259b78be6f..0b5d19bda1a 100644 --- a/templates/galaxy_client_app.mako +++ b/templates/galaxy_client_app.mako @@ -83,7 +83,7 @@ ${ h.dumps( get_config_dict() )} users_api_controller = trans.webapp.api_controllers[ 'users' ] tags_used = [] for tag in users_api_controller.get_user_tags_used( trans, user=trans.user ): - tag = tag | h + tag = escape( tag ) if tag: tags_used.append( tag ) user_dict[ 'tags_used' ] = tags_used @@ -106,6 +106,8 @@ ${ h.dumps( get_config_dict() )} except Exception, exc: pass + #TODO: no logging available? + #log.exception( exc ) return user_dict %> diff --git a/templates/tagging_common.mako b/templates/tagging_common.mako index 35ccfb4550a..b85388b793f 100644 --- a/templates/tagging_common.mako +++ b/templates/tagging_common.mako @@ -89,7 +89,7 @@ <%def name="render_tool_tagging_elements()"> <% elt_id = int ( floor ( random()*maxint ) ) - tags = trans.app.tag_handler.get_tool_tags( trans ) + tags = trans.app.tag_handler.get_tool_tags() %> ${self.render_tagging_element_html(elt_id=elt_id, \ tags=tags, \ @@ -105,7 +105,7 @@ ## Build HTML. <% elt_id = int ( floor ( random()*maxint ) ) - community_tags = trans.app.tag_handler.get_community_tags( trans, item=tagged_item, limit=5 ) + community_tags = trans.app.tag_handler.get_community_tags( item=tagged_item, limit=5 ) %> ${self.render_tagging_element_html(elt_id=elt_id, \ tags=community_tags, \ diff --git a/templates/user/change_password.mako b/templates/user/change_password.mako new file mode 100644 index 00000000000..14030c3d8b9 --- /dev/null +++ b/templates/user/change_password.mako @@ -0,0 +1,31 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +
+
+
Change Password
+ %if token: + + %else: +
+ + +
+ %endif +
+ + +
+
+ + +
+
+ +
+
+
diff --git a/templates/user/index.mako b/templates/user/index.mako index 019ad82adc1..9cade2ae098 100644 --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -6,7 +6,8 @@
    %if t.webapp.name == 'galaxy': %if not trans.app.config.use_remote_user: -
  • ${_('Manage your information')} (email, password, etc.)
    • +
  • ${_('Manage your information')} (email, address, etc.)
    • +
  • ${_('Change your password')}
    • %endif
  • ${_('Change default permissions')} for new histories
  • ${_('Manage your API keys')}
    • @@ -17,6 +18,7 @@
  • ${_('Logout')} ${_('of all user sessions')}
    • %else:
  • ${_('Manage your information')}
    • +
  • ${_('Change your password')}
  • ${_('Manage your API keys')}
  • ${_('Manage your email alerts')}
  • ${_('Logout')} ${_('of all user sessions')}
    • diff --git a/templates/user/info.mako b/templates/user/info.mako index 20ae4744ae0..21603ece67c 100644 --- a/templates/user/info.mako +++ b/templates/user/info.mako @@ -7,7 +7,7 @@