February 2015 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 05 Feb '15

05 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9eeb924b5204/ Changeset: 9eeb924b5204 User: dannon Date: 2015-02-05 13:12:54+00:00 Summary: Add lunr library for toolbox (and potentially more things in the future) search. Affected #: 5 files diff -r 85b1de6a6ebdfe30e14b96f8dc7d13105ae04c2b -r 9eeb924b5204ff10bac0998612549de468f9bc2a client/GruntFile.js --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -69,11 +69,11 @@ 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" ] + "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 diff -r 85b1de6a6ebdfe30e14b96f8dc7d13105ae04c2b -r 9eeb924b5204ff10bac0998612549de468f9bc2a client/bower.json --- a/client/bower.json +++ b/client/bower.json @@ -32,7 +32,8 @@ "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" + "jquery-migrate": "~1.2.1", + "lunr.js": "git://github.com/olivernn/lunr.js.git#~0.5.7" }, "resolutions": { "jquery": "~1.11.1" diff -r 85b1de6a6ebdfe30e14b96f8dc7d13105ae04c2b -r 9eeb924b5204ff10bac0998612549de468f9bc2a client/galaxy/scripts/libs/lunr.js --- /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 + })) +})() This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/19079eea7d22/ Changeset: 19079eea7d22 User: dannon Date: 2015-02-05 13:32:25+00:00 Summary: Add require, TODO for where to integrate lunr. Affected #: 3 files diff -r 9eeb924b5204ff10bac0998612549de468f9bc2a -r 19079eea7d2285d701866b0df77beeff20a677e8 client/galaxy/scripts/mvc/tools.js --- a/client/galaxy/scripts/mvc/tools.js +++ b/client/galaxy/scripts/mvc/tools.js @@ -2,7 +2,7 @@ * Model, view, and controller objects for Galaxy tools and tool panel. */ - define( ["libs/underscore", "viz/trackster/util", "mvc/data" ], + define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr.js" ], function(_, util, data) { /** @@ -14,7 +14,7 @@ show: function() { this.set("hidden", false); }, - + hide: function() { this.set("hidden", true); }, @@ -22,7 +22,7 @@ toggle: function() { this.set("hidden", !this.get("hidden")); }, - + is_visible: function() { return !this.attributes.hidden; } @@ -88,7 +88,7 @@ } }); -/** +/** * A select tool parameter. */ var SelectToolParameter = ToolParameter.extend({ @@ -157,7 +157,7 @@ }); tool.get('inputs').remove(incompatible_inputs); }, - + /** * Returns object copy, optionally including only inputs that can be sampled. */ @@ -177,12 +177,12 @@ return copy; }, - + apply_search_results: function(results) { ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); return this.is_visible(); }, - + /** * Set a tool input's value. */ @@ -191,24 +191,24 @@ return input.get('name') === name; }).set('value', value); }, - + /** * Set many input values at once. */ set_input_values: function(inputs_dict) { var self = this; _.each(_.keys(inputs_dict), function(input_name) { - self.set_input_value(input_name, inputs_dict[input_name]); + self.set_input_value(input_name, inputs_dict[input_name]); }); }, - + /** * Run tool; returns a Deferred that resolves to the tool's output(s). */ run: function() { return this._run(); }, - + /** * Rerun tool using regions and a target dataset. */ @@ -230,7 +230,7 @@ }); return input_dict; }, - + /** * Run tool; returns a Deferred that resolves to the tool's output(s). * NOTE: this method is a helper method and should not be called directly. @@ -259,7 +259,7 @@ return response !== "pending"; } }); - + // Run job and resolve run_deferred to tool outputs. $.when(ss_deferred.go()).then(function(result) { run_deferred.resolve(new data.DatasetCollection().reset(result)); @@ -296,20 +296,20 @@ elems: [], open: false }, - + clear_search_results: function() { _.each(this.attributes.elems, function(elt) { elt.show(); }); - + this.show(); this.set("open", false); }, - + apply_search_results: function(results) { var all_hidden = true, cur_label; - _.each(this.attributes.elems, function(elt) { + _.each(this.attributes.elems, function(elt) { if (elt instanceof ToolSectionLabel) { cur_label = elt; cur_label.hide(); @@ -323,7 +323,7 @@ } } }); - + if (all_hidden) { this.hide(); } @@ -340,6 +340,11 @@ * indicates that query was not run; if not null, results are from search using * query. */ + +/** + * TODO: Integrate lunr search here with tools from API instead of making + * repeated requests. + */ var ToolSearch = Backbone.Model.extend({ defaults: { search_hint_string: "search tools", @@ -353,23 +358,23 @@ // ESC (27) will clear the input field and tool search filters clear_key: 27 }, - + initialize: function() { this.on("change:query", this.do_search); }, - + /** * Do the search and update the results. */ do_search: function() { var query = this.attributes.query; - + // If query is too short, do not search. if (query.length < this.attributes.min_chars_for_search) { this.set("results", null); return; } - + // Do search via AJAX. var q = query + '*'; // Stop previous ajax-request @@ -388,12 +393,12 @@ }, "json" ); }, 200 ); }, - + clear_search: function() { this.set("query", ""); this.set("results", null); } - + }); _.extend(ToolSearch.prototype, VisibilityMixin); @@ -433,7 +438,7 @@ return new ToolSectionLabel(elt_dict); } }; - + return _.map(response, parse_elt); }, @@ -448,14 +453,14 @@ } }); }, - + apply_search_results: function() { var results = this.get('tool_search').get('results'); if (results === null) { this.clear_search_results(); return; } - + var cur_label = null; this.get('layout').each(function(panel_elt) { if (panel_elt instanceof ToolSectionLabel) { @@ -479,13 +484,13 @@ }); /** - * View classes for Galaxy tools and tool panel. - * + * View classes for Galaxy tools and tool panel. + * * Views use precompiled Handlebars templates for rendering. Views update as needed * based on (a) model/collection events and (b) user interactions; in this sense, * they are controllers are well and the HTML is the real view in the MVC architecture. */ - + /** * Base view that handles visibility based on model's hidden attribute. */ @@ -496,9 +501,9 @@ }, update_visible: function() { ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); - } + } }); - + /** * Link to a tool. */ @@ -509,7 +514,7 @@ // create element var $link = $('<div/>'); $link.append(Handlebars.templates.tool_link(this.model.toJSON())); - + // open upload dialog for upload tool if (this.model.id === 'upload1') { $link.find('a').on('click', function(e) { @@ -517,7 +522,7 @@ Galaxy.upload.show(); }); } - + // add element this.$el.append($link); return this; @@ -543,7 +548,7 @@ var ToolSectionView = BaseView.extend({ tagName: 'div', className: 'toolSectionWrapper', - + initialize: function() { BaseView.prototype.initialize.call(this); this.model.on("change:open", this.update_open, this); @@ -552,7 +557,7 @@ render: function() { // Build using template. this.$el.append( Handlebars.templates.panel_section(this.model.toJSON()) ); - + // Add tools to section. var section_body = this.$el.find(".toolSectionBody"); _.each(this.model.attributes.elems, function(elt) { @@ -572,25 +577,25 @@ }); return this; }, - + events: { 'click .toolSectionTitle > a': 'toggle' }, - - /** + + /** * Toggle visibility of tool section. */ toggle: function() { this.model.set("open", !this.model.attributes.open); }, - + /** * Update whether section is open or close. */ update_open: function() { (this.model.attributes.open ? this.$el.children(".toolSectionBody").slideDown("fast") : - this.$el.children(".toolSectionBody").slideUp("fast") + this.$el.children(".toolSectionBody").slideUp("fast") ); } }); @@ -599,13 +604,13 @@ tagName: 'div', id: 'tool-search', className: 'bar', - + events: { 'click': 'focus_and_select', 'keyup :input': 'query_changed', 'click #search-clear-btn': 'clear' }, - + render: function() { this.$el.append( Handlebars.templates.tool_search(this.model.toJSON()) ); if (!this.model.is_visible()) { @@ -614,18 +619,18 @@ this.$el.find('[title]').tooltip(); return this; }, - + focus_and_select: function() { this.$el.find(":input").focus().select(); }, - + clear: function() { this.model.clear_search(); this.$el.find(":input").val(this.model.attributes.search_hint_string); this.focus_and_select(); return false; }, - + query_changed: function( evData ) { // check for the 'clear key' (ESC) first if( ( this.model.attributes.clear_key ) && @@ -644,22 +649,22 @@ var ToolPanelView = Backbone.View.extend({ tagName: 'div', className: 'toolMenu', - + /** * Set up view. */ initialize: function() { this.model.get('tool_search').on("change:results", this.handle_search_results, this); }, - + render: function() { var self = this; - + // Render search. var search_view = new ToolSearchView( { model: this.model.get('tool_search') } ); search_view.render(); self.$el.append(search_view.$el); - + // Render panel. this.model.get('layout').each(function(panel_elt) { if (panel_elt instanceof ToolSection) { @@ -678,20 +683,20 @@ self.$el.append(label_view.$el); } }); - + // Setup tool link click eventing. self.$el.find("a.tool-link").click(function(e) { // Tool id is always the first class. - var + var tool_id = $(this).attr('class').split(/\s+/)[0], tool = self.model.get('tools').get(tool_id); - + self.trigger("tool_link_click", e, tool); }); - + return this; }, - + handle_search_results: function() { var results = this.model.get('tool_search').get('results'); if (results && results.length === 0) { @@ -708,7 +713,7 @@ */ var ToolFormView = Backbone.View.extend({ className: 'toolForm', - + render: function() { this.$el.children().remove(); this.$el.append( Handlebars.templates.tool_form(this.model.toJSON()) ); @@ -720,22 +725,22 @@ */ var IntegratedToolMenuAndView = Backbone.View.extend({ className: 'toolMenuAndView', - + initialize: function() { this.tool_panel_view = new ToolPanelView({collection: this.collection}); this.tool_form_view = new ToolFormView(); }, - + render: function() { // Render and append tool panel. this.tool_panel_view.render(); this.tool_panel_view.$el.css("float", "left"); this.$el.append(this.tool_panel_view.$el); - + // Append tool form view. this.tool_form_view.$el.hide(); this.$el.append(this.tool_form_view.$el); - + // On tool link click, show tool. var self = this; this.tool_panel_view.on("tool_link_click", function(e, tool) { @@ -745,7 +750,7 @@ self.show_tool(tool); }); }, - + /** * Fetch and display tool. */ diff -r 9eeb924b5204ff10bac0998612549de468f9bc2a -r 19079eea7d2285d701866b0df77beeff20a677e8 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -2,7 +2,7 @@ * Model, view, and controller objects for Galaxy tools and tool panel. */ - define( ["libs/underscore", "viz/trackster/util", "mvc/data" ], + define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr.js" ], function(_, util, data) { /** @@ -14,7 +14,7 @@ show: function() { this.set("hidden", false); }, - + hide: function() { this.set("hidden", true); }, @@ -22,7 +22,7 @@ toggle: function() { this.set("hidden", !this.get("hidden")); }, - + is_visible: function() { return !this.attributes.hidden; } @@ -88,7 +88,7 @@ } }); -/** +/** * A select tool parameter. */ var SelectToolParameter = ToolParameter.extend({ @@ -157,7 +157,7 @@ }); tool.get('inputs').remove(incompatible_inputs); }, - + /** * Returns object copy, optionally including only inputs that can be sampled. */ @@ -177,12 +177,12 @@ return copy; }, - + apply_search_results: function(results) { ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); return this.is_visible(); }, - + /** * Set a tool input's value. */ @@ -191,24 +191,24 @@ return input.get('name') === name; }).set('value', value); }, - + /** * Set many input values at once. */ set_input_values: function(inputs_dict) { var self = this; _.each(_.keys(inputs_dict), function(input_name) { - self.set_input_value(input_name, inputs_dict[input_name]); + self.set_input_value(input_name, inputs_dict[input_name]); }); }, - + /** * Run tool; returns a Deferred that resolves to the tool's output(s). */ run: function() { return this._run(); }, - + /** * Rerun tool using regions and a target dataset. */ @@ -230,7 +230,7 @@ }); return input_dict; }, - + /** * Run tool; returns a Deferred that resolves to the tool's output(s). * NOTE: this method is a helper method and should not be called directly. @@ -259,7 +259,7 @@ return response !== "pending"; } }); - + // Run job and resolve run_deferred to tool outputs. $.when(ss_deferred.go()).then(function(result) { run_deferred.resolve(new data.DatasetCollection().reset(result)); @@ -296,20 +296,20 @@ elems: [], open: false }, - + clear_search_results: function() { _.each(this.attributes.elems, function(elt) { elt.show(); }); - + this.show(); this.set("open", false); }, - + apply_search_results: function(results) { var all_hidden = true, cur_label; - _.each(this.attributes.elems, function(elt) { + _.each(this.attributes.elems, function(elt) { if (elt instanceof ToolSectionLabel) { cur_label = elt; cur_label.hide(); @@ -323,7 +323,7 @@ } } }); - + if (all_hidden) { this.hide(); } @@ -340,6 +340,11 @@ * indicates that query was not run; if not null, results are from search using * query. */ + +/** + * TODO: Integrate lunr search here with tools from API instead of making + * repeated requests. + */ var ToolSearch = Backbone.Model.extend({ defaults: { search_hint_string: "search tools", @@ -353,23 +358,23 @@ // ESC (27) will clear the input field and tool search filters clear_key: 27 }, - + initialize: function() { this.on("change:query", this.do_search); }, - + /** * Do the search and update the results. */ do_search: function() { var query = this.attributes.query; - + // If query is too short, do not search. if (query.length < this.attributes.min_chars_for_search) { this.set("results", null); return; } - + // Do search via AJAX. var q = query + '*'; // Stop previous ajax-request @@ -388,12 +393,12 @@ }, "json" ); }, 200 ); }, - + clear_search: function() { this.set("query", ""); this.set("results", null); } - + }); _.extend(ToolSearch.prototype, VisibilityMixin); @@ -433,7 +438,7 @@ return new ToolSectionLabel(elt_dict); } }; - + return _.map(response, parse_elt); }, @@ -448,14 +453,14 @@ } }); }, - + apply_search_results: function() { var results = this.get('tool_search').get('results'); if (results === null) { this.clear_search_results(); return; } - + var cur_label = null; this.get('layout').each(function(panel_elt) { if (panel_elt instanceof ToolSectionLabel) { @@ -479,13 +484,13 @@ }); /** - * View classes for Galaxy tools and tool panel. - * + * View classes for Galaxy tools and tool panel. + * * Views use precompiled Handlebars templates for rendering. Views update as needed * based on (a) model/collection events and (b) user interactions; in this sense, * they are controllers are well and the HTML is the real view in the MVC architecture. */ - + /** * Base view that handles visibility based on model's hidden attribute. */ @@ -496,9 +501,9 @@ }, update_visible: function() { ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() ); - } + } }); - + /** * Link to a tool. */ @@ -509,7 +514,7 @@ // create element var $link = $('<div/>'); $link.append(Handlebars.templates.tool_link(this.model.toJSON())); - + // open upload dialog for upload tool if (this.model.id === 'upload1') { $link.find('a').on('click', function(e) { @@ -517,7 +522,7 @@ Galaxy.upload.show(); }); } - + // add element this.$el.append($link); return this; @@ -543,7 +548,7 @@ var ToolSectionView = BaseView.extend({ tagName: 'div', className: 'toolSectionWrapper', - + initialize: function() { BaseView.prototype.initialize.call(this); this.model.on("change:open", this.update_open, this); @@ -552,7 +557,7 @@ render: function() { // Build using template. this.$el.append( Handlebars.templates.panel_section(this.model.toJSON()) ); - + // Add tools to section. var section_body = this.$el.find(".toolSectionBody"); _.each(this.model.attributes.elems, function(elt) { @@ -572,25 +577,25 @@ }); return this; }, - + events: { 'click .toolSectionTitle > a': 'toggle' }, - - /** + + /** * Toggle visibility of tool section. */ toggle: function() { this.model.set("open", !this.model.attributes.open); }, - + /** * Update whether section is open or close. */ update_open: function() { (this.model.attributes.open ? this.$el.children(".toolSectionBody").slideDown("fast") : - this.$el.children(".toolSectionBody").slideUp("fast") + this.$el.children(".toolSectionBody").slideUp("fast") ); } }); @@ -599,13 +604,13 @@ tagName: 'div', id: 'tool-search', className: 'bar', - + events: { 'click': 'focus_and_select', 'keyup :input': 'query_changed', 'click #search-clear-btn': 'clear' }, - + render: function() { this.$el.append( Handlebars.templates.tool_search(this.model.toJSON()) ); if (!this.model.is_visible()) { @@ -614,18 +619,18 @@ this.$el.find('[title]').tooltip(); return this; }, - + focus_and_select: function() { this.$el.find(":input").focus().select(); }, - + clear: function() { this.model.clear_search(); this.$el.find(":input").val(this.model.attributes.search_hint_string); this.focus_and_select(); return false; }, - + query_changed: function( evData ) { // check for the 'clear key' (ESC) first if( ( this.model.attributes.clear_key ) && @@ -644,22 +649,22 @@ var ToolPanelView = Backbone.View.extend({ tagName: 'div', className: 'toolMenu', - + /** * Set up view. */ initialize: function() { this.model.get('tool_search').on("change:results", this.handle_search_results, this); }, - + render: function() { var self = this; - + // Render search. var search_view = new ToolSearchView( { model: this.model.get('tool_search') } ); search_view.render(); self.$el.append(search_view.$el); - + // Render panel. this.model.get('layout').each(function(panel_elt) { if (panel_elt instanceof ToolSection) { @@ -678,20 +683,20 @@ self.$el.append(label_view.$el); } }); - + // Setup tool link click eventing. self.$el.find("a.tool-link").click(function(e) { // Tool id is always the first class. - var + var tool_id = $(this).attr('class').split(/\s+/)[0], tool = self.model.get('tools').get(tool_id); - + self.trigger("tool_link_click", e, tool); }); - + return this; }, - + handle_search_results: function() { var results = this.model.get('tool_search').get('results'); if (results && results.length === 0) { @@ -708,7 +713,7 @@ */ var ToolFormView = Backbone.View.extend({ className: 'toolForm', - + render: function() { this.$el.children().remove(); this.$el.append( Handlebars.templates.tool_form(this.model.toJSON()) ); @@ -720,22 +725,22 @@ */ var IntegratedToolMenuAndView = Backbone.View.extend({ className: 'toolMenuAndView', - + initialize: function() { this.tool_panel_view = new ToolPanelView({collection: this.collection}); this.tool_form_view = new ToolFormView(); }, - + render: function() { // Render and append tool panel. this.tool_panel_view.render(); this.tool_panel_view.$el.css("float", "left"); this.$el.append(this.tool_panel_view.$el); - + // Append tool form view. this.tool_form_view.$el.hide(); this.$el.append(this.tool_form_view.$el); - + // On tool link click, show tool. var self = this; this.tool_panel_view.on("tool_link_click", function(e, tool) { @@ -745,7 +750,7 @@ self.show_tool(tool); }); }, - + /** * Fetch and display tool. */ diff -r 9eeb924b5204ff10bac0998612549de468f9bc2a -r 19079eea7d2285d701866b0df77beeff20a677e8 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){var z=$("<div/>");z.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){z.find("a").on("click",function(A){A.preventDefault();Galaxy.upload.show()})}this.$el.append(z);return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/lunr.js"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){var z=$("<div/>");z.append(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){z.find("a").on("click",function(A){A.preventDefault();Galaxy.upload.show()})}this.$el.append(z);return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Minor bug fixes for main.py (webless Galaxy entry point).
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/85b1de6a6ebd/ Changeset: 85b1de6a6ebd User: natefoo Date: 2015-02-05 04:40:59+00:00 Summary: Minor bug fixes for main.py (webless Galaxy entry point). Affected #: 1 file diff -r 00f4c600b89fdd52b0296e8bfc599a16485838b2 -r 85b1de6a6ebdfe30e14b96f8dc7d13105ae04c2b lib/galaxy/main.py --- a/lib/galaxy/main.py +++ b/lib/galaxy/main.py @@ -36,7 +36,7 @@ # Vaguely Python 2.6 compatibile ArgumentParser import try: - from argparser import ArgumentParser + from argparse import ArgumentParser except ImportError: from optparse import OptionParser @@ -202,9 +202,6 @@ def main(): - if Daemonize is None: - raise ImportError(REQUIRES_DAEMONIZE_MESSAGE) - arg_parser = ArgumentParser(description=DESCRIPTION) GalaxyConfigBuilder.populate_options(arg_parser) args = arg_parser.parse_args() @@ -217,6 +214,9 @@ log.setLevel(logging.DEBUG) log.propagate = False if args.daemonize: + if Daemonize is None: + raise ImportError(REQUIRES_DAEMONIZE_MESSAGE) + keep_fds = [] if args.daemon_log_file: fh = logging.FileHandler(args.daemon_log_file, "w") Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Allow reloading External Display applications without restarting Galaxy.
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/00f4c600b89f/ Changeset: 00f4c600b89f User: dan Date: 2015-02-04 21:12:03+00:00 Summary: Allow reloading External Display applications without restarting Galaxy. Affected #: 5 files diff -r dee88f35c796e413ae071a49716dff1a9238d66c -r 00f4c600b89fdd52b0296e8bfc599a16485838b2 lib/galaxy/datatypes/display_applications/application.py --- a/lib/galaxy/datatypes/display_applications/application.py +++ b/lib/galaxy/datatypes/display_applications/application.py @@ -167,23 +167,21 @@ class DisplayApplication( object ): @classmethod def from_file( cls, filename, datatypes_registry ): - return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) + return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry, filename=filename ) @classmethod - def from_elem( cls, elem, datatypes_registry ): + def from_elem( cls, elem, datatypes_registry, filename=None ): + att_dict = cls._get_attributes_from_elem( elem ) + rval = DisplayApplication( att_dict['id'], att_dict['name'], datatypes_registry, att_dict['version'], filename=filename, elem=elem ) + rval._load_links_from_elem( elem ) + return rval + @classmethod + def _get_attributes_from_elem( cls, elem ): display_id = elem.get( 'id', None ) assert display_id, "ID tag is required for a Display Application" name = elem.get( 'name', display_id ) version = elem.get( 'version', None ) - rval = DisplayApplication( display_id, name, datatypes_registry, version ) - for link_elem in elem.findall( 'link' ): - link = DisplayApplicationLink.from_elem( link_elem, rval ) - if link: - rval.links[ link.id ] = link - for dynamic_links in elem.findall( 'dynamic_links' ): - for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): - rval.links[ link.id ] = link - return rval - def __init__( self, display_id, name, datatypes_registry, version = None ): + return dict( id=display_id, name=name, version=version ) + def __init__( self, display_id, name, datatypes_registry, version = None, filename=None, elem=None ): self.id = display_id self.name = name self.datatypes_registry = datatypes_registry @@ -191,6 +189,16 @@ version = "1.0.0" self.version = version self.links = odict() + self._filename = filename + self._elem = elem + def _load_links_from_elem( self, elem ): + for link_elem in elem.findall( 'link' ): + link = DisplayApplicationLink.from_elem( link_elem, self ) + if link: + self.links[ link.id ] = link + for dynamic_links in elem.findall( 'dynamic_links' ): + for link in DynamicDisplayApplicationBuilder( dynamic_links, self, self.datatypes_registry.build_sites ): + self.links[ link.id ] = link def get_link( self, link_name, data, dataset_hash, user_hash, trans, app_kwds ): #returns a link object with data knowledge to generate links return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans, app_kwds ) @@ -200,3 +208,23 @@ if link_value.filter_by_dataset( data, trans ): filtered.links[link_name] = link_value return filtered + def reload( self ): + if self._filename: + elem = parse_xml( self._filename ).getroot() + elif self._elem: + elem = self._elem + else: + raise Exception( "Unable to reload DisplayApplication %s." % ( self.name ) ) + # All toolshed-specific attributes added by e.g the registry will remain + attr_dict = self._get_attributes_from_elem( elem ) + # We will not allow changing the id at this time (we'll need to fix several mappings upstream to handle this case) + assert attr_dict.get( 'id' ) == self.id, ValueError( "You cannot reload a Display application where the ID has changed. You will need to restart the server instead." ) + # clear old links + for key in self.links.keys(): + del self.links[key] + # Set new attributes + for key, value in attr_dict.iteritems(): + setattr( self, key, value ) + # Load new links + self._load_links_from_elem( elem ) + return self diff -r dee88f35c796e413ae071a49716dff1a9238d66c -r 00f4c600b89fdd52b0296e8bfc599a16485838b2 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -621,6 +621,26 @@ self.log.debug( "Adding inherited display application '%s' to datatype '%s'" % ( display_app.id, extension ) ) d_type1.add_display_application( display_app ) + def reload_display_applications( self, display_application_ids=None ): + """ + Reloads display applications: by id, or all if no ids provided + Returns tuple( [reloaded_ids], [failed_ids] ) + """ + if not display_application_ids: + display_application_ids = self.display_applications.keys() + elif not isinstance( display_application_ids, list ): + display_application_ids = [ display_application_ids ] + reloaded = [] + failed = [] + for display_application_id in display_application_ids: + try: + self.display_applications[ display_application_id ].reload() + reloaded.append( display_application_id ) + except Exception, e: + self.log.debug( 'Requested to reload display application "%s", but failed: %s.', display_application_id, e ) + failed.append( display_application_id ) + return ( reloaded, failed ) + def load_external_metadata_tool( self, toolbox ): """Adds a tool which is used to set external metadata""" # We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated diff -r dee88f35c796e413ae071a49716dff1a9238d66c -r 00f4c600b89fdd52b0296e8bfc599a16485838b2 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -883,3 +883,21 @@ message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) ) status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) ) return trans.fill_template( 'admin/view_data_tables_registry.mako', message=message, status=status ) + + @web.expose + @web.require_admin + def display_applications( self, trans, **kwd ): + return trans.fill_template( 'admin/view_display_applications.mako', display_applications=trans.app.datatypes_registry.display_applications ) + + @web.expose + @web.require_admin + def reload_display_application( self, trans, **kwd ): + reloaded, failed = trans.app.datatypes_registry.reload_display_applications( kwd.get( 'id' ) ) + if not reloaded and failed: + return trans.show_error_message( 'Unable to reload any of the %i requested display applications ("%s").' % ( len( failed ), '", "'.join( failed ) ) ) + if failed: + return trans.show_warn_message( 'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").' + % ( len( reloaded ), '", "'.join( reloaded ), len( failed ), '", "'.join( failed ) ) ) + if not reloaded: + return trans.show_warn_message( 'You need to request at least one display application to reload.' ) + return trans.show_ok_message( 'Reloaded %i requested display applications ("%s").' % ( len( reloaded ), '", "'.join( reloaded ) ) ) diff -r dee88f35c796e413ae071a49716dff1a9238d66c -r 00f4c600b89fdd52b0296e8bfc599a16485838b2 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -75,6 +75,7 @@ <div class="toolSectionBg"><div class="toolTitle"><a href="${h.url_for( controller='admin', action='view_datatypes_registry' )}" target="galaxy_main">View data types registry</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='view_tool_data_tables' )}" target="galaxy_main">View data tables registry</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='display_applications' )}" target="galaxy_main">View display applications</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='tool_versions' )}" target="galaxy_main">View tool lineage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='package_tool' )}" target="galaxy_main">Download tool tarball</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='reload_tool' )}" target="galaxy_main">Reload a tool's configuration</a></div> diff -r dee88f35c796e413ae071a49716dff1a9238d66c -r 00f4c600b89fdd52b0296e8bfc599a16485838b2 templates/webapps/galaxy/admin/view_display_applications.mako --- /dev/null +++ b/templates/webapps/galaxy/admin/view_display_applications.mako @@ -0,0 +1,48 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">There are currently ${len( display_applications )} <a class="icon-btn" href="${ h.url_for( controller='admin', action='reload_display_application' ) }" title="Reload all display applications" data-placement="bottom"> + <span class="fa fa-refresh"></span> + </a> display applications loaded.</div> + <div class="toolFormBody"> + <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> + <tr> + <th bgcolor="#D8D8D8">Reload</th> + <th bgcolor="#D8D8D8">Name</th> + <th bgcolor="#D8D8D8">ID</th> + <th bgcolor="#D8D8D8">Version</th> + <th bgcolor="#D8D8D8">Links</th> + <th bgcolor="#D8D8D8">Filename</th> + </tr> + <% ctr = 0 %> + %for display_app in display_applications.values(): + %if ctr % 2 == 1: + <tr class="odd_row"> + %else: + <tr class="tr"> + %endif + <td> + <a class="icon-btn" href="${ h.url_for( controller='admin', action='reload_display_application', id=display_app.id ) }" title="Reload ${ display_app.name | h } display application" data-placement="bottom"> + <span class="fa fa-refresh"></span> + </a> + </td> + <td>${ display_app.name | h }</td> + <td>${ display_app.id | h }</td> + <td>${ display_app.version | h }</td> + <td><ul> + %for link in display_app.links.values(): + <li>${ link.name | h }</li> + %endfor + </ul></td> + <td>${ display_app._filename | h }</td> + </tr> + <% ctr += 1 %> + %endfor + </table> + </div> +</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merged in dan/galaxy-central-prs (pull request #659)
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dee88f35c796/ Changeset: dee88f35c796 User: dannon Date: 2015-02-04 17:45:56+00:00 Summary: Merged in dan/galaxy-central-prs (pull request #659) In API, when removing or refreshing a data table, send the reload signal to the worker queue. Change return values of reload and delete to be the new table contents, instead of the only-internally-useful 'version'. Affected #: 1 file diff -r 7c04c98d7b6af49164615bf3988942a19a1fc620 -r dee88f35c796e413ae071a49716dff1a9238d66c lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -5,6 +5,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_raw as expose_api_raw from galaxy.web.base.controller import BaseAPIController +import galaxy.queue_worker class ToolData( BaseAPIController ): @@ -36,7 +37,11 @@ """ decoded_tool_data_id = id data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id) - return data_table.reload_from_files() + data_table.reload_from_files() + galaxy.queue_worker.send_control_task( trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': decoded_tool_data_id} ) + return self._data_table( decoded_tool_data_id ).to_dict( view='element' ) @web.require_admin @@ -78,7 +83,11 @@ trans.response.status = 400 return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) - return data_table.remove_entry(split_values) + data_table.remove_entry(split_values) + galaxy.queue_worker.send_control_task( trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': decoded_tool_data_id} ) + return self._data_table( decoded_tool_data_id ).to_dict( view='element' ) @web.require_admin @expose_api Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5435d68586aa/ Changeset: 5435d68586aa User: dan Date: 2015-02-04 15:02:20+00:00 Summary: In API, when removing or refreshing a data table, send the reload signal to the worker queue. Change return values of reload and delete to be the new table contents, instead of the only-internally-useful 'version'. Affected #: 1 file diff -r 9bc22ec1a8156fe640fd049399cb39c8755eef73 -r 5435d68586aa09f74391504030b6d30eb627f66e lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -5,6 +5,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_raw as expose_api_raw from galaxy.web.base.controller import BaseAPIController +import galaxy.queue_worker class ToolData( BaseAPIController ): @@ -36,7 +37,11 @@ """ decoded_tool_data_id = id data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id) - return data_table.reload_from_files() + data_table.reload_from_files() + galaxy.queue_worker.send_control_task( trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': decoded_tool_data_id} ) + return self._data_table( decoded_tool_data_id ).to_dict( view='element' ) @web.require_admin @@ -78,7 +83,11 @@ trans.response.status = 400 return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) - return data_table.remove_entry(split_values) + data_table.remove_entry(split_values) + galaxy.queue_worker.send_control_task( trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': decoded_tool_data_id} ) + return self._data_table( decoded_tool_data_id ).to_dict( view='element' ) @web.require_admin @expose_api https://bitbucket.org/galaxy/galaxy-central/commits/dee88f35c796/ Changeset: dee88f35c796 User: dannon Date: 2015-02-04 17:45:56+00:00 Summary: Merged in dan/galaxy-central-prs (pull request #659) In API, when removing or refreshing a data table, send the reload signal to the worker queue. Change return values of reload and delete to be the new table contents, instead of the only-internally-useful 'version'. Affected #: 1 file diff -r 7c04c98d7b6af49164615bf3988942a19a1fc620 -r dee88f35c796e413ae071a49716dff1a9238d66c lib/galaxy/webapps/galaxy/api/tool_data.py --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -5,6 +5,7 @@ from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_raw as expose_api_raw from galaxy.web.base.controller import BaseAPIController +import galaxy.queue_worker class ToolData( BaseAPIController ): @@ -36,7 +37,11 @@ """ decoded_tool_data_id = id data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id) - return data_table.reload_from_files() + data_table.reload_from_files() + galaxy.queue_worker.send_control_task( trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': decoded_tool_data_id} ) + return self._data_table( decoded_tool_data_id ).to_dict( view='element' ) @web.require_admin @@ -78,7 +83,11 @@ trans.response.status = 400 return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list()))) - return data_table.remove_entry(split_values) + data_table.remove_entry(split_values) + galaxy.queue_worker.send_control_task( trans, 'reload_tool_data_tables', + noop_self=True, + kwargs={'table_name': decoded_tool_data_id} ) + return self._data_table( decoded_tool_data_id ).to_dict( view='element' ) @web.require_admin @expose_api Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Update hgignore to include all .lock, .pid, and .log files.
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7c04c98d7b6a/ Changeset: 7c04c98d7b6a User: dannon Date: 2015-02-04 17:07:01+00:00 Summary: Update hgignore to include all .lock, .pid, and .log files. Affected #: 1 file diff -r f0ae870b22e955a6668dd46e55b31e708184abb4 -r 7c04c98d7b6af49164615bf3988942a19a1fc620 .hgignore --- a/.hgignore +++ b/.hgignore @@ -30,9 +30,9 @@ *.pyc # Galaxy Runtime Files -paster.lock -paster.log -paster.pid +*.lock +*.log +*.pid # Tool Shed Runtime Files tool_shed_webapp.lock Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/09bfb4f3f60d/ Changeset: 09bfb4f3f60d User: dannon Date: 2015-02-04 15:33:07+00:00 Summary: Initial version of session_timeout. Still needs client side work to handle API/web.json requests better but that turned out to be a large project -- see TODOs for more details. Affected #: 5 files diff -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 -r 09bfb4f3f60d4fa31bc4f0ed91151cc60d0c6256 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -392,6 +392,13 @@ #inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. + +# Galaxy Session Timeout +# This provides a timeout (in minutes) after which a user will have to log back in. +# A duration of 0 disables this feature. +#session_duration = 0 + + # -- Analytics # You can enter tracking code here to track visitor's behavior diff -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 -r 09bfb4f3f60d4fa31bc4f0ed91151cc60d0c6256 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -171,6 +171,7 @@ self.instance_resource_url = kwargs.get( 'instance_resource_url', None ) self.registration_warning_message = kwargs.get( 'registration_warning_message', None ) self.ga_code = kwargs.get( 'ga_code', None ) + self.session_duration = int(kwargs.get( 'session_duration', 0 )) # Get the disposable email domains blacklist file and its contents self.blacklist_location = kwargs.get( 'blacklist_file', None ) self.blacklist_content = None diff -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 -r 09bfb4f3f60d4fa31bc4f0ed91151cc60d0c6256 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1335,7 +1335,7 @@ FAILED_METADATA = 'failed_metadata', RESUBMITTED = 'resubmitted' ) # failed_metadata and resubmitted are only valid as DatasetInstance states currently - + non_ready_states = ( states.UPLOAD, states.QUEUED, @@ -2997,6 +2997,7 @@ self.is_valid = is_valid self.prev_session_id = prev_session_id self.histories = [] + self.last_action = galaxy.model.orm.now.now() def add_history( self, history, association=None ): if association is None: diff -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 -r 09bfb4f3f60d4fa31bc4f0ed91151cc60d0c6256 lib/galaxy/model/migrate/versions/0128_session_timeout.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0128_session_timeout.py @@ -0,0 +1,50 @@ +""" +Migration script to add session update time (used for timeouts) +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + + lastaction_column = Column( "last_action", DateTime, default=now ) + __add_column( lastaction_column, "galaxy_session", metadata ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + + __drop_column( "last_action", "galaxy_session", metadata ) + + +def __add_column(column, table_name, metadata, **kwds): + try: + table = Table( table_name, metadata, autoload=True ) + column.create( table, **kwds ) + except Exception as e: + print str(e) + log.exception( "Adding column %s failed." % column) + + +def __drop_column( column_name, table_name, metadata ): + try: + table = Table( table_name, metadata, autoload=True ) + getattr( table.c, column_name ).drop() + except Exception as e: + print str(e) + log.exception( "Dropping column %s failed." % column_name ) diff -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 -r 09bfb4f3f60d4fa31bc4f0ed91151cc60d0c6256 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -1,5 +1,6 @@ """ """ +import datetime import inspect import os import hashlib @@ -210,6 +211,32 @@ self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) if config.require_login: self._ensure_logged_in_user( environ, session_cookie ) + if config.session_duration and not self.environ.get('is_api_request', False): + # TODO DBTODO Session-based API requests need to be handled + # correctly here. Disabled for now. The issue is that API + # request response error codes aren't handled in a consistent + # way on the client side. All ajax calls from the client need + # to go through a single point of control where we can do things + # like redirect/etc. This is API calls as well as something + # like 40 @web.json requests that might not get handled well on + # the clientside. + # + # Make sure we're not past the duration, and either log out or + # update timestamp. + now = datetime.datetime.now() + expiration_time = self.galaxy_session.update_time + datetime.timedelta(minutes=config.session_duration) + if expiration_time < now: + # Expiration time has passed. + self.handle_user_logout() + self.response.send_redirect( url_for( controller='user', + action='login', + message="You have been logged out due to inactivity. Please log in again to continue using Galaxy.", + status='info', + use_panels=True ) ) + else: + self.galaxy_session.update_time = datetime.datetime.now() + self.sa_session.add(self.galaxy_session) + self.sa_session.flush() def setup_i18n( self ): locales = [] https://bitbucket.org/galaxy/galaxy-central/commits/d3a4dca4bfa5/ Changeset: d3a4dca4bfa5 User: dannon Date: 2015-02-04 16:06:53+00:00 Summary: Handle timeout correctly for API requests. There's still the issue of clients potentially not understanding this, and of course the @web.json requests. Affected #: 1 file diff -r 09bfb4f3f60d4fa31bc4f0ed91151cc60d0c6256 -r d3a4dca4bfa571599494a315343c2e635fbc7b5f lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -211,7 +211,7 @@ self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) if config.require_login: self._ensure_logged_in_user( environ, session_cookie ) - if config.session_duration and not self.environ.get('is_api_request', False): + if config.session_duration: # TODO DBTODO Session-based API requests need to be handled # correctly here. Disabled for now. The issue is that API # request response error codes aren't handled in a consistent @@ -228,7 +228,12 @@ if expiration_time < now: # Expiration time has passed. self.handle_user_logout() - self.response.send_redirect( url_for( controller='user', + if self.environ.get('is_api_request', False): + self.response.status = 401 + self.user = None + self.galaxy_session = None + else: + self.response.send_redirect( url_for( controller='user', action='login', message="You have been logged out due to inactivity. Please log in again to continue using Galaxy.", status='info', https://bitbucket.org/galaxy/galaxy-central/commits/2d7653d16e02/ Changeset: 2d7653d16e02 User: dannon Date: 2015-02-04 16:07:58+00:00 Summary: Update commentary per previous commit re: API request handling. Affected #: 1 file diff -r d3a4dca4bfa571599494a315343c2e635fbc7b5f -r 2d7653d16e02119e9028c63b4a4920f46a7cefa6 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -212,14 +212,11 @@ if config.require_login: self._ensure_logged_in_user( environ, session_cookie ) if config.session_duration: - # TODO DBTODO Session-based API requests need to be handled - # correctly here. Disabled for now. The issue is that API - # request response error codes aren't handled in a consistent - # way on the client side. All ajax calls from the client need - # to go through a single point of control where we can do things - # like redirect/etc. This is API calls as well as something - # like 40 @web.json requests that might not get handled well on - # the clientside. + # TODO DBTODO All ajax calls from the client need to go through + # a single point of control where we can do things like + # redirect/etc. This is API calls as well as something like 40 + # @web.json requests that might not get handled well on the + # clientside. # # Make sure we're not past the duration, and either log out or # update timestamp. https://bitbucket.org/galaxy/galaxy-central/commits/f0ae870b22e9/ Changeset: f0ae870b22e9 User: dannon Date: 2015-02-04 16:08:25+00:00 Summary: pep8 webapp.py. Affected #: 1 file diff -r 2d7653d16e02119e9028c63b4a4920f46a7cefa6 -r f0ae870b22e955a6668dd46e55b31e708184abb4 lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -231,10 +231,10 @@ self.galaxy_session = None else: self.response.send_redirect( url_for( controller='user', - action='login', - message="You have been logged out due to inactivity. Please log in again to continue using Galaxy.", - status='info', - use_panels=True ) ) + action='login', + message="You have been logged out due to inactivity. Please log in again to continue using Galaxy.", + status='info', + use_panels=True ) ) else: self.galaxy_session.update_time = datetime.datetime.now() self.sa_session.add(self.galaxy_session) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: UI, client build: change source for jquery-migrate (no version change)
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11c8048ae648/ Changeset: 11c8048ae648 User: carlfeberhard Date: 2015-02-04 15:04:20+00:00 Summary: UI, client build: change source for jquery-migrate (no version change) Affected #: 4 files diff -r 9bc22ec1a8156fe640fd049399cb39c8755eef73 -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 client/GruntFile.js --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -68,13 +68,13 @@ // 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-official": [ "index.js", "jquery/jquery.migrate.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" ] //"backbone": [ "backbone.js", "backbone/backbone.js" ], - "handlebars": [ "handlebars.runtime.js", "handlebars.runtime.js" ] // these need to be updated and tested //"require": [ "build/require.js", "require.js" ], diff -r 9bc22ec1a8156fe640fd049399cb39c8755eef73 -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 client/bower.json --- a/client/bower.json +++ b/client/bower.json @@ -9,7 +9,6 @@ "homepage": "usegalaxy.org", "dependencies": { "jquery": "~1.11.1", - "jquery-migrate-official": "http://code.jquery.com/jquery-migrate-1.2.1.js", "traceKit": "*", "ravenjs": "~1.1.16", "require": "*", @@ -32,7 +31,8 @@ "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" + "handlebars": "~2.0.0", + "jquery-migrate": "~1.2.1" }, "resolutions": { "jquery": "~1.11.1" diff -r 9bc22ec1a8156fe640fd049399cb39c8755eef73 -r 11c8048ae648d3b8ddae7f180f6bbde4aac4fb83 client/galaxy/scripts/libs/jquery/jquery.migrate.js --- a/client/galaxy/scripts/libs/jquery/jquery.migrate.js +++ b/client/galaxy/scripts/libs/jquery/jquery.migrate.js @@ -1,521 +1,521 @@ -/*! - * jQuery Migrate - v1.2.1 - 2013-05-08 - * https://github.com/jquery/jquery-migrate - * Copyright 2005, 2013 jQuery Foundation, Inc. and other contributors; Licensed MIT - */ -(function( jQuery, window, undefined ) { -// See http://bugs.jquery.com/ticket/13335 -// "use strict"; - - -var warnedAbout = {}; - -// List of warnings already given; public read only -jQuery.migrateWarnings = []; - -// Set to true to prevent console output; migrateWarnings still maintained -// jQuery.migrateMute = false; - -// Show a message on the console so devs know we're active -if ( !jQuery.migrateMute && window.console && window.console.log ) { - window.console.log("JQMIGRATE: Logging is active"); -} - -// Set to false to disable traces that appear with warnings -if ( jQuery.migrateTrace === undefined ) { - jQuery.migrateTrace = true; -} - -// Forget any warnings we've already given; public -jQuery.migrateReset = function() { - warnedAbout = {}; - jQuery.migrateWarnings.length = 0; -}; - -function migrateWarn( msg) { - var console = window.console; - if ( !warnedAbout[ msg ] ) { - warnedAbout[ msg ] = true; - jQuery.migrateWarnings.push( msg ); - if ( console && console.warn && !jQuery.migrateMute ) { - console.warn( "JQMIGRATE: " + msg ); - if ( jQuery.migrateTrace && console.trace ) { - console.trace(); - } - } - } -} - -function migrateWarnProp( obj, prop, value, msg ) { - if ( Object.defineProperty ) { - // On ES5 browsers (non-oldIE), warn if the code tries to get prop; - // allow property to be overwritten in case some other plugin wants it - try { - Object.defineProperty( obj, prop, { - configurable: true, - enumerable: true, - get: function() { - migrateWarn( msg ); - return value; - }, - set: function( newValue ) { - migrateWarn( msg ); - value = newValue; - } - }); - return; - } catch( err ) { - // IE8 is a dope about Object.defineProperty, can't warn there - } - } - - // Non-ES5 (or broken) browser; just set the property - jQuery._definePropertyBroken = true; - obj[ prop ] = value; -} - -if ( document.compatMode === "BackCompat" ) { - // jQuery has never supported or tested Quirks Mode - migrateWarn( "jQuery is not compatible with Quirks Mode" ); -} - - -var attrFn = jQuery( "<input/>", { size: 1 } ).attr("size") && jQuery.attrFn, - oldAttr = jQuery.attr, - valueAttrGet = jQuery.attrHooks.value && jQuery.attrHooks.value.get || - function() { return null; }, - valueAttrSet = jQuery.attrHooks.value && jQuery.attrHooks.value.set || - function() { return undefined; }, - rnoType = /^(?:input|button)$/i, - rnoAttrNodeType = /^[238]$/, - rboolean = /^(?:autofocus|autoplay|async|checked|controls|defer|disabled|hidden|loop|multiple|open|readonly|required|scoped|selected)$/i, - ruseDefault = /^(?:checked|selected)$/i; - -// jQuery.attrFn -migrateWarnProp( jQuery, "attrFn", attrFn || {}, "jQuery.attrFn is deprecated" ); - -jQuery.attr = function( elem, name, value, pass ) { - var lowerName = name.toLowerCase(), - nType = elem && elem.nodeType; - - if ( pass ) { - // Since pass is used internally, we only warn for new jQuery - // versions where there isn't a pass arg in the formal params - if ( oldAttr.length < 4 ) { - migrateWarn("jQuery.fn.attr( props, pass ) is deprecated"); - } - if ( elem && !rnoAttrNodeType.test( nType ) && - (attrFn ? name in attrFn : jQuery.isFunction(jQuery.fn[name])) ) { - return jQuery( elem )[ name ]( value ); - } - } - - // Warn if user tries to set `type`, since it breaks on IE 6/7/8; by checking - // for disconnected elements we don't warn on $( "<button>", { type: "button" } ). - if ( name === "type" && value !== undefined && rnoType.test( elem.nodeName ) && elem.parentNode ) { - migrateWarn("Can't change the 'type' of an input or button in IE 6/7/8"); - } - - // Restore boolHook for boolean property/attribute synchronization - if ( !jQuery.attrHooks[ lowerName ] && rboolean.test( lowerName ) ) { - jQuery.attrHooks[ lowerName ] = { - get: function( elem, name ) { - // Align boolean attributes with corresponding properties - // Fall back to attribute presence where some booleans are not supported - var attrNode, - property = jQuery.prop( elem, name ); - return property === true || typeof property !== "boolean" && - ( attrNode = elem.getAttributeNode(name) ) && attrNode.nodeValue !== false ? - - name.toLowerCase() : - undefined; - }, - set: function( elem, value, name ) { - var propName; - if ( value === false ) { - // Remove boolean attributes when set to false - jQuery.removeAttr( elem, name ); - } else { - // value is true since we know at this point it's type boolean and not false - // Set boolean attributes to the same name and set the DOM property - propName = jQuery.propFix[ name ] || name; - if ( propName in elem ) { - // Only set the IDL specifically if it already exists on the element - elem[ propName ] = true; - } - - elem.setAttribute( name, name.toLowerCase() ); - } - return name; - } - }; - - // Warn only for attributes that can remain distinct from their properties post-1.9 - if ( ruseDefault.test( lowerName ) ) { - migrateWarn( "jQuery.fn.attr('" + lowerName + "') may use property instead of attribute" ); - } - } - - return oldAttr.call( jQuery, elem, name, value ); -}; - -// attrHooks: value -jQuery.attrHooks.value = { - get: function( elem, name ) { - var nodeName = ( elem.nodeName || "" ).toLowerCase(); - if ( nodeName === "button" ) { - return valueAttrGet.apply( this, arguments ); - } - if ( nodeName !== "input" && nodeName !== "option" ) { - migrateWarn("jQuery.fn.attr('value') no longer gets properties"); - } - return name in elem ? - elem.value : - null; - }, - set: function( elem, value ) { - var nodeName = ( elem.nodeName || "" ).toLowerCase(); - if ( nodeName === "button" ) { - return valueAttrSet.apply( this, arguments ); - } - if ( nodeName !== "input" && nodeName !== "option" ) { - migrateWarn("jQuery.fn.attr('value', val) no longer sets properties"); - } - // Does not return so that setAttribute is also used - elem.value = value; - } -}; - - -var matched, browser, - oldInit = jQuery.fn.init, - oldParseJSON = jQuery.parseJSON, - // Note: XSS check is done below after string is trimmed - rquickExpr = /^([^<]*)(<[\w\W]+>)([^>]*)$/; - -// $(html) "looks like html" rule change -jQuery.fn.init = function( selector, context, rootjQuery ) { - var match; - - if ( selector && typeof selector === "string" && !jQuery.isPlainObject( context ) && - (match = rquickExpr.exec( jQuery.trim( selector ) )) && match[ 0 ] ) { - // This is an HTML string according to the "old" rules; is it still? - if ( selector.charAt( 0 ) !== "<" ) { - migrateWarn("$(html) HTML strings must start with '<' character"); - } - if ( match[ 3 ] ) { - migrateWarn("$(html) HTML text after last tag is ignored"); - } - // Consistently reject any HTML-like string starting with a hash (#9521) - // Note that this may break jQuery 1.6.x code that otherwise would work. - if ( match[ 0 ].charAt( 0 ) === "#" ) { - migrateWarn("HTML string cannot start with a '#' character"); - jQuery.error("JQMIGRATE: Invalid selector string (XSS)"); - } - // Now process using loose rules; let pre-1.8 play too - if ( context && context.context ) { - // jQuery object as context; parseHTML expects a DOM object - context = context.context; - } - if ( jQuery.parseHTML ) { - return oldInit.call( this, jQuery.parseHTML( match[ 2 ], context, true ), - context, rootjQuery ); - } - } - return oldInit.apply( this, arguments ); -}; -jQuery.fn.init.prototype = jQuery.fn; - -// Let $.parseJSON(falsy_value) return null -jQuery.parseJSON = function( json ) { - if ( !json && json !== null ) { - migrateWarn("jQuery.parseJSON requires a valid JSON string"); - return null; - } - return oldParseJSON.apply( this, arguments ); -}; - -jQuery.uaMatch = function( ua ) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec( ua ) || - /(webkit)[ \/]([\w.]+)/.exec( ua ) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec( ua ) || - /(msie) ([\w.]+)/.exec( ua ) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec( ua ) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; -}; - -// Don't clobber any existing jQuery.browser in case it's different -if ( !jQuery.browser ) { - matched = jQuery.uaMatch( navigator.userAgent ); - browser = {}; - - if ( matched.browser ) { - browser[ matched.browser ] = true; - browser.version = matched.version; - } - - // Chrome is Webkit, but Webkit is also Safari. - if ( browser.chrome ) { - browser.webkit = true; - } else if ( browser.webkit ) { - browser.safari = true; - } - - jQuery.browser = browser; -} - -// Warn if the code tries to get jQuery.browser -migrateWarnProp( jQuery, "browser", jQuery.browser, "jQuery.browser is deprecated" ); - -jQuery.sub = function() { - function jQuerySub( selector, context ) { - return new jQuerySub.fn.init( selector, context ); - } - jQuery.extend( true, jQuerySub, this ); - jQuerySub.superclass = this; - jQuerySub.fn = jQuerySub.prototype = this(); - jQuerySub.fn.constructor = jQuerySub; - jQuerySub.sub = this.sub; - jQuerySub.fn.init = function init( selector, context ) { - if ( context && context instanceof jQuery && !(context instanceof jQuerySub) ) { - context = jQuerySub( context ); - } - - return jQuery.fn.init.call( this, selector, context, rootjQuerySub ); - }; - jQuerySub.fn.init.prototype = jQuerySub.fn; - var rootjQuerySub = jQuerySub(document); - migrateWarn( "jQuery.sub() is deprecated" ); - return jQuerySub; -}; - - -// Ensure that $.ajax gets the new parseJSON defined in core.js -jQuery.ajaxSetup({ - converters: { - "text json": jQuery.parseJSON - } -}); - - -var oldFnData = jQuery.fn.data; - -jQuery.fn.data = function( name ) { - var ret, evt, - elem = this[0]; - - // Handles 1.7 which has this behavior and 1.8 which doesn't - if ( elem && name === "events" && arguments.length === 1 ) { - ret = jQuery.data( elem, name ); - evt = jQuery._data( elem, name ); - if ( ( ret === undefined || ret === evt ) && evt !== undefined ) { - migrateWarn("Use of jQuery.fn.data('events') is deprecated"); - return evt; - } - } - return oldFnData.apply( this, arguments ); -}; - - -var rscriptType = /\/(java|ecma)script/i, - oldSelf = jQuery.fn.andSelf || jQuery.fn.addBack; - -jQuery.fn.andSelf = function() { - migrateWarn("jQuery.fn.andSelf() replaced by jQuery.fn.addBack()"); - return oldSelf.apply( this, arguments ); -}; - -// Since jQuery.clean is used internally on older versions, we only shim if it's missing -if ( !jQuery.clean ) { - jQuery.clean = function( elems, context, fragment, scripts ) { - // Set context per 1.8 logic - context = context || document; - context = !context.nodeType && context[0] || context; - context = context.ownerDocument || context; - - migrateWarn("jQuery.clean() is deprecated"); - - var i, elem, handleScript, jsTags, - ret = []; - - jQuery.merge( ret, jQuery.buildFragment( elems, context ).childNodes ); - - // Complex logic lifted directly from jQuery 1.8 - if ( fragment ) { - // Special handling of each script element - handleScript = function( elem ) { - // Check if we consider it executable - if ( !elem.type || rscriptType.test( elem.type ) ) { - // Detach the script and store it in the scripts array (if provided) or the fragment - // Return truthy to indicate that it has been handled - return scripts ? - scripts.push( elem.parentNode ? elem.parentNode.removeChild( elem ) : elem ) : - fragment.appendChild( elem ); - } - }; - - for ( i = 0; (elem = ret[i]) != null; i++ ) { - // Check if we're done after handling an executable script - if ( !( jQuery.nodeName( elem, "script" ) && handleScript( elem ) ) ) { - // Append to fragment and handle embedded scripts - fragment.appendChild( elem ); - if ( typeof elem.getElementsByTagName !== "undefined" ) { - // handleScript alters the DOM, so use jQuery.merge to ensure snapshot iteration - jsTags = jQuery.grep( jQuery.merge( [], elem.getElementsByTagName("script") ), handleScript ); - - // Splice the scripts into ret after their former ancestor and advance our index beyond them - ret.splice.apply( ret, [i + 1, 0].concat( jsTags ) ); - i += jsTags.length; - } - } - } - } - - return ret; - }; -} - -var eventAdd = jQuery.event.add, - eventRemove = jQuery.event.remove, - eventTrigger = jQuery.event.trigger, - oldToggle = jQuery.fn.toggle, - oldLive = jQuery.fn.live, - oldDie = jQuery.fn.die, - ajaxEvents = "ajaxStart|ajaxStop|ajaxSend|ajaxComplete|ajaxError|ajaxSuccess", - rajaxEvent = new RegExp( "\\b(?:" + ajaxEvents + ")\\b" ), - rhoverHack = /(?:^|\s)hover(\.\S+|)\b/, - hoverHack = function( events ) { - if ( typeof( events ) !== "string" || jQuery.event.special.hover ) { - return events; - } - if ( rhoverHack.test( events ) ) { - migrateWarn("'hover' pseudo-event is deprecated, use 'mouseenter mouseleave'"); - } - return events && events.replace( rhoverHack, "mouseenter$1 mouseleave$1" ); - }; - -// Event props removed in 1.9, put them back if needed; no practical way to warn them -if ( jQuery.event.props && jQuery.event.props[ 0 ] !== "attrChange" ) { - jQuery.event.props.unshift( "attrChange", "attrName", "relatedNode", "srcElement" ); -} - -// Undocumented jQuery.event.handle was "deprecated" in jQuery 1.7 -if ( jQuery.event.dispatch ) { - migrateWarnProp( jQuery.event, "handle", jQuery.event.dispatch, "jQuery.event.handle is undocumented and deprecated" ); -} - -// Support for 'hover' pseudo-event and ajax event warnings -jQuery.event.add = function( elem, types, handler, data, selector ){ - if ( elem !== document && rajaxEvent.test( types ) ) { - migrateWarn( "AJAX events should be attached to document: " + types ); - } - eventAdd.call( this, elem, hoverHack( types || "" ), handler, data, selector ); -}; -jQuery.event.remove = function( elem, types, handler, selector, mappedTypes ){ - eventRemove.call( this, elem, hoverHack( types ) || "", handler, selector, mappedTypes ); -}; - -jQuery.fn.error = function() { - var args = Array.prototype.slice.call( arguments, 0); - migrateWarn("jQuery.fn.error() is deprecated"); - args.splice( 0, 0, "error" ); - if ( arguments.length ) { - return this.bind.apply( this, args ); - } - // error event should not bubble to window, although it does pre-1.7 - this.triggerHandler.apply( this, args ); - return this; -}; - -jQuery.fn.toggle = function( fn, fn2 ) { - - // Don't mess with animation or css toggles - if ( !jQuery.isFunction( fn ) || !jQuery.isFunction( fn2 ) ) { - return oldToggle.apply( this, arguments ); - } - migrateWarn("jQuery.fn.toggle(handler, handler...) is deprecated"); - - // Save reference to arguments for access in closure - var args = arguments, - guid = fn.guid || jQuery.guid++, - i = 0, - toggler = function( event ) { - // Figure out which function to execute - var lastToggle = ( jQuery._data( this, "lastToggle" + fn.guid ) || 0 ) % i; - jQuery._data( this, "lastToggle" + fn.guid, lastToggle + 1 ); - - // Make sure that clicks stop - event.preventDefault(); - - // and execute the function - return args[ lastToggle ].apply( this, arguments ) || false; - }; - - // link all the functions, so any of them can unbind this click handler - toggler.guid = guid; - while ( i < args.length ) { - args[ i++ ].guid = guid; - } - - return this.click( toggler ); -}; - -jQuery.fn.live = function( types, data, fn ) { - migrateWarn("jQuery.fn.live() is deprecated"); - if ( oldLive ) { - return oldLive.apply( this, arguments ); - } - jQuery( this.context ).on( types, this.selector, data, fn ); - return this; -}; - -jQuery.fn.die = function( types, fn ) { - migrateWarn("jQuery.fn.die() is deprecated"); - if ( oldDie ) { - return oldDie.apply( this, arguments ); - } - jQuery( this.context ).off( types, this.selector || "**", fn ); - return this; -}; - -// Turn global events into document-triggered events -jQuery.event.trigger = function( event, data, elem, onlyHandlers ){ - if ( !elem && !rajaxEvent.test( event ) ) { - migrateWarn( "Global events are undocumented and deprecated" ); - } - return eventTrigger.call( this, event, data, elem || document, onlyHandlers ); -}; -jQuery.each( ajaxEvents.split("|"), - function( _, name ) { - jQuery.event.special[ name ] = { - setup: function() { - var elem = this; - - // The document needs no shimming; must be !== for oldIE - if ( elem !== document ) { - jQuery.event.add( document, name + "." + jQuery.guid, function() { - jQuery.event.trigger( name, null, elem, true ); - }); - jQuery._data( this, name, jQuery.guid++ ); - } - return false; - }, - teardown: function() { - if ( this !== document ) { - jQuery.event.remove( document, name + "." + jQuery._data( this, name ) ); - } - return false; - } - }; - } -); - - -})( jQuery, window ); +/*! + * jQuery Migrate - v1.2.1 - 2013-05-08 + * https://github.com/jquery/jquery-migrate + * Copyright 2005, 2013 jQuery Foundation, Inc. and other contributors; Licensed MIT + */ +(function( jQuery, window, undefined ) { +// See http://bugs.jquery.com/ticket/13335 +// "use strict"; + + +var warnedAbout = {}; + +// List of warnings already given; public read only +jQuery.migrateWarnings = []; + +// Set to true to prevent console output; migrateWarnings still maintained +// jQuery.migrateMute = false; + +// Show a message on the console so devs know we're active +if ( !jQuery.migrateMute && window.console && window.console.log ) { + window.console.log("JQMIGRATE: Logging is active"); +} + +// Set to false to disable traces that appear with warnings +if ( jQuery.migrateTrace === undefined ) { + jQuery.migrateTrace = true; +} + +// Forget any warnings we've already given; public +jQuery.migrateReset = function() { + warnedAbout = {}; + jQuery.migrateWarnings.length = 0; +}; + +function migrateWarn( msg) { + var console = window.console; + if ( !warnedAbout[ msg ] ) { + warnedAbout[ msg ] = true; + jQuery.migrateWarnings.push( msg ); + if ( console && console.warn && !jQuery.migrateMute ) { + console.warn( "JQMIGRATE: " + msg ); + if ( jQuery.migrateTrace && console.trace ) { + console.trace(); + } + } + } +} + +function migrateWarnProp( obj, prop, value, msg ) { + if ( Object.defineProperty ) { + // On ES5 browsers (non-oldIE), warn if the code tries to get prop; + // allow property to be overwritten in case some other plugin wants it + try { + Object.defineProperty( obj, prop, { + configurable: true, + enumerable: true, + get: function() { + migrateWarn( msg ); + return value; + }, + set: function( newValue ) { + migrateWarn( msg ); + value = newValue; + } + }); + return; + } catch( err ) { + // IE8 is a dope about Object.defineProperty, can't warn there + } + } + + // Non-ES5 (or broken) browser; just set the property + jQuery._definePropertyBroken = true; + obj[ prop ] = value; +} + +if ( document.compatMode === "BackCompat" ) { + // jQuery has never supported or tested Quirks Mode + migrateWarn( "jQuery is not compatible with Quirks Mode" ); +} + + +var attrFn = jQuery( "<input/>", { size: 1 } ).attr("size") && jQuery.attrFn, + oldAttr = jQuery.attr, + valueAttrGet = jQuery.attrHooks.value && jQuery.attrHooks.value.get || + function() { return null; }, + valueAttrSet = jQuery.attrHooks.value && jQuery.attrHooks.value.set || + function() { return undefined; }, + rnoType = /^(?:input|button)$/i, + rnoAttrNodeType = /^[238]$/, + rboolean = /^(?:autofocus|autoplay|async|checked|controls|defer|disabled|hidden|loop|multiple|open|readonly|required|scoped|selected)$/i, + ruseDefault = /^(?:checked|selected)$/i; + +// jQuery.attrFn +migrateWarnProp( jQuery, "attrFn", attrFn || {}, "jQuery.attrFn is deprecated" ); + +jQuery.attr = function( elem, name, value, pass ) { + var lowerName = name.toLowerCase(), + nType = elem && elem.nodeType; + + if ( pass ) { + // Since pass is used internally, we only warn for new jQuery + // versions where there isn't a pass arg in the formal params + if ( oldAttr.length < 4 ) { + migrateWarn("jQuery.fn.attr( props, pass ) is deprecated"); + } + if ( elem && !rnoAttrNodeType.test( nType ) && + (attrFn ? name in attrFn : jQuery.isFunction(jQuery.fn[name])) ) { + return jQuery( elem )[ name ]( value ); + } + } + + // Warn if user tries to set `type`, since it breaks on IE 6/7/8; by checking + // for disconnected elements we don't warn on $( "<button>", { type: "button" } ). + if ( name === "type" && value !== undefined && rnoType.test( elem.nodeName ) && elem.parentNode ) { + migrateWarn("Can't change the 'type' of an input or button in IE 6/7/8"); + } + + // Restore boolHook for boolean property/attribute synchronization + if ( !jQuery.attrHooks[ lowerName ] && rboolean.test( lowerName ) ) { + jQuery.attrHooks[ lowerName ] = { + get: function( elem, name ) { + // Align boolean attributes with corresponding properties + // Fall back to attribute presence where some booleans are not supported + var attrNode, + property = jQuery.prop( elem, name ); + return property === true || typeof property !== "boolean" && + ( attrNode = elem.getAttributeNode(name) ) && attrNode.nodeValue !== false ? + + name.toLowerCase() : + undefined; + }, + set: function( elem, value, name ) { + var propName; + if ( value === false ) { + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else { + // value is true since we know at this point it's type boolean and not false + // Set boolean attributes to the same name and set the DOM property + propName = jQuery.propFix[ name ] || name; + if ( propName in elem ) { + // Only set the IDL specifically if it already exists on the element + elem[ propName ] = true; + } + + elem.setAttribute( name, name.toLowerCase() ); + } + return name; + } + }; + + // Warn only for attributes that can remain distinct from their properties post-1.9 + if ( ruseDefault.test( lowerName ) ) { + migrateWarn( "jQuery.fn.attr('" + lowerName + "') may use property instead of attribute" ); + } + } + + return oldAttr.call( jQuery, elem, name, value ); +}; + +// attrHooks: value +jQuery.attrHooks.value = { + get: function( elem, name ) { + var nodeName = ( elem.nodeName || "" ).toLowerCase(); + if ( nodeName === "button" ) { + return valueAttrGet.apply( this, arguments ); + } + if ( nodeName !== "input" && nodeName !== "option" ) { + migrateWarn("jQuery.fn.attr('value') no longer gets properties"); + } + return name in elem ? + elem.value : + null; + }, + set: function( elem, value ) { + var nodeName = ( elem.nodeName || "" ).toLowerCase(); + if ( nodeName === "button" ) { + return valueAttrSet.apply( this, arguments ); + } + if ( nodeName !== "input" && nodeName !== "option" ) { + migrateWarn("jQuery.fn.attr('value', val) no longer sets properties"); + } + // Does not return so that setAttribute is also used + elem.value = value; + } +}; + + +var matched, browser, + oldInit = jQuery.fn.init, + oldParseJSON = jQuery.parseJSON, + // Note: XSS check is done below after string is trimmed + rquickExpr = /^([^<]*)(<[\w\W]+>)([^>]*)$/; + +// $(html) "looks like html" rule change +jQuery.fn.init = function( selector, context, rootjQuery ) { + var match; + + if ( selector && typeof selector === "string" && !jQuery.isPlainObject( context ) && + (match = rquickExpr.exec( jQuery.trim( selector ) )) && match[ 0 ] ) { + // This is an HTML string according to the "old" rules; is it still? + if ( selector.charAt( 0 ) !== "<" ) { + migrateWarn("$(html) HTML strings must start with '<' character"); + } + if ( match[ 3 ] ) { + migrateWarn("$(html) HTML text after last tag is ignored"); + } + // Consistently reject any HTML-like string starting with a hash (#9521) + // Note that this may break jQuery 1.6.x code that otherwise would work. + if ( match[ 0 ].charAt( 0 ) === "#" ) { + migrateWarn("HTML string cannot start with a '#' character"); + jQuery.error("JQMIGRATE: Invalid selector string (XSS)"); + } + // Now process using loose rules; let pre-1.8 play too + if ( context && context.context ) { + // jQuery object as context; parseHTML expects a DOM object + context = context.context; + } + if ( jQuery.parseHTML ) { + return oldInit.call( this, jQuery.parseHTML( match[ 2 ], context, true ), + context, rootjQuery ); + } + } + return oldInit.apply( this, arguments ); +}; +jQuery.fn.init.prototype = jQuery.fn; + +// Let $.parseJSON(falsy_value) return null +jQuery.parseJSON = function( json ) { + if ( !json && json !== null ) { + migrateWarn("jQuery.parseJSON requires a valid JSON string"); + return null; + } + return oldParseJSON.apply( this, arguments ); +}; + +jQuery.uaMatch = function( ua ) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec( ua ) || + /(webkit)[ \/]([\w.]+)/.exec( ua ) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec( ua ) || + /(msie) ([\w.]+)/.exec( ua ) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec( ua ) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; +}; + +// Don't clobber any existing jQuery.browser in case it's different +if ( !jQuery.browser ) { + matched = jQuery.uaMatch( navigator.userAgent ); + browser = {}; + + if ( matched.browser ) { + browser[ matched.browser ] = true; + browser.version = matched.version; + } + + // Chrome is Webkit, but Webkit is also Safari. + if ( browser.chrome ) { + browser.webkit = true; + } else if ( browser.webkit ) { + browser.safari = true; + } + + jQuery.browser = browser; +} + +// Warn if the code tries to get jQuery.browser +migrateWarnProp( jQuery, "browser", jQuery.browser, "jQuery.browser is deprecated" ); + +jQuery.sub = function() { + function jQuerySub( selector, context ) { + return new jQuerySub.fn.init( selector, context ); + } + jQuery.extend( true, jQuerySub, this ); + jQuerySub.superclass = this; + jQuerySub.fn = jQuerySub.prototype = this(); + jQuerySub.fn.constructor = jQuerySub; + jQuerySub.sub = this.sub; + jQuerySub.fn.init = function init( selector, context ) { + if ( context && context instanceof jQuery && !(context instanceof jQuerySub) ) { + context = jQuerySub( context ); + } + + return jQuery.fn.init.call( this, selector, context, rootjQuerySub ); + }; + jQuerySub.fn.init.prototype = jQuerySub.fn; + var rootjQuerySub = jQuerySub(document); + migrateWarn( "jQuery.sub() is deprecated" ); + return jQuerySub; +}; + + +// Ensure that $.ajax gets the new parseJSON defined in core.js +jQuery.ajaxSetup({ + converters: { + "text json": jQuery.parseJSON + } +}); + + +var oldFnData = jQuery.fn.data; + +jQuery.fn.data = function( name ) { + var ret, evt, + elem = this[0]; + + // Handles 1.7 which has this behavior and 1.8 which doesn't + if ( elem && name === "events" && arguments.length === 1 ) { + ret = jQuery.data( elem, name ); + evt = jQuery._data( elem, name ); + if ( ( ret === undefined || ret === evt ) && evt !== undefined ) { + migrateWarn("Use of jQuery.fn.data('events') is deprecated"); + return evt; + } + } + return oldFnData.apply( this, arguments ); +}; + + +var rscriptType = /\/(java|ecma)script/i, + oldSelf = jQuery.fn.andSelf || jQuery.fn.addBack; + +jQuery.fn.andSelf = function() { + migrateWarn("jQuery.fn.andSelf() replaced by jQuery.fn.addBack()"); + return oldSelf.apply( this, arguments ); +}; + +// Since jQuery.clean is used internally on older versions, we only shim if it's missing +if ( !jQuery.clean ) { + jQuery.clean = function( elems, context, fragment, scripts ) { + // Set context per 1.8 logic + context = context || document; + context = !context.nodeType && context[0] || context; + context = context.ownerDocument || context; + + migrateWarn("jQuery.clean() is deprecated"); + + var i, elem, handleScript, jsTags, + ret = []; + + jQuery.merge( ret, jQuery.buildFragment( elems, context ).childNodes ); + + // Complex logic lifted directly from jQuery 1.8 + if ( fragment ) { + // Special handling of each script element + handleScript = function( elem ) { + // Check if we consider it executable + if ( !elem.type || rscriptType.test( elem.type ) ) { + // Detach the script and store it in the scripts array (if provided) or the fragment + // Return truthy to indicate that it has been handled + return scripts ? + scripts.push( elem.parentNode ? elem.parentNode.removeChild( elem ) : elem ) : + fragment.appendChild( elem ); + } + }; + + for ( i = 0; (elem = ret[i]) != null; i++ ) { + // Check if we're done after handling an executable script + if ( !( jQuery.nodeName( elem, "script" ) && handleScript( elem ) ) ) { + // Append to fragment and handle embedded scripts + fragment.appendChild( elem ); + if ( typeof elem.getElementsByTagName !== "undefined" ) { + // handleScript alters the DOM, so use jQuery.merge to ensure snapshot iteration + jsTags = jQuery.grep( jQuery.merge( [], elem.getElementsByTagName("script") ), handleScript ); + + // Splice the scripts into ret after their former ancestor and advance our index beyond them + ret.splice.apply( ret, [i + 1, 0].concat( jsTags ) ); + i += jsTags.length; + } + } + } + } + + return ret; + }; +} + +var eventAdd = jQuery.event.add, + eventRemove = jQuery.event.remove, + eventTrigger = jQuery.event.trigger, + oldToggle = jQuery.fn.toggle, + oldLive = jQuery.fn.live, + oldDie = jQuery.fn.die, + ajaxEvents = "ajaxStart|ajaxStop|ajaxSend|ajaxComplete|ajaxError|ajaxSuccess", + rajaxEvent = new RegExp( "\\b(?:" + ajaxEvents + ")\\b" ), + rhoverHack = /(?:^|\s)hover(\.\S+|)\b/, + hoverHack = function( events ) { + if ( typeof( events ) !== "string" || jQuery.event.special.hover ) { + return events; + } + if ( rhoverHack.test( events ) ) { + migrateWarn("'hover' pseudo-event is deprecated, use 'mouseenter mouseleave'"); + } + return events && events.replace( rhoverHack, "mouseenter$1 mouseleave$1" ); + }; + +// Event props removed in 1.9, put them back if needed; no practical way to warn them +if ( jQuery.event.props && jQuery.event.props[ 0 ] !== "attrChange" ) { + jQuery.event.props.unshift( "attrChange", "attrName", "relatedNode", "srcElement" ); +} + +// Undocumented jQuery.event.handle was "deprecated" in jQuery 1.7 +if ( jQuery.event.dispatch ) { + migrateWarnProp( jQuery.event, "handle", jQuery.event.dispatch, "jQuery.event.handle is undocumented and deprecated" ); +} + +// Support for 'hover' pseudo-event and ajax event warnings +jQuery.event.add = function( elem, types, handler, data, selector ){ + if ( elem !== document && rajaxEvent.test( types ) ) { + migrateWarn( "AJAX events should be attached to document: " + types ); + } + eventAdd.call( this, elem, hoverHack( types || "" ), handler, data, selector ); +}; +jQuery.event.remove = function( elem, types, handler, selector, mappedTypes ){ + eventRemove.call( this, elem, hoverHack( types ) || "", handler, selector, mappedTypes ); +}; + +jQuery.fn.error = function() { + var args = Array.prototype.slice.call( arguments, 0); + migrateWarn("jQuery.fn.error() is deprecated"); + args.splice( 0, 0, "error" ); + if ( arguments.length ) { + return this.bind.apply( this, args ); + } + // error event should not bubble to window, although it does pre-1.7 + this.triggerHandler.apply( this, args ); + return this; +}; + +jQuery.fn.toggle = function( fn, fn2 ) { + + // Don't mess with animation or css toggles + if ( !jQuery.isFunction( fn ) || !jQuery.isFunction( fn2 ) ) { + return oldToggle.apply( this, arguments ); + } + migrateWarn("jQuery.fn.toggle(handler, handler...) is deprecated"); + + // Save reference to arguments for access in closure + var args = arguments, + guid = fn.guid || jQuery.guid++, + i = 0, + toggler = function( event ) { + // Figure out which function to execute + var lastToggle = ( jQuery._data( this, "lastToggle" + fn.guid ) || 0 ) % i; + jQuery._data( this, "lastToggle" + fn.guid, lastToggle + 1 ); + + // Make sure that clicks stop + event.preventDefault(); + + // and execute the function + return args[ lastToggle ].apply( this, arguments ) || false; + }; + + // link all the functions, so any of them can unbind this click handler + toggler.guid = guid; + while ( i < args.length ) { + args[ i++ ].guid = guid; + } + + return this.click( toggler ); +}; + +jQuery.fn.live = function( types, data, fn ) { + migrateWarn("jQuery.fn.live() is deprecated"); + if ( oldLive ) { + return oldLive.apply( this, arguments ); + } + jQuery( this.context ).on( types, this.selector, data, fn ); + return this; +}; + +jQuery.fn.die = function( types, fn ) { + migrateWarn("jQuery.fn.die() is deprecated"); + if ( oldDie ) { + return oldDie.apply( this, arguments ); + } + jQuery( this.context ).off( types, this.selector || "**", fn ); + return this; +}; + +// Turn global events into document-triggered events +jQuery.event.trigger = function( event, data, elem, onlyHandlers ){ + if ( !elem && !rajaxEvent.test( event ) ) { + migrateWarn( "Global events are undocumented and deprecated" ); + } + return eventTrigger.call( this, event, data, elem || document, onlyHandlers ); +}; +jQuery.each( ajaxEvents.split("|"), + function( _, name ) { + jQuery.event.special[ name ] = { + setup: function() { + var elem = this; + + // The document needs no shimming; must be !== for oldIE + if ( elem !== document ) { + jQuery.event.add( document, name + "." + jQuery.guid, function() { + jQuery.event.trigger( name, null, elem, true ); + }); + jQuery._data( this, name, jQuery.guid++ ); + } + return false; + }, + teardown: function() { + if ( this !== document ) { + jQuery.event.remove( document, name + "." + jQuery._data( this, name ) ); + } + return false; + } + }; + } +); + + +})( jQuery, window ); This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI, client build: sync underscore version in grunt file and libs at 1.7.0
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9bc22ec1a815/ Changeset: 9bc22ec1a815 User: carlfeberhard Date: 2015-02-04 14:42:59+00:00 Summary: UI, client build: sync underscore version in grunt file and libs at 1.7.0 Affected #: 3 files diff -r 334ae138b7b66dbaa95292213aab86ccc08efcae -r 9bc22ec1a8156fe640fd049399cb39c8755eef73 client/GruntFile.js --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -72,7 +72,7 @@ "traceKit": [ "tracekit.js", "tracekit.js" ], "ravenjs": [ "dist/raven.js", "raven.js" ], - //"underscore": [ "underscore.js", "underscore.js" ], + "underscore": [ "underscore.js", "underscore.js" ], //"backbone": [ "backbone.js", "backbone/backbone.js" ], "handlebars": [ "handlebars.runtime.js", "handlebars.runtime.js" ] diff -r 334ae138b7b66dbaa95292213aab86ccc08efcae -r 9bc22ec1a8156fe640fd049399cb39c8755eef73 client/galaxy/scripts/libs/underscore.js --- a/client/galaxy/scripts/libs/underscore.js +++ b/client/galaxy/scripts/libs/underscore.js @@ -1159,7 +1159,6 @@ return value; }; - // Predicate-generating functions. Often useful outside of Underscore. _.constant = function(value) { return function() { return value; diff -r 334ae138b7b66dbaa95292213aab86ccc08efcae -r 9bc22ec1a8156fe640fd049399cb39c8755eef73 static/scripts/libs/underscore.js --- a/static/scripts/libs/underscore.js +++ b/static/scripts/libs/underscore.js @@ -1159,7 +1159,6 @@ return value; }; - // Predicate-generating functions. Often useful outside of Underscore. _.constant = function(value) { return function() { return value; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI, client build: correct handlebars bower source, update handlebars.runtime to 2.0.0, recompile templates w/ 2.0.0 precompiler
by commits-noreply＠bitbucket.org 04 Feb '15

04 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/334ae138b7b6/ Changeset: 334ae138b7b6 User: carlfeberhard Date: 2015-02-04 14:20:48+00:00 Summary: UI, client build: correct handlebars bower source, update handlebars.runtime to 2.0.0, recompile templates w/ 2.0.0 precompiler Affected #: 17 files diff -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 -r 334ae138b7b66dbaa95292213aab86ccc08efcae client/GruntFile.js --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -74,6 +74,7 @@ "ravenjs": [ "dist/raven.js", "raven.js" ], //"underscore": [ "underscore.js", "underscore.js" ], //"backbone": [ "backbone.js", "backbone/backbone.js" ], + "handlebars": [ "handlebars.runtime.js", "handlebars.runtime.js" ] // these need to be updated and tested //"require": [ "build/require.js", "require.js" ], @@ -105,8 +106,6 @@ // [ "", "jquery/jquery-ui.js" ] //], - // building the runtime library is not so simple - //"handlebars.js": [ "", "handlebars.runtime.js" ] } }); diff -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 -r 334ae138b7b66dbaa95292213aab86ccc08efcae client/bower.json --- a/client/bower.json +++ b/client/bower.json @@ -32,7 +32,7 @@ "jstree": "~3.0.9", "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2", "jquery.event.drag-drop": "~2.2.1", - "handlebars.js": "~2.0.0" + "handlebars": "~2.0.0" }, "resolutions": { "jquery": "~1.11.1" diff -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 -r 334ae138b7b66dbaa95292213aab86ccc08efcae client/galaxy/scripts/libs/handlebars.runtime.js --- 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 @@ 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<j; i++) { - if (data) { data.index = i; } - ret = ret + fn(context[i], { data: data }); - } - } else { - for(var key in context) { - if(context.hasOwnProperty(key)) { - if(data) { data.key = key; } - ret = ret + fn(context[key], {data: data}); - i++; + SafeString.prototype.toString = function() { + return "" + this.string; + }; + + __exports__ = SafeString; + return __exports__; +})(); + +// handlebars/utils.js +var __module2__ = (function(__dependency1__) { + "use strict"; + var __exports__ = {}; + /*jshint -W004 */ + var SafeString = __dependency1__; + + var escape = { + "&": "&", + "<": "<", + ">": ">", + '"': """, + "'": "'", + "`": "`" + }; + + 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<j; i++) { + if (data) { + data.index = i; + data.first = (i === 0); + data.last = (i === (context.length-1)); + + if (contextPath) { + data.contextPath = contextPath + i; + } + } + ret = ret + fn(context[i], { data: data }); + } + } else { + for(var key in context) { + if(context.hasOwnProperty(key)) { + if(data) { + data.key = key; + data.index = i; + data.first = (i === 0); + + if (contextPath) { + data.contextPath = contextPath + key; + } + } + ret = ret + fn(context[key], {data: data}); + i++; + } + } + } + } + + if(i === 0){ + ret = inverse(this); + } + + return ret; + }); + + instance.registerHelper('if', function(conditional, options) { + if (isFunction(conditional)) { conditional = conditional.call(this); } + + // Default behavior is to render the positive path if the value is truthy and not empty. + // The `includeZero` option may be set to treat the condtional as purely not empty based on the + // behavior of isEmpty. Effectively this determines if 0 is handled by the positive path or negative. + if ((!options.hash.includeZero && !conditional) || Utils.isEmpty(conditional)) { + return options.inverse(this); + } else { + return options.fn(this); + } + }); + + instance.registerHelper('unless', function(conditional, options) { + return instance.helpers['if'].call(this, conditional, {fn: options.inverse, inverse: options.fn, hash: options.hash}); + }); + + instance.registerHelper('with', function(context, options) { + if (isFunction(context)) { context = context.call(this); } + + var fn = options.fn; + + if (!Utils.isEmpty(context)) { + if (options.data && options.ids) { + var data = createFrame(options.data); + data.contextPath = Utils.appendContextPath(options.data.contextPath, options.ids[0]); + options = {data:data}; + } + + return fn(context, options); + } else { + return options.inverse(this); + } + }); + + instance.registerHelper('log', function(message, options) { + var level = options.data && options.data.level != null ? parseInt(options.data.level, 10) : 1; + instance.log(level, message); + }); + + instance.registerHelper('lookup', function(obj, field) { + return obj && obj[field]; + }); + } + + var logger = { + methodMap: { 0: 'debug', 1: 'info', 2: 'warn', 3: 'error' }, + + // State enum + DEBUG: 0, + INFO: 1, + WARN: 2, + ERROR: 3, + level: 3, + + // can be overridden in the host environment + log: function(level, message) { + if (logger.level <= level) { + var method = logger.methodMap[level]; + if (typeof console !== 'undefined' && console[method]) { + console[method].call(console, message); + } + } + } + }; + __exports__.logger = logger; + var log = logger.log; + __exports__.log = log; + var createFrame = function(object) { + var frame = Utils.extend({}, object); + frame._parent = object; + return frame; + }; + __exports__.createFrame = createFrame; + return __exports__; +})(__module2__, __module4__); + +// handlebars/runtime.js +var __module5__ = (function(__dependency1__, __dependency2__, __dependency3__) { + "use strict"; + var __exports__ = {}; + var Utils = __dependency1__; + var Exception = __dependency2__; + var COMPILER_REVISION = __dependency3__.COMPILER_REVISION; + var REVISION_CHANGES = __dependency3__.REVISION_CHANGES; + var createFrame = __dependency3__.createFrame; + + function checkRevision(compilerInfo) { + var compilerRevision = compilerInfo && compilerInfo[0] || 1, + currentRevision = COMPILER_REVISION; + + if (compilerRevision !== currentRevision) { + if (compilerRevision < currentRevision) { + var runtimeVersions = REVISION_CHANGES[currentRevision], + compilerVersions = REVISION_CHANGES[compilerRevision]; + throw new Exception("Template was precompiled with an older version of Handlebars than the current runtime. "+ + "Please update your precompiler to a newer version ("+runtimeVersions+") or downgrade your runtime to an older version ("+compilerVersions+")."); + } else { + // Use the embedded version info since the runtime doesn't know about this revision yet + throw new Exception("Template was precompiled with a newer version of Handlebars than the current runtime. "+ + "Please update your runtime to a newer version ("+compilerInfo[1]+")."); + } + } + } + + __exports__.checkRevision = checkRevision;// TODO: Remove this line and break up compilePartial + + function template(templateSpec, env) { + /* istanbul ignore next */ + if (!env) { + throw new Exception("No environment passed to template"); + } + if (!templateSpec || !templateSpec.main) { + throw new Exception('Unknown template object: ' + typeof templateSpec); + } + + // Note: Using env.VM references rather than local var references throughout this section to allow + // for external users to override these as psuedo-supported APIs. + env.VM.checkRevision(templateSpec.compiler); + + var invokePartialWrapper = function(partial, indent, name, context, hash, helpers, partials, data, depths) { + if (hash) { + context = Utils.extend({}, context, hash); + } + + var result = env.VM.invokePartial.call(this, partial, name, context, helpers, partials, data, depths); + + if (result == null && env.compile) { + var options = { helpers: helpers, partials: partials, data: data, depths: depths }; + partials[name] = env.compile(partial, { data: data !== undefined, compat: templateSpec.compat }, env); + result = partials[name](context, options); + } + if (result != null) { + if (indent) { + var lines = result.split('\n'); + for (var i = 0, l = lines.length; i < l; i++) { + if (!lines[i] && i + 1 === l) { + break; + } + + lines[i] = indent + lines[i]; + } + result = lines.join('\n'); + } + return result; + } else { + throw new Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); + } + }; + // Just add water var container = { - escapeExpression: Handlebars.Utils.escapeExpression, - invokePartial: Handlebars.VM.invokePartial, + lookup: function(depths, name) { + var len = depths.length; + for (var i = 0; i < len; i++) { + if (depths[i] && depths[i][name] != null) { + return depths[i][name]; + } + } + }, + lambda: function(current, context) { + return typeof current === 'function' ? current.call(context) : current; + }, + + escapeExpression: Utils.escapeExpression, + invokePartial: invokePartialWrapper, + + fn: function(i) { + return templateSpec[i]; + }, + programs: [], - program: function(i, fn, data) { - var programWrapper = this.programs[i]; - if(data) { - programWrapper = Handlebars.VM.program(i, fn, data); + program: function(i, data, depths) { + var programWrapper = this.programs[i], + fn = this.fn(i); + if (data || depths) { + programWrapper = program(this, i, fn, data, depths); } else if (!programWrapper) { - programWrapper = this.programs[i] = Handlebars.VM.program(i, fn); + programWrapper = this.programs[i] = program(this, i, fn); } return programWrapper; }, + + data: function(data, depth) { + while (data && depth--) { + data = data._parent; + } + return data; + }, merge: function(param, common) { var ret = param || common; - if (param && common) { - ret = {}; - Handlebars.Utils.extend(ret, common); - Handlebars.Utils.extend(ret, param); + if (param && common && (param !== common)) { + ret = Utils.extend({}, common, param); } + return ret; }, - programWithDepth: Handlebars.VM.programWithDepth, - noop: Handlebars.VM.noop, - compilerInfo: null + + noop: env.VM.noop, + compilerInfo: templateSpec.compiler }; - return function(context, options) { + var ret = function(context, options) { options = options || {}; - var result = templateSpec.call(container, Handlebars, context, options.helpers, options.partials, options.data); + var data = options.data; - var compilerInfo = container.compilerInfo || [], - compilerRevision = compilerInfo[0] || 1, - currentRevision = Handlebars.COMPILER_REVISION; - - if (compilerRevision !== currentRevision) { - if (compilerRevision < currentRevision) { - var runtimeVersions = Handlebars.REVISION_CHANGES[currentRevision], - compilerVersions = Handlebars.REVISION_CHANGES[compilerRevision]; - throw "Template was precompiled with an older version of Handlebars than the current runtime. "+ - "Please update your precompiler to a newer version ("+runtimeVersions+") or downgrade your runtime to an older version ("+compilerVersions+")."; - } else { - // Use the embedded version info since the runtime doesn't know about this revision yet - throw "Template was precompiled with a newer version of Handlebars than the current runtime. "+ - "Please update your runtime to a newer version ("+compilerInfo[1]+")."; - } + ret._setup(options); + if (!options.partial && templateSpec.useData) { + data = initData(context, data); + } + var depths; + if (templateSpec.useDepths) { + depths = options.depths ? [context].concat(options.depths) : [context]; } - return result; + return templateSpec.main.call(container, context, container.helpers, container.partials, data, depths); }; - }, + ret.isTop = true; - programWithDepth: function(i, fn, data /*, $depth */) { - var args = Array.prototype.slice.call(arguments, 3); + ret._setup = function(options) { + if (!options.partial) { + container.helpers = container.merge(options.helpers, env.helpers); - var program = function(context, options) { + if (templateSpec.usePartial) { + container.partials = container.merge(options.partials, env.partials); + } + } else { + container.helpers = options.helpers; + container.partials = options.partials; + } + }; + + ret._child = function(i, data, depths) { + if (templateSpec.useDepths && !depths) { + throw new Exception('must pass parent depths'); + } + + return program(container, i, templateSpec[i], data, depths); + }; + return ret; + } + + __exports__.template = template;function program(container, i, fn, data, depths) { + var prog = function(context, options) { options = options || {}; - return fn.apply(this, [context, options.data || data].concat(args)); + return fn.call(container, context, container.helpers, container.partials, options.data || data, depths && [context].concat(depths)); }; - program.program = i; - program.depth = args.length; - return program; - }, - program: function(i, fn, data) { - var program = function(context, options) { - options = options || {}; + prog.program = i; + prog.depth = depths ? depths.length : 0; + return prog; + } - return fn(context, options.data || data); - }; - program.program = i; - program.depth = 0; - return program; - }, - noop: function() { return ""; }, - invokePartial: function(partial, name, context, helpers, partials, data) { - var options = { helpers: helpers, partials: partials, data: data }; + __exports__.program = program;function invokePartial(partial, name, context, helpers, partials, data, depths) { + var options = { partial: true, helpers: helpers, partials: partials, data: data, depths: depths }; if(partial === undefined) { - throw new Handlebars.Exception("The partial " + name + " could not be found"); + throw new Exception("The partial " + name + " could not be found"); } else if(partial instanceof Function) { return partial(context, options); - } else if (!Handlebars.compile) { - throw new Handlebars.Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); - } else { - partials[name] = Handlebars.compile(partial, {data: data !== undefined}); - return partials[name](context, options); } } -}; -Handlebars.template = Handlebars.VM.template; -; -// lib/handlebars/browser-suffix.js -})(Handlebars); -; + __exports__.invokePartial = invokePartial;function noop() { return ""; } + + __exports__.noop = noop;function initData(context, data) { + if (!data || !('root' in data)) { + data = data ? createFrame(data) : {}; + data.root = context; + } + return data; + } + return __exports__; +})(__module2__, __module4__, __module1__); + +// handlebars.runtime.js +var __module0__ = (function(__dependency1__, __dependency2__, __dependency3__, __dependency4__, __dependency5__) { + "use strict"; + var __exports__; + /*globals Handlebars: true */ + var base = __dependency1__; + + // Each of these augment the Handlebars object. No need to setup here. + // (This is done to easily share code between commonjs and browse envs) + var SafeString = __dependency2__; + var Exception = __dependency3__; + var Utils = __dependency4__; + var runtime = __dependency5__; + + // For compatibility and usage outside of module systems, make the Handlebars object a namespace + var create = function() { + var hb = new base.HandlebarsEnvironment(); + + Utils.extend(hb, base); + hb.SafeString = SafeString; + hb.Exception = Exception; + hb.Utils = Utils; + hb.escapeExpression = Utils.escapeExpression; + + hb.VM = runtime; + hb.template = function(spec) { + return runtime.template(spec, hb); + }; + + return hb; + }; + + var Handlebars = create(); + Handlebars.create = create; + + Handlebars['default'] = Handlebars; + + __exports__ = Handlebars; + return __exports__; +})(__module1__, __module3__, __module4__, __module2__, __module5__); + + return __module0__; +})); diff -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 -r 334ae138b7b66dbaa95292213aab86ccc08efcae client/galaxy/scripts/templates/compiled/panel_section.js --- a/client/galaxy/scripts/templates/compiled/panel_section.js +++ b/client/galaxy/scripts/templates/compiled/panel_section.js @@ -1,24 +1,13 @@ (function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['panel_section'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression; - - - buffer += "<div class=\"toolSectionTitle\" id=\"title_"; - if (stack1 = helpers.id) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\">\n <a href=\"javascript:void(0)\"><span>"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span></a>\n</div>\n<div id=\""; - if (stack1 = helpers.id) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) +templates['panel_section'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) { + var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression; + return "<div class=\"toolSectionTitle\" id=\"title_" + + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper))) + + "\">\n <a href=\"javascript:void(0)\"><span>" + + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper))) + + "</span></a>\n</div>\n<div id=\"" + + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper))) + "\" class=\"toolSectionBody\" style=\"display: none; \">\n <div class=\"toolSectionBg\"></div>\n<div>"; - return buffer; - }); +},"useData":true}); })(); \ No newline at end of file diff -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 -r 334ae138b7b66dbaa95292213aab86ccc08efcae client/galaxy/scripts/templates/compiled/tool_form.js --- a/client/galaxy/scripts/templates/compiled/tool_form.js +++ b/client/galaxy/scripts/templates/compiled/tool_form.js @@ -1,49 +1,26 @@ (function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['tool_form'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"form-row\">\n <label for=\""; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\">"; - if (stack1 = helpers.label) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) +templates['tool_form'] = template({"1":function(depth0,helpers,partials,data) { + var stack1, helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression, buffer = " <div class=\"form-row\">\n <label for=\"" + + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper))) + + "\">" + + escapeExpression(((helper = (helper = helpers.label || (depth0 != null ? depth0.label : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"label","hash":{},"data":data}) : helper))) + ":</label>\n <div class=\"form-row-input\">\n "; - if (stack1 = helpers.html) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.html; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n "; - if (stack1 = helpers.help) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.help; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n "; - return buffer; - } - - buffer += "<div class=\"toolFormTitle\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + " (version "; - if (stack1 = helpers.version) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.version; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + ")</div>\n <div class=\"toolFormBody\">\n "; - stack1 = helpers.each.call(depth0, depth0.inputs, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">"; - if (stack1 = helpers.help) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.help; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) + stack1 = ((helper = (helper = helpers.html || (depth0 != null ? depth0.html : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"html","hash":{},"data":data}) : helper)); + if (stack1 != null) { buffer += stack1; } + return buffer + "\n </div>\n <div class=\"toolParamHelp\" style=\"clear: both;\">\n " + + escapeExpression(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"help","hash":{},"data":data}) : helper))) + + "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n"; +},"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) { + var stack1, helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression, buffer = "<div class=\"toolFormTitle\">" + + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper))) + + " (version " + + escapeExpression(((helper = (helper = helpers.version || (depth0 != null ? depth0.version : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"version","hash":{},"data":data}) : helper))) + + ")</div>\n <div class=\"toolFormBody\">\n"; + stack1 = helpers.each.call(depth0, (depth0 != null ? depth0.inputs : depth0), {"name":"each","hash":{},"fn":this.program(1, data),"inverse":this.noop,"data":data}); + if (stack1 != null) { buffer += stack1; } + return buffer + " </div>\n <div class=\"form-row form-actions\">\n <input type=\"submit\" class=\"btn btn-primary\" name=\"runtool_btn\" value=\"Execute\">\n</div>\n<div class=\"toolHelp\">\n <div class=\"toolHelpBody\">" + + escapeExpression(((helper = (helper = helpers.help || (depth0 != null ? depth0.help : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"help","hash":{},"data":data}) : helper))) + "</div>\n</div>"; - return buffer; - }); +},"useData":true}); })(); \ No newline at end of file diff -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 -r 334ae138b7b66dbaa95292213aab86ccc08efcae client/galaxy/scripts/templates/compiled/tool_link.js --- a/client/galaxy/scripts/templates/compiled/tool_link.js +++ b/client/galaxy/scripts/templates/compiled/tool_link.js @@ -1,35 +1,18 @@ (function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['tool_link'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression; - - - buffer += "<a class=\""; - if (stack1 = helpers.id) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + " tool-link\" href=\""; - if (stack1 = helpers.link) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.link; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\" target=\""; - if (stack1 = helpers.target) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\" minsizehint=\""; - if (stack1 = helpers.min_width) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.min_width; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</a> "; - if (stack1 = helpers.description) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.description; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1); - return buffer; - }); +templates['tool_link'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) { + var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression; + return "<a class=\"" + + escapeExpression(((helper = (helper = helpers.id || (depth0 != null ? depth0.id : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"id","hash":{},"data":data}) : helper))) + + " tool-link\" href=\"" + + escapeExpression(((helper = (helper = helpers.link || (depth0 != null ? depth0.link : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"link","hash":{},"data":data}) : helper))) + + "\" target=\"" + + escapeExpression(((helper = (helper = helpers.target || (depth0 != null ? depth0.target : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"target","hash":{},"data":data}) : helper))) + + "\" minsizehint=\"" + + escapeExpression(((helper = (helper = helpers.min_width || (depth0 != null ? depth0.min_width : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"min_width","hash":{},"data":data}) : helper))) + + "\">" + + escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"name","hash":{},"data":data}) : helper))) + + "</a> " + + escapeExpression(((helper = (helper = helpers.description || (depth0 != null ? depth0.description : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"description","hash":{},"data":data}) : helper))); +},"useData":true}); })(); \ No newline at end of file diff -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 -r 334ae138b7b66dbaa95292213aab86ccc08efcae client/galaxy/scripts/templates/compiled/tool_search.js --- a/client/galaxy/scripts/templates/compiled/tool_search.js +++ b/client/galaxy/scripts/templates/compiled/tool_search.js @@ -1,20 +1,11 @@ (function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['tool_search'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression; - - - buffer += "<input type=\"text\" name=\"query\" value=\""; - if (stack1 = helpers.search_hint_string) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.search_hint_string; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<a id=\"search-clear-btn\" title=\"clear search (esc)\"></a>\n<img src=\""; - if (stack1 = helpers.spinner_url) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.spinner_url; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) +templates['tool_search'] = template({"compiler":[6,">= 2.0.0-beta.1"],"main":function(depth0,helpers,partials,data) { + var helper, functionType="function", helperMissing=helpers.helperMissing, escapeExpression=this.escapeExpression; + return "<input type=\"text\" name=\"query\" value=\"" + + escapeExpression(((helper = (helper = helpers.search_hint_string || (depth0 != null ? depth0.search_hint_string : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"search_hint_string","hash":{},"data":data}) : helper))) + + "\" id=\"tool-search-query\" autocomplete=\"off\" class=\"search-query parent-width\" />\n<a id=\"search-clear-btn\" title=\"clear search (esc)\"></a>\n<img src=\"" + + escapeExpression(((helper = (helper = helpers.spinner_url || (depth0 != null ? depth0.spinner_url : depth0)) != null ? helper : helperMissing),(typeof helper === functionType ? helper.call(depth0, {"name":"spinner_url","hash":{},"data":data}) : helper))) + "\" id=\"search-spinner\" class=\"search-spinner\"/>"; - return buffer; - }); +},"useData":true}); })(); \ No newline at end of file This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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