diff --git a/.ci/pep8_sources.txt b/.ci/pep8_sources.txt index 0ff00105a65..01ed8dca4cd 100644 --- a/.ci/pep8_sources.txt +++ b/.ci/pep8_sources.txt @@ -19,10 +19,11 @@ lib/galaxy/tools/toolbox lib/galaxy/tools/{errors,loader_directory,test}.py lib/galaxy/util/{__init__,json,permutations,plugin_config,properties,simplegraph,sockets,sleeper,streamball,submodules}.py lib/galaxy/web/{proxy,security} +lib/galaxy/web/base/{__init__,interactive_environments}.py lib/galaxy/web/formatting.py lib/galaxy/webapps/__init__.py lib/galaxy/webapps/galaxy/__init__.py -lib/galaxy/webapps/galaxy/api/{__init__,dataset_collections,datatypes,job_files,provenance,users}.py +lib/galaxy/webapps/galaxy/api/{__init__,authenticate,dataset_collections,datatypes,folder_contents,folders,lda_datasets,job_files,libraries,library_contents,provenance,remote_files,search,users}.py lib/galaxy/webapps/galaxy/controllers/{__init__,admin,cloudlaunch,workflow}.py lib/galaxy/webapps/reports/app.py lib/galaxy/webapps/reports/controllers/{__init__,jobs,query,workflows}.py diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 38f5c527afd..7888a623415 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,8 +1,9 @@ # Contributing -This document briefly describes how to contribute to the -galaxy-central core project - also checkout our 2013 Galaxy Community -Conference presentation] on the topic +This document briefly describes how to contribute to the [core +galaxy project](https://github.com/galaxyproject/galaxy) - +also checkout our 2013 Galaxy Community +Conference presentation on the topic ([video](http://vimeo.com/channels/581875/73486255), [presentation](https://wiki.galaxyproject.org/Documents/Presentations/GCC2013?action=AttachFile&do=view&target=BakerContribute.pdf)). For information on contributing more broadly to the Galaxy ecosystem and a @@ -25,6 +26,11 @@ the [development mailing list](http://dev.list.galaxyproject.org/). ## How to Contribute +* All changes to the [core galaxy project](https://github.com/galaxyproject/galaxy) + should be made through pull requests to this repository except when + serious security vulnerabilities must simulatenously be made to multiple + previously released versions of Galaxy. + * If you are new to Git - please check out the very useful tutorials on the [GitHub training hub](https://training.github.com/kit/) * Make sure you have a free [GitHub account](https://github.com/) @@ -42,7 +48,7 @@ the [development mailing list](http://dev.list.galaxyproject.org/). checkout dev`). * Most bug fixes to previously release components (things in galaxy-dist) - should be made against the `master` branch (`git checkout master`). + should be made against the recent `release_XX.XX` branch (`git checkout release_XX.XX`). * Serious security problems should not be fixed via pull request - please responsibly disclose these by e-mailing them (with or @@ -66,11 +72,12 @@ the [development mailing list](http://dev.list.galaxyproject.org/). tests as part of the pull request review process and may request the output of these tests. -* Commit and push your changes to your Bitbucket fork. +* Commit and push your changes to your + [fork](https://help.github.com/articles/pushing-to-a-remote/). * Open a [pull - request](https://confluence.atlassian.com/display/BITBUCKET/Fork+a+Repo,+Compare+Code,+and+Create+a+Pull+Request) - with these changes. You pull request message should include: + request](https://help.github.com/articles/creating-a-pull-request/) + with these changes. You pull request message ideally should include: * A description of why the change should be made. diff --git a/client/GruntFile.js b/client/GruntFile.js index 3065871ef90..918c2dec8af 100644 --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -85,7 +85,6 @@ module.exports = function(grunt) { "ravenjs": [ "dist/raven.js", "raven.js" ], "underscore": [ "underscore.js", "underscore.js" ], "handlebars": [ "handlebars.runtime.js", "handlebars.runtime.js" ], - "lunr.js": [ "lunr.js", "lunr.js" ], "backbone": [ "backbone.js", "backbone/backbone.js" ], // these need to be updated and tested diff --git a/client/bower.json b/client/bower.json index f5f22afbdfb..c1c9f187fa9 100644 --- a/client/bower.json +++ b/client/bower.json @@ -32,8 +32,7 @@ "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2", "threedubmedia.jquery.event": "*", "handlebars": "~2.0.0", - "jquery-migrate": "~1.2.1", - "lunr.js": "git://github.com/olivernn/lunr.js.git#~0.5.7" + "jquery-migrate": "~1.2.1" }, "resolutions": { "jquery": "~1.11.1" diff --git a/client/galaxy/scripts/libs/lunr.js b/client/galaxy/scripts/libs/lunr.js deleted file mode 100644 index b5bacd97960..00000000000 --- a/client/galaxy/scripts/libs/lunr.js +++ /dev/null @@ -1,1910 +0,0 @@ -/** - * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 0.5.7 - * Copyright (C) 2014 Oliver Nightingale - * MIT Licensed - * @license - */ - -(function(){ - -/** - * Convenience function for instantiating a new lunr index and configuring it - * with the default pipeline functions and the passed config function. - * - * When using this convenience function a new index will be created with the - * following functions already in the pipeline: - * - * lunr.StopWordFilter - filters out any stop words before they enter the - * index - * - * lunr.stemmer - stems the tokens before entering the index. - * - * Example: - * - * var idx = lunr(function () { - * this.field('title', 10) - * this.field('tags', 100) - * this.field('body') - * - * this.ref('cid') - * - * this.pipeline.add(function () { - * // some custom pipeline function - * }) - * - * }) - * - * @param {Function} config A function that will be called with the new instance - * of the lunr.Index as both its context and first parameter. It can be used to - * customize the instance of new lunr.Index. - * @namespace - * @module - * @returns {lunr.Index} - * - */ -var lunr = function (config) { - var idx = new lunr.Index - - idx.pipeline.add( - lunr.trimmer, - lunr.stopWordFilter, - lunr.stemmer - ) - - if (config) config.call(idx, idx) - - return idx -} - -lunr.version = "0.5.7" -/*! - * lunr.utils - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * A namespace containing utils for the rest of the lunr library - */ -lunr.utils = {} - -/** - * Print a warning message to the console. - * - * @param {String} message The message to be printed. - * @memberOf Utils - */ -lunr.utils.warn = (function (global) { - return function (message) { - if (global.console && console.warn) { - console.warn(message) - } - } -})(this) - -/*! - * lunr.EventEmitter - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.EventEmitter is an event emitter for lunr. It manages adding and removing event handlers and triggering events and their handlers. - * - * @constructor - */ -lunr.EventEmitter = function () { - this.events = {} -} - -/** - * Binds a handler function to a specific event(s). - * - * Can bind a single function to many different events in one call. - * - * @param {String} [eventName] The name(s) of events to bind this function to. - * @param {Function} handler The function to call when an event is fired. - * @memberOf EventEmitter - */ -lunr.EventEmitter.prototype.addListener = function () { - var args = Array.prototype.slice.call(arguments), - fn = args.pop(), - names = args - - if (typeof fn !== "function") throw new TypeError ("last argument must be a function") - - names.forEach(function (name) { - if (!this.hasHandler(name)) this.events[name] = [] - this.events[name].push(fn) - }, this) -} - -/** - * Removes a handler function from a specific event. - * - * @param {String} eventName The name of the event to remove this function from. - * @param {Function} handler The function to remove from an event. - * @memberOf EventEmitter - */ -lunr.EventEmitter.prototype.removeListener = function (name, fn) { - if (!this.hasHandler(name)) return - - var fnIndex = this.events[name].indexOf(fn) - this.events[name].splice(fnIndex, 1) - - if (!this.events[name].length) delete this.events[name] -} - -/** - * Calls all functions bound to the given event. - * - * Additional data can be passed to the event handler as arguments to `emit` - * after the event name. - * - * @param {String} eventName The name of the event to emit. - * @memberOf EventEmitter - */ -lunr.EventEmitter.prototype.emit = function (name) { - if (!this.hasHandler(name)) return - - var args = Array.prototype.slice.call(arguments, 1) - - this.events[name].forEach(function (fn) { - fn.apply(undefined, args) - }) -} - -/** - * Checks whether a handler has ever been stored against an event. - * - * @param {String} eventName The name of the event to check. - * @private - * @memberOf EventEmitter - */ -lunr.EventEmitter.prototype.hasHandler = function (name) { - return name in this.events -} - -/*! - * lunr.tokenizer - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * A function for splitting a string into tokens ready to be inserted into - * the search index. - * - * @module - * @param {String} obj The string to convert into tokens - * @returns {Array} - */ -lunr.tokenizer = function (obj) { - if (!arguments.length || obj == null || obj == undefined) return [] - if (Array.isArray(obj)) return obj.map(function (t) { return t.toLowerCase() }) - - var str = obj.toString().replace(/^\s+/, '') - - for (var i = str.length - 1; i >= 0; i--) { - if (/\S/.test(str.charAt(i))) { - str = str.substring(0, i + 1) - break - } - } - - return str - .split(/(?:\s+|\-)/) - .filter(function (token) { - return !!token - }) - .map(function (token) { - return token.toLowerCase() - }) -} -/*! - * lunr.Pipeline - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.Pipelines maintain an ordered list of functions to be applied to all - * tokens in documents entering the search index and queries being ran against - * the index. - * - * An instance of lunr.Index created with the lunr shortcut will contain a - * pipeline with a stop word filter and an English language stemmer. Extra - * functions can be added before or after either of these functions or these - * default functions can be removed. - * - * When run the pipeline will call each function in turn, passing a token, the - * index of that token in the original list of all tokens and finally a list of - * all the original tokens. - * - * The output of functions in the pipeline will be passed to the next function - * in the pipeline. To exclude a token from entering the index the function - * should return undefined, the rest of the pipeline will not be called with - * this token. - * - * For serialisation of pipelines to work, all functions used in an instance of - * a pipeline should be registered with lunr.Pipeline. Registered functions can - * then be loaded. If trying to load a serialised pipeline that uses functions - * that are not registered an error will be thrown. - * - * If not planning on serialising the pipeline then registering pipeline functions - * is not necessary. - * - * @constructor - */ -lunr.Pipeline = function () { - this._stack = [] -} - -lunr.Pipeline.registeredFunctions = {} - -/** - * Register a function with the pipeline. - * - * Functions that are used in the pipeline should be registered if the pipeline - * needs to be serialised, or a serialised pipeline needs to be loaded. - * - * Registering a function does not add it to a pipeline, functions must still be - * added to instances of the pipeline for them to be used when running a pipeline. - * - * @param {Function} fn The function to check for. - * @param {String} label The label to register this function with - * @memberOf Pipeline - */ -lunr.Pipeline.registerFunction = function (fn, label) { - if (label in this.registeredFunctions) { - lunr.utils.warn('Overwriting existing registered function: ' + label) - } - - fn.label = label - lunr.Pipeline.registeredFunctions[fn.label] = fn -} - -/** - * Warns if the function is not registered as a Pipeline function. - * - * @param {Function} fn The function to check for. - * @private - * @memberOf Pipeline - */ -lunr.Pipeline.warnIfFunctionNotRegistered = function (fn) { - var isRegistered = fn.label && (fn.label in this.registeredFunctions) - - if (!isRegistered) { - lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\n', fn) - } -} - -/** - * Loads a previously serialised pipeline. - * - * All functions to be loaded must already be registered with lunr.Pipeline. - * If any function from the serialised data has not been registered then an - * error will be thrown. - * - * @param {Object} serialised The serialised pipeline to load. - * @returns {lunr.Pipeline} - * @memberOf Pipeline - */ -lunr.Pipeline.load = function (serialised) { - var pipeline = new lunr.Pipeline - - serialised.forEach(function (fnName) { - var fn = lunr.Pipeline.registeredFunctions[fnName] - - if (fn) { - pipeline.add(fn) - } else { - throw new Error ('Cannot load un-registered function: ' + fnName) - } - }) - - return pipeline -} - -/** - * Adds new functions to the end of the pipeline. - * - * Logs a warning if the function has not been registered. - * - * @param {Function} functions Any number of functions to add to the pipeline. - * @memberOf Pipeline - */ -lunr.Pipeline.prototype.add = function () { - var fns = Array.prototype.slice.call(arguments) - - fns.forEach(function (fn) { - lunr.Pipeline.warnIfFunctionNotRegistered(fn) - this._stack.push(fn) - }, this) -} - -/** - * Adds a single function after a function that already exists in the - * pipeline. - * - * Logs a warning if the function has not been registered. - * - * @param {Function} existingFn A function that already exists in the pipeline. - * @param {Function} newFn The new function to add to the pipeline. - * @memberOf Pipeline - */ -lunr.Pipeline.prototype.after = function (existingFn, newFn) { - lunr.Pipeline.warnIfFunctionNotRegistered(newFn) - - var pos = this._stack.indexOf(existingFn) + 1 - this._stack.splice(pos, 0, newFn) -} - -/** - * Adds a single function before a function that already exists in the - * pipeline. - * - * Logs a warning if the function has not been registered. - * - * @param {Function} existingFn A function that already exists in the pipeline. - * @param {Function} newFn The new function to add to the pipeline. - * @memberOf Pipeline - */ -lunr.Pipeline.prototype.before = function (existingFn, newFn) { - lunr.Pipeline.warnIfFunctionNotRegistered(newFn) - - var pos = this._stack.indexOf(existingFn) - this._stack.splice(pos, 0, newFn) -} - -/** - * Removes a function from the pipeline. - * - * @param {Function} fn The function to remove from the pipeline. - * @memberOf Pipeline - */ -lunr.Pipeline.prototype.remove = function (fn) { - var pos = this._stack.indexOf(fn) - this._stack.splice(pos, 1) -} - -/** - * Runs the current list of functions that make up the pipeline against the - * passed tokens. - * - * @param {Array} tokens The tokens to run through the pipeline. - * @returns {Array} - * @memberOf Pipeline - */ -lunr.Pipeline.prototype.run = function (tokens) { - var out = [], - tokenLength = tokens.length, - stackLength = this._stack.length - - for (var i = 0; i < tokenLength; i++) { - var token = tokens[i] - - for (var j = 0; j < stackLength; j++) { - token = this._stack[j](token, i, tokens) - if (token === void 0) break - }; - - if (token !== void 0) out.push(token) - }; - - return out -} - -/** - * Resets the pipeline by removing any existing processors. - * - * @memberOf Pipeline - */ -lunr.Pipeline.prototype.reset = function () { - this._stack = [] -} - -/** - * Returns a representation of the pipeline ready for serialisation. - * - * Logs a warning if the function has not been registered. - * - * @returns {Array} - * @memberOf Pipeline - */ -lunr.Pipeline.prototype.toJSON = function () { - return this._stack.map(function (fn) { - lunr.Pipeline.warnIfFunctionNotRegistered(fn) - - return fn.label - }) -} -/*! - * lunr.Vector - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.Vectors implement vector related operations for - * a series of elements. - * - * @constructor - */ -lunr.Vector = function () { - this._magnitude = null - this.list = undefined - this.length = 0 -} - -/** - * lunr.Vector.Node is a simple struct for each node - * in a lunr.Vector. - * - * @private - * @param {Number} The index of the node in the vector. - * @param {Object} The data at this node in the vector. - * @param {lunr.Vector.Node} The node directly after this node in the vector. - * @constructor - * @memberOf Vector - */ -lunr.Vector.Node = function (idx, val, next) { - this.idx = idx - this.val = val - this.next = next -} - -/** - * Inserts a new value at a position in a vector. - * - * @param {Number} The index at which to insert a value. - * @param {Object} The object to insert in the vector. - * @memberOf Vector. - */ -lunr.Vector.prototype.insert = function (idx, val) { - var list = this.list - - if (!list) { - this.list = new lunr.Vector.Node (idx, val, list) - return this.length++ - } - - var prev = list, - next = list.next - - while (next != undefined) { - if (idx < next.idx) { - prev.next = new lunr.Vector.Node (idx, val, next) - return this.length++ - } - - prev = next, next = next.next - } - - prev.next = new lunr.Vector.Node (idx, val, next) - return this.length++ -} - -/** - * Calculates the magnitude of this vector. - * - * @returns {Number} - * @memberOf Vector - */ -lunr.Vector.prototype.magnitude = function () { - if (this._magniture) return this._magnitude - var node = this.list, - sumOfSquares = 0, - val - - while (node) { - val = node.val - sumOfSquares += val * val - node = node.next - } - - return this._magnitude = Math.sqrt(sumOfSquares) -} - -/** - * Calculates the dot product of this vector and another vector. - * - * @param {lunr.Vector} otherVector The vector to compute the dot product with. - * @returns {Number} - * @memberOf Vector - */ -lunr.Vector.prototype.dot = function (otherVector) { - var node = this.list, - otherNode = otherVector.list, - dotProduct = 0 - - while (node && otherNode) { - if (node.idx < otherNode.idx) { - node = node.next - } else if (node.idx > otherNode.idx) { - otherNode = otherNode.next - } else { - dotProduct += node.val * otherNode.val - node = node.next - otherNode = otherNode.next - } - } - - return dotProduct -} - -/** - * Calculates the cosine similarity between this vector and another - * vector. - * - * @param {lunr.Vector} otherVector The other vector to calculate the - * similarity with. - * @returns {Number} - * @memberOf Vector - */ -lunr.Vector.prototype.similarity = function (otherVector) { - return this.dot(otherVector) / (this.magnitude() * otherVector.magnitude()) -} -/*! - * lunr.SortedSet - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.SortedSets are used to maintain an array of uniq values in a sorted - * order. - * - * @constructor - */ -lunr.SortedSet = function () { - this.length = 0 - this.elements = [] -} - -/** - * Loads a previously serialised sorted set. - * - * @param {Array} serialisedData The serialised set to load. - * @returns {lunr.SortedSet} - * @memberOf SortedSet - */ -lunr.SortedSet.load = function (serialisedData) { - var set = new this - - set.elements = serialisedData - set.length = serialisedData.length - - return set -} - -/** - * Inserts new items into the set in the correct position to maintain the - * order. - * - * @param {Object} The objects to add to this set. - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.add = function () { - Array.prototype.slice.call(arguments).forEach(function (element) { - if (~this.indexOf(element)) return - this.elements.splice(this.locationFor(element), 0, element) - }, this) - - this.length = this.elements.length -} - -/** - * Converts this sorted set into an array. - * - * @returns {Array} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.toArray = function () { - return this.elements.slice() -} - -/** - * Creates a new array with the results of calling a provided function on every - * element in this sorted set. - * - * Delegates to Array.prototype.map and has the same signature. - * - * @param {Function} fn The function that is called on each element of the - * set. - * @param {Object} ctx An optional object that can be used as the context - * for the function fn. - * @returns {Array} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.map = function (fn, ctx) { - return this.elements.map(fn, ctx) -} - -/** - * Executes a provided function once per sorted set element. - * - * Delegates to Array.prototype.forEach and has the same signature. - * - * @param {Function} fn The function that is called on each element of the - * set. - * @param {Object} ctx An optional object that can be used as the context - * @memberOf SortedSet - * for the function fn. - */ -lunr.SortedSet.prototype.forEach = function (fn, ctx) { - return this.elements.forEach(fn, ctx) -} - -/** - * Returns the index at which a given element can be found in the - * sorted set, or -1 if it is not present. - * - * @param {Object} elem The object to locate in the sorted set. - * @param {Number} start An optional index at which to start searching from - * within the set. - * @param {Number} end An optional index at which to stop search from within - * the set. - * @returns {Number} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.indexOf = function (elem, start, end) { - var start = start || 0, - end = end || this.elements.length, - sectionLength = end - start, - pivot = start + Math.floor(sectionLength / 2), - pivotElem = this.elements[pivot] - - if (sectionLength <= 1) { - if (pivotElem === elem) { - return pivot - } else { - return -1 - } - } - - if (pivotElem < elem) return this.indexOf(elem, pivot, end) - if (pivotElem > elem) return this.indexOf(elem, start, pivot) - if (pivotElem === elem) return pivot -} - -/** - * Returns the position within the sorted set that an element should be - * inserted at to maintain the current order of the set. - * - * This function assumes that the element to search for does not already exist - * in the sorted set. - * - * @param {Object} elem The elem to find the position for in the set - * @param {Number} start An optional index at which to start searching from - * within the set. - * @param {Number} end An optional index at which to stop search from within - * the set. - * @returns {Number} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.locationFor = function (elem, start, end) { - var start = start || 0, - end = end || this.elements.length, - sectionLength = end - start, - pivot = start + Math.floor(sectionLength / 2), - pivotElem = this.elements[pivot] - - if (sectionLength <= 1) { - if (pivotElem > elem) return pivot - if (pivotElem < elem) return pivot + 1 - } - - if (pivotElem < elem) return this.locationFor(elem, pivot, end) - if (pivotElem > elem) return this.locationFor(elem, start, pivot) -} - -/** - * Creates a new lunr.SortedSet that contains the elements in the intersection - * of this set and the passed set. - * - * @param {lunr.SortedSet} otherSet The set to intersect with this set. - * @returns {lunr.SortedSet} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.intersect = function (otherSet) { - var intersectSet = new lunr.SortedSet, - i = 0, j = 0, - a_len = this.length, b_len = otherSet.length, - a = this.elements, b = otherSet.elements - - while (true) { - if (i > a_len - 1 || j > b_len - 1) break - - if (a[i] === b[j]) { - intersectSet.add(a[i]) - i++, j++ - continue - } - - if (a[i] < b[j]) { - i++ - continue - } - - if (a[i] > b[j]) { - j++ - continue - } - }; - - return intersectSet -} - -/** - * Makes a copy of this set - * - * @returns {lunr.SortedSet} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.clone = function () { - var clone = new lunr.SortedSet - - clone.elements = this.toArray() - clone.length = clone.elements.length - - return clone -} - -/** - * Creates a new lunr.SortedSet that contains the elements in the union - * of this set and the passed set. - * - * @param {lunr.SortedSet} otherSet The set to union with this set. - * @returns {lunr.SortedSet} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.union = function (otherSet) { - var longSet, shortSet, unionSet - - if (this.length >= otherSet.length) { - longSet = this, shortSet = otherSet - } else { - longSet = otherSet, shortSet = this - } - - unionSet = longSet.clone() - - unionSet.add.apply(unionSet, shortSet.toArray()) - - return unionSet -} - -/** - * Returns a representation of the sorted set ready for serialisation. - * - * @returns {Array} - * @memberOf SortedSet - */ -lunr.SortedSet.prototype.toJSON = function () { - return this.toArray() -} -/*! - * lunr.Index - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.Index is object that manages a search index. It contains the indexes - * and stores all the tokens and document lookups. It also provides the main - * user facing API for the library. - * - * @constructor - */ -lunr.Index = function () { - this._fields = [] - this._ref = 'id' - this.pipeline = new lunr.Pipeline - this.documentStore = new lunr.Store - this.tokenStore = new lunr.TokenStore - this.corpusTokens = new lunr.SortedSet - this.eventEmitter = new lunr.EventEmitter - - this._idfCache = {} - - this.on('add', 'remove', 'update', (function () { - this._idfCache = {} - }).bind(this)) -} - -/** - * Bind a handler to events being emitted by the index. - * - * The handler can be bound to many events at the same time. - * - * @param {String} [eventName] The name(s) of events to bind the function to. - * @param {Function} handler The serialised set to load. - * @memberOf Index - */ -lunr.Index.prototype.on = function () { - var args = Array.prototype.slice.call(arguments) - return this.eventEmitter.addListener.apply(this.eventEmitter, args) -} - -/** - * Removes a handler from an event being emitted by the index. - * - * @param {String} eventName The name of events to remove the function from. - * @param {Function} handler The serialised set to load. - * @memberOf Index - */ -lunr.Index.prototype.off = function (name, fn) { - return this.eventEmitter.removeListener(name, fn) -} - -/** - * Loads a previously serialised index. - * - * Issues a warning if the index being imported was serialised - * by a different version of lunr. - * - * @param {Object} serialisedData The serialised set to load. - * @returns {lunr.Index} - * @memberOf Index - */ -lunr.Index.load = function (serialisedData) { - if (serialisedData.version !== lunr.version) { - lunr.utils.warn('version mismatch: current ' + lunr.version + ' importing ' + serialisedData.version) - } - - var idx = new this - - idx._fields = serialisedData.fields - idx._ref = serialisedData.ref - - idx.documentStore = lunr.Store.load(serialisedData.documentStore) - idx.tokenStore = lunr.TokenStore.load(serialisedData.tokenStore) - idx.corpusTokens = lunr.SortedSet.load(serialisedData.corpusTokens) - idx.pipeline = lunr.Pipeline.load(serialisedData.pipeline) - - return idx -} - -/** - * Adds a field to the list of fields that will be searchable within documents - * in the index. - * - * An optional boost param can be passed to affect how much tokens in this field - * rank in search results, by default the boost value is 1. - * - * Fields should be added before any documents are added to the index, fields - * that are added after documents are added to the index will only apply to new - * documents added to the index. - * - * @param {String} fieldName The name of the field within the document that - * should be indexed - * @param {Number} boost An optional boost that can be applied to terms in this - * field. - * @returns {lunr.Index} - * @memberOf Index - */ -lunr.Index.prototype.field = function (fieldName, opts) { - var opts = opts || {}, - field = { name: fieldName, boost: opts.boost || 1 } - - this._fields.push(field) - return this -} - -/** - * Sets the property used to uniquely identify documents added to the index, - * by default this property is 'id'. - * - * This should only be changed before adding documents to the index, changing - * the ref property without resetting the index can lead to unexpected results. - * - * @param {String} refName The property to use to uniquely identify the - * documents in the index. - * @param {Boolean} emitEvent Whether to emit add events, defaults to true - * @returns {lunr.Index} - * @memberOf Index - */ -lunr.Index.prototype.ref = function (refName) { - this._ref = refName - return this -} - -/** - * Add a document to the index. - * - * This is the way new documents enter the index, this function will run the - * fields from the document through the index's pipeline and then add it to - * the index, it will then show up in search results. - * - * An 'add' event is emitted with the document that has been added and the index - * the document has been added to. This event can be silenced by passing false - * as the second argument to add. - * - * @param {Object} doc The document to add to the index. - * @param {Boolean} emitEvent Whether or not to emit events, default true. - * @memberOf Index - */ -lunr.Index.prototype.add = function (doc, emitEvent) { - var docTokens = {}, - allDocumentTokens = new lunr.SortedSet, - docRef = doc[this._ref], - emitEvent = emitEvent === undefined ? true : emitEvent - - this._fields.forEach(function (field) { - var fieldTokens = this.pipeline.run(lunr.tokenizer(doc[field.name])) - - docTokens[field.name] = fieldTokens - lunr.SortedSet.prototype.add.apply(allDocumentTokens, fieldTokens) - }, this) - - this.documentStore.set(docRef, allDocumentTokens) - lunr.SortedSet.prototype.add.apply(this.corpusTokens, allDocumentTokens.toArray()) - - for (var i = 0; i < allDocumentTokens.length; i++) { - var token = allDocumentTokens.elements[i] - var tf = this._fields.reduce(function (memo, field) { - var fieldLength = docTokens[field.name].length - - if (!fieldLength) return memo - - var tokenCount = docTokens[field.name].filter(function (t) { return t === token }).length - - return memo + (tokenCount / fieldLength * field.boost) - }, 0) - - this.tokenStore.add(token, { ref: docRef, tf: tf }) - }; - - if (emitEvent) this.eventEmitter.emit('add', doc, this) -} - -/** - * Removes a document from the index. - * - * To make sure documents no longer show up in search results they can be - * removed from the index using this method. - * - * The document passed only needs to have the same ref property value as the - * document that was added to the index, they could be completely different - * objects. - * - * A 'remove' event is emitted with the document that has been removed and the index - * the document has been removed from. This event can be silenced by passing false - * as the second argument to remove. - * - * @param {Object} doc The document to remove from the index. - * @param {Boolean} emitEvent Whether to emit remove events, defaults to true - * @memberOf Index - */ -lunr.Index.prototype.remove = function (doc, emitEvent) { - var docRef = doc[this._ref], - emitEvent = emitEvent === undefined ? true : emitEvent - - if (!this.documentStore.has(docRef)) return - - var docTokens = this.documentStore.get(docRef) - - this.documentStore.remove(docRef) - - docTokens.forEach(function (token) { - this.tokenStore.remove(token, docRef) - }, this) - - if (emitEvent) this.eventEmitter.emit('remove', doc, this) -} - -/** - * Updates a document in the index. - * - * When a document contained within the index gets updated, fields changed, - * added or removed, to make sure it correctly matched against search queries, - * it should be updated in the index. - * - * This method is just a wrapper around `remove` and `add` - * - * An 'update' event is emitted with the document that has been updated and the index. - * This event can be silenced by passing false as the second argument to update. Only - * an update event will be fired, the 'add' and 'remove' events of the underlying calls - * are silenced. - * - * @param {Object} doc The document to update in the index. - * @param {Boolean} emitEvent Whether to emit update events, defaults to true - * @see Index.prototype.remove - * @see Index.prototype.add - * @memberOf Index - */ -lunr.Index.prototype.update = function (doc, emitEvent) { - var emitEvent = emitEvent === undefined ? true : emitEvent - - this.remove(doc, false) - this.add(doc, false) - - if (emitEvent) this.eventEmitter.emit('update', doc, this) -} - -/** - * Calculates the inverse document frequency for a token within the index. - * - * @param {String} token The token to calculate the idf of. - * @see Index.prototype.idf - * @private - * @memberOf Index - */ -lunr.Index.prototype.idf = function (term) { - var cacheKey = "@" + term - if (Object.prototype.hasOwnProperty.call(this._idfCache, cacheKey)) return this._idfCache[cacheKey] - - var documentFrequency = this.tokenStore.count(term), - idf = 1 - - if (documentFrequency > 0) { - idf = 1 + Math.log(this.tokenStore.length / documentFrequency) - } - - return this._idfCache[cacheKey] = idf -} - -/** - * Searches the index using the passed query. - * - * Queries should be a string, multiple words are allowed and will lead to an - * AND based query, e.g. `idx.search('foo bar')` will run a search for - * documents containing both 'foo' and 'bar'. - * - * All query tokens are passed through the same pipeline that document tokens - * are passed through, so any language processing involved will be run on every - * query term. - * - * Each query term is expanded, so that the term 'he' might be expanded to - * 'hello' and 'help' if those terms were already included in the index. - * - * Matching documents are returned as an array of objects, each object contains - * the matching document ref, as set for this index, and the similarity score - * for this document against the query. - * - * @param {String} query The query to search the index with. - * @returns {Object} - * @see Index.prototype.idf - * @see Index.prototype.documentVector - * @memberOf Index - */ -lunr.Index.prototype.search = function (query) { - var queryTokens = this.pipeline.run(lunr.tokenizer(query)), - queryVector = new lunr.Vector, - documentSets = [], - fieldBoosts = this._fields.reduce(function (memo, f) { return memo + f.boost }, 0) - - var hasSomeToken = queryTokens.some(function (token) { - return this.tokenStore.has(token) - }, this) - - if (!hasSomeToken) return [] - - queryTokens - .forEach(function (token, i, tokens) { - var tf = 1 / tokens.length * this._fields.length * fieldBoosts, - self = this - - var set = this.tokenStore.expand(token).reduce(function (memo, key) { - var pos = self.corpusTokens.indexOf(key), - idf = self.idf(key), - similarityBoost = 1, - set = new lunr.SortedSet - - // if the expanded key is not an exact match to the token then - // penalise the score for this key by how different the key is - // to the token. - if (key !== token) { - var diff = Math.max(3, key.length - token.length) - similarityBoost = 1 / Math.log(diff) - } - - // calculate the query tf-idf score for this token - // applying an similarityBoost to ensure exact matches - // these rank higher than expanded terms - if (pos > -1) queryVector.insert(pos, tf * idf * similarityBoost) - - // add all the documents that have this key into a set - Object.keys(self.tokenStore.get(key)).forEach(function (ref) { set.add(ref) }) - - return memo.union(set) - }, new lunr.SortedSet) - - documentSets.push(set) - }, this) - - var documentSet = documentSets.reduce(function (memo, set) { - return memo.intersect(set) - }) - - return documentSet - .map(function (ref) { - return { ref: ref, score: queryVector.similarity(this.documentVector(ref)) } - }, this) - .sort(function (a, b) { - return b.score - a.score - }) -} - -/** - * Generates a vector containing all the tokens in the document matching the - * passed documentRef. - * - * The vector contains the tf-idf score for each token contained in the - * document with the passed documentRef. The vector will contain an element - * for every token in the indexes corpus, if the document does not contain that - * token the element will be 0. - * - * @param {Object} documentRef The ref to find the document with. - * @returns {lunr.Vector} - * @private - * @memberOf Index - */ -lunr.Index.prototype.documentVector = function (documentRef) { - var documentTokens = this.documentStore.get(documentRef), - documentTokensLength = documentTokens.length, - documentVector = new lunr.Vector - - for (var i = 0; i < documentTokensLength; i++) { - var token = documentTokens.elements[i], - tf = this.tokenStore.get(token)[documentRef].tf, - idf = this.idf(token) - - documentVector.insert(this.corpusTokens.indexOf(token), tf * idf) - }; - - return documentVector -} - -/** - * Returns a representation of the index ready for serialisation. - * - * @returns {Object} - * @memberOf Index - */ -lunr.Index.prototype.toJSON = function () { - return { - version: lunr.version, - fields: this._fields, - ref: this._ref, - documentStore: this.documentStore.toJSON(), - tokenStore: this.tokenStore.toJSON(), - corpusTokens: this.corpusTokens.toJSON(), - pipeline: this.pipeline.toJSON() - } -} - -/** - * Applies a plugin to the current index. - * - * A plugin is a function that is called with the index as its context. - * Plugins can be used to customise or extend the behaviour the index - * in some way. A plugin is just a function, that encapsulated the custom - * behaviour that should be applied to the index. - * - * The plugin function will be called with the index as its argument, additional - * arguments can also be passed when calling use. The function will be called - * with the index as its context. - * - * Example: - * - * var myPlugin = function (idx, arg1, arg2) { - * // `this` is the index to be extended - * // apply any extensions etc here. - * } - * - * var idx = lunr(function () { - * this.use(myPlugin, 'arg1', 'arg2') - * }) - * - * @param {Function} plugin The plugin to apply. - * @memberOf Index - */ -lunr.Index.prototype.use = function (plugin) { - var args = Array.prototype.slice.call(arguments, 1) - args.unshift(this) - plugin.apply(this, args) -} -/*! - * lunr.Store - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.Store is a simple key-value store used for storing sets of tokens for - * documents stored in index. - * - * @constructor - * @module - */ -lunr.Store = function () { - this.store = {} - this.length = 0 -} - -/** - * Loads a previously serialised store - * - * @param {Object} serialisedData The serialised store to load. - * @returns {lunr.Store} - * @memberOf Store - */ -lunr.Store.load = function (serialisedData) { - var store = new this - - store.length = serialisedData.length - store.store = Object.keys(serialisedData.store).reduce(function (memo, key) { - memo[key] = lunr.SortedSet.load(serialisedData.store[key]) - return memo - }, {}) - - return store -} - -/** - * Stores the given tokens in the store against the given id. - * - * @param {Object} id The key used to store the tokens against. - * @param {Object} tokens The tokens to store against the key. - * @memberOf Store - */ -lunr.Store.prototype.set = function (id, tokens) { - if (!this.has(id)) this.length++ - this.store[id] = tokens -} - -/** - * Retrieves the tokens from the store for a given key. - * - * @param {Object} id The key to lookup and retrieve from the store. - * @returns {Object} - * @memberOf Store - */ -lunr.Store.prototype.get = function (id) { - return this.store[id] -} - -/** - * Checks whether the store contains a key. - * - * @param {Object} id The id to look up in the store. - * @returns {Boolean} - * @memberOf Store - */ -lunr.Store.prototype.has = function (id) { - return id in this.store -} - -/** - * Removes the value for a key in the store. - * - * @param {Object} id The id to remove from the store. - * @memberOf Store - */ -lunr.Store.prototype.remove = function (id) { - if (!this.has(id)) return - - delete this.store[id] - this.length-- -} - -/** - * Returns a representation of the store ready for serialisation. - * - * @returns {Object} - * @memberOf Store - */ -lunr.Store.prototype.toJSON = function () { - return { - store: this.store, - length: this.length - } -} - -/*! - * lunr.stemmer - * Copyright (C) 2014 Oliver Nightingale - * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt - */ - -/** - * lunr.stemmer is an english language stemmer, this is a JavaScript - * implementation of the PorterStemmer taken from http://tartaurs.org/~martin - * - * @module - * @param {String} str The string to stem - * @returns {String} - * @see lunr.Pipeline - */ -lunr.stemmer = (function(){ - var step2list = { - "ational" : "ate", - "tional" : "tion", - "enci" : "ence", - "anci" : "ance", - "izer" : "ize", - "bli" : "ble", - "alli" : "al", - "entli" : "ent", - "eli" : "e", - "ousli" : "ous", - "ization" : "ize", - "ation" : "ate", - "ator" : "ate", - "alism" : "al", - "iveness" : "ive", - "fulness" : "ful", - "ousness" : "ous", - "aliti" : "al", - "iviti" : "ive", - "biliti" : "ble", - "logi" : "log" - }, - - step3list = { - "icate" : "ic", - "ative" : "", - "alize" : "al", - "iciti" : "ic", - "ical" : "ic", - "ful" : "", - "ness" : "" - }, - - c = "[^aeiou]", // consonant - v = "[aeiouy]", // vowel - C = c + "[^aeiouy]*", // consonant sequence - V = v + "[aeiou]*", // vowel sequence - - mgr0 = "^(" + C + ")?" + V + C, // [C]VC... is m>0 - meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$", // [C]VC[V] is m=1 - mgr1 = "^(" + C + ")?" + V + C + V + C, // [C]VCVC... is m>1 - s_v = "^(" + C + ")?" + v; // vowel in stem - - var re_mgr0 = new RegExp(mgr0); - var re_mgr1 = new RegExp(mgr1); - var re_meq1 = new RegExp(meq1); - var re_s_v = new RegExp(s_v); - - var re_1a = /^(.+?)(ss|i)es$/; - var re2_1a = /^(.+?)([^s])s$/; - var re_1b = /^(.+?)eed$/; - var re2_1b = /^(.+?)(ed|ing)$/; - var re_1b_2 = /.$/; - var re2_1b_2 = /(at|bl|iz)$/; - var re3_1b_2 = new RegExp("([^aeiouylsz])\\1$"); - var re4_1b_2 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - - var re_1c = /^(.+?[^aeiou])y$/; - var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - - var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - - var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - var re2_4 = /^(.+?)(s|t)(ion)$/; - - var re_5 = /^(.+?)e$/; - var re_5_1 = /ll$/; - var re3_5 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - - var porterStemmer = function porterStemmer(w) { - var stem, - suffix, - firstch, - re, - re2, - re3, - re4; - - if (w.length < 3) { return w; } - - firstch = w.substr(0,1); - if (firstch == "y") { - w = firstch.toUpperCase() + w.substr(1); - } - - // Step 1a - re = re_1a - re2 = re2_1a; - - if (re.test(w)) { w = w.replace(re,"$1$2"); } - else if (re2.test(w)) { w = w.replace(re2,"$1$2"); } - - // Step 1b - re = re_1b; - re2 = re2_1b; - if (re.test(w)) { - var fp = re.exec(w); - re = re_mgr0; - if (re.test(fp[1])) { - re = re_1b_2; - w = w.replace(re,""); - } - } else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = re_s_v; - if (re2.test(stem)) { - w = stem; - re2 = re2_1b_2; - re3 = re3_1b_2; - re4 = re4_1b_2; - if (re2.test(w)) { w = w + "e"; } - else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,""); } - else if (re4.test(w)) { w = w + "e"; } - } - } - - // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say) - re = re_1c; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - w = stem + "i"; - } - - // Step 2 - re = re_2; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = re_mgr0; - if (re.test(stem)) { - w = stem + step2list[suffix]; - } - } - - // Step 3 - re = re_3; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = re_mgr0; - if (re.test(stem)) { - w = stem + step3list[suffix]; - } - } - - // Step 4 - re = re_4; - re2 = re2_4; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = re_mgr1; - if (re.test(stem)) { - w = stem; - } - } else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = re_mgr1; - if (re2.test(stem)) { - w = stem; - } - } - - // Step 5 - re = re_5; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = re_mgr1; - re2 = re_meq1; - re3 = re3_5; - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) { - w = stem; - } - } - - re = re_5_1; - re2 = re_mgr1; - if (re.test(w) && re2.test(w)) { - re = re_1b_2; - w = w.replace(re,""); - } - - // and turn initial Y back to y - - if (firstch == "y") { - w = firstch.toLowerCase() + w.substr(1); - } - - return w; - }; - - return porterStemmer; -})(); - -lunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer') -/*! - * lunr.stopWordFilter - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.stopWordFilter is an English language stop word list filter, any words - * contained in the list will not be passed through the filter. - * - * This is intended to be used in the Pipeline. If the token does not pass the - * filter then undefined will be returned. - * - * @module - * @param {String} token The token to pass through the filter - * @returns {String} - * @see lunr.Pipeline - */ -lunr.stopWordFilter = function (token) { - if (lunr.stopWordFilter.stopWords.indexOf(token) === -1) return token -} - -lunr.stopWordFilter.stopWords = new lunr.SortedSet -lunr.stopWordFilter.stopWords.length = 119 -lunr.stopWordFilter.stopWords.elements = [ - "", - "a", - "able", - "about", - "across", - "after", - "all", - "almost", - "also", - "am", - "among", - "an", - "and", - "any", - "are", - "as", - "at", - "be", - "because", - "been", - "but", - "by", - "can", - "cannot", - "could", - "dear", - "did", - "do", - "does", - "either", - "else", - "ever", - "every", - "for", - "from", - "get", - "got", - "had", - "has", - "have", - "he", - "her", - "hers", - "him", - "his", - "how", - "however", - "i", - "if", - "in", - "into", - "is", - "it", - "its", - "just", - "least", - "let", - "like", - "likely", - "may", - "me", - "might", - "most", - "must", - "my", - "neither", - "no", - "nor", - "not", - "of", - "off", - "often", - "on", - "only", - "or", - "other", - "our", - "own", - "rather", - "said", - "say", - "says", - "she", - "should", - "since", - "so", - "some", - "than", - "that", - "the", - "their", - "them", - "then", - "there", - "these", - "they", - "this", - "tis", - "to", - "too", - "twas", - "us", - "wants", - "was", - "we", - "were", - "what", - "when", - "where", - "which", - "while", - "who", - "whom", - "why", - "will", - "with", - "would", - "yet", - "you", - "your" -] - -lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter') -/*! - * lunr.trimmer - * Copyright (C) 2014 Oliver Nightingale - */ - -/** - * lunr.trimmer is a pipeline function for trimming non word - * characters from the begining and end of tokens before they - * enter the index. - * - * This implementation may not work correctly for non latin - * characters and should either be removed or adapted for use - * with languages with non-latin characters. - * - * @module - * @param {String} token The token to pass through the filter - * @returns {String} - * @see lunr.Pipeline - */ -lunr.trimmer = function (token) { - return token - .replace(/^\W+/, '') - .replace(/\W+$/, '') -} - -lunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer') -/*! - * lunr.stemmer - * Copyright (C) 2014 Oliver Nightingale - * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt - */ - -/** - * lunr.TokenStore is used for efficient storing and lookup of the reverse - * index of token to document ref. - * - * @constructor - */ -lunr.TokenStore = function () { - this.root = { docs: {} } - this.length = 0 -} - -/** - * Loads a previously serialised token store - * - * @param {Object} serialisedData The serialised token store to load. - * @returns {lunr.TokenStore} - * @memberOf TokenStore - */ -lunr.TokenStore.load = function (serialisedData) { - var store = new this - - store.root = serialisedData.root - store.length = serialisedData.length - - return store -} - -/** - * Adds a new token doc pair to the store. - * - * By default this function starts at the root of the current store, however - * it can start at any node of any token store if required. - * - * @param {String} token The token to store the doc under - * @param {Object} doc The doc to store against the token - * @param {Object} root An optional node at which to start looking for the - * correct place to enter the doc, by default the root of this lunr.TokenStore - * is used. - * @memberOf TokenStore - */ -lunr.TokenStore.prototype.add = function (token, doc, root) { - var root = root || this.root, - key = token[0], - rest = token.slice(1) - - if (!(key in root)) root[key] = {docs: {}} - - if (rest.length === 0) { - root[key].docs[doc.ref] = doc - this.length += 1 - return - } else { - return this.add(rest, doc, root[key]) - } -} - -/** - * Checks whether this key is contained within this lunr.TokenStore. - * - * By default this function starts at the root of the current store, however - * it can start at any node of any token store if required. - * - * @param {String} token The token to check for - * @param {Object} root An optional node at which to start - * @memberOf TokenStore - */ -lunr.TokenStore.prototype.has = function (token) { - if (!token) return false - - var node = this.root - - for (var i = 0; i < token.length; i++) { - if (!node[token[i]]) return false - - node = node[token[i]] - } - - return true -} - -/** - * Retrieve a node from the token store for a given token. - * - * By default this function starts at the root of the current store, however - * it can start at any node of any token store if required. - * - * @param {String} token The token to get the node for. - * @param {Object} root An optional node at which to start. - * @returns {Object} - * @see TokenStore.prototype.get - * @memberOf TokenStore - */ -lunr.TokenStore.prototype.getNode = function (token) { - if (!token) return {} - - var node = this.root - - for (var i = 0; i < token.length; i++) { - if (!node[token[i]]) return {} - - node = node[token[i]] - } - - return node -} - -/** - * Retrieve the documents for a node for the given token. - * - * By default this function starts at the root of the current store, however - * it can start at any node of any token store if required. - * - * @param {String} token The token to get the documents for. - * @param {Object} root An optional node at which to start. - * @returns {Object} - * @memberOf TokenStore - */ -lunr.TokenStore.prototype.get = function (token, root) { - return this.getNode(token, root).docs || {} -} - -lunr.TokenStore.prototype.count = function (token, root) { - return Object.keys(this.get(token, root)).length -} - -/** - * Remove the document identified by ref from the token in the store. - * - * By default this function starts at the root of the current store, however - * it can start at any node of any token store if required. - * - * @param {String} token The token to get the documents for. - * @param {String} ref The ref of the document to remove from this token. - * @param {Object} root An optional node at which to start. - * @returns {Object} - * @memberOf TokenStore - */ -lunr.TokenStore.prototype.remove = function (token, ref) { - if (!token) return - var node = this.root - - for (var i = 0; i < token.length; i++) { - if (!(token[i] in node)) return - node = node[token[i]] - } - - delete node.docs[ref] -} - -/** - * Find all the possible suffixes of the passed token using tokens - * currently in the store. - * - * @param {String} token The token to expand. - * @returns {Array} - * @memberOf TokenStore - */ -lunr.TokenStore.prototype.expand = function (token, memo) { - var root = this.getNode(token), - docs = root.docs || {}, - memo = memo || [] - - if (Object.keys(docs).length) memo.push(token) - - Object.keys(root) - .forEach(function (key) { - if (key === 'docs') return - - memo.concat(this.expand(token + key, memo)) - }, this) - - return memo -} - -/** - * Returns a representation of the token store ready for serialisation. - * - * @returns {Object} - * @memberOf TokenStore - */ -lunr.TokenStore.prototype.toJSON = function () { - return { - root: this.root, - length: this.length - } -} - - - /** - * export the module via AMD, CommonJS or as a browser global - * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js - */ - ;(function (root, factory) { - if (typeof define === 'function' && define.amd) { - // AMD. Register as an anonymous module. - define(factory) - } else if (typeof exports === 'object') { - /** - * Node. Does not work with strict CommonJS, but - * only CommonJS-like enviroments that support module.exports, - * like Node. - */ - module.exports = factory() - } else { - // Browser globals (root is window) - root.lunr = factory() - } - }(this, function () { - /** - * Just return a value to define the module export. - * This example returns an object, but the module - * can return a function as the exported value. - */ - return lunr - })) -})() diff --git a/client/galaxy/scripts/mvc/tools.js b/client/galaxy/scripts/mvc/tools.js index 032d6fbe051..abd017b075b 100644 --- a/client/galaxy/scripts/mvc/tools.js +++ b/client/galaxy/scripts/mvc/tools.js @@ -2,8 +2,8 @@ * Model, view, and controller objects for Galaxy tools and tool panel. */ - define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/lunr" ], - function(_, util, data, lunr) { + define( ["libs/underscore", "viz/trackster/util", "mvc/data" ], + function(_, util, data) { /** * Mixin for tracking model visibility. @@ -340,11 +340,6 @@ _.extend(ToolSection.prototype, VisibilityMixin); * 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", diff --git a/client/galaxy/scripts/viz/circster.js b/client/galaxy/scripts/viz/circster.js index a673d971891..756d8e3f085 100644 --- a/client/galaxy/scripts/viz/circster.js +++ b/client/galaxy/scripts/viz/circster.js @@ -1,16 +1,20 @@ // load required libraries -require( -[ +require([ 'utils/utils', - 'mvc/ui/icon-button', - 'libs/farbtastic', -], function(mod_utils, mod_icon_btn) +], function(mod_utils) { // load css mod_utils.cssLoadFile("static/style/circster.css"); }); -define(["libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(_, d3, visualization, config) { +define([ + "libs/underscore", + "libs/d3", + "viz/visualization", + "utils/config", + 'mvc/ui/icon-button', + 'libs/farbtastic' +], function(_, d3, visualization, config, mod_icon_btn) { /** * Utility class for working with SVG. @@ -71,7 +75,7 @@ var UsesTicks = { else { tick_coords = [1, 0, 4, 0]; text_coords = [0, 4, ".35em", ""]; - + } ticks.append("line") @@ -80,7 +84,7 @@ var UsesTicks = { .attr("x2", tick_coords[2]) .attr("y1", tick_coords[3]) .style("stroke", "#000"); - + return ticks.append("text") .attr("x", text_coords[0]) .attr("y", text_coords[1]) @@ -98,11 +102,11 @@ var UsesTicks = { // Use default of 2 sig. digits. if (sigDigits === undefined) sigDigits = 2; - + // Verify input number if (num === null) return null; - + // Calculate return value var rval = null; if (Math.abs(num) < 1) { @@ -141,7 +145,7 @@ var CircsterLabelTrack = Backbone.Model.extend({}); */ var CircsterView = Backbone.View.extend({ className: 'circster', - + initialize: function(options) { this.genome = options.genome; this.label_arc_height = 50; @@ -188,7 +192,7 @@ var CircsterView = Backbone.View.extend({ track_gap = this.model.get('config').get_value('track_gap'), // Subtract 20 to make sure chrom labels are on screen. min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20, - // Compute radius start based on model, will be centered + // Compute radius start based on model, will be centered // and fit entirely inside element by default. radius_start = min_dimension / 2 - circular_tracks.length * (dataset_arc_height + track_gap) + @@ -198,14 +202,14 @@ var CircsterView = Backbone.View.extend({ // Compute range of track starting radii. tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap); - + // Map from track start to bounds. var self = this; return _.map(tracks_start_radii, function(radius) { return [radius, radius + dataset_arc_height]; }); }, - + /** * Renders circular tracks, chord tracks, and label tracks. */ @@ -254,7 +258,7 @@ var CircsterView = Backbone.View.extend({ })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g').attr('class', 'tracks'); - + // -- Render circular tracks. -- // Create a view for each track in the visualization and render. @@ -266,12 +270,12 @@ var CircsterView = Backbone.View.extend({ genome: self.genome, total_gap: total_gap }); - + view.render(); - + return view; }); - + // -- Render chords tracks. -- this.chords_views = chords_tracks.map(function(track) { @@ -289,10 +293,10 @@ var CircsterView = Backbone.View.extend({ }); // -- Render label track. -- - + // Track bounds are: // (a) outer radius of last circular track; - // (b) + // (b) var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1], track_bounds = [ outermost_radius, @@ -305,7 +309,7 @@ var CircsterView = Backbone.View.extend({ genome: self.genome, total_gap: total_gap }); - + this.label_track_view.render(); }, @@ -356,7 +360,7 @@ var CircsterView = Backbone.View.extend({ // Update label track. /* - FIXME: should never have to update label track because vis always expands to fit area + FIXME: should never have to update label track because vis always expands to fit area within label track. var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; track_bounds[1] = track_bounds[0]; @@ -373,7 +377,7 @@ var CircsterView = Backbone.View.extend({ var track_view = this.circular_views[options.index]; this.circular_views.splice(options.index, 1); track_view.$el.remove(); - + // Recompute and update track bounds. var new_track_bounds = this.get_tracks_bounds(); _.each(this.circular_views, function(track_view, i) { @@ -392,7 +396,7 @@ var CircsterView = Backbone.View.extend({ _.each(this.chords_views, function(track_view) { track_view.update_radius_bounds(new_track_bounds[0]); }); - + } }); @@ -455,7 +459,7 @@ var CircsterTrackView = Backbone.View.extend({ // Append titles to paths. chroms_paths.append("title").text(function(d) { return d.data.chrom; }); - + // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. -- var self = this, @@ -490,7 +494,7 @@ var CircsterTrackView = Backbone.View.extend({ var new_d = d3.svg.arc() .innerRadius(this.radius_bounds[0]) .outerRadius(this.radius_bounds[1]); - + this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d); this._transition_chrom_data(); @@ -511,7 +515,7 @@ var CircsterTrackView = Backbone.View.extend({ } // -- Scale increased, so render visible data with more detail. -- - + var self = this, utils = new SVGUtils(); @@ -539,7 +543,7 @@ var CircsterTrackView = Backbone.View.extend({ $.when(data_deferred).then(function(data) { // Remove current data path. path_elt.remove(); - + // Update data bounds with new data. self._update_data_bounds(); @@ -598,12 +602,12 @@ var CircsterTrackView = Backbone.View.extend({ _transition_labels: function() {}, /** - * Update data bounds. If there are new_bounds, use them; otherwise use + * Update data bounds. If there are new_bounds, use them; otherwise use * default data bounds. */ _update_data_bounds: function(new_bounds) { var old_bounds = this.data_bounds; - this.data_bounds = new_bounds || + this.data_bounds = new_bounds || this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome)); this._transition_chrom_data(); }, @@ -624,7 +628,7 @@ var CircsterTrackView = Backbone.View.extend({ // Set min, max value in config so that they can be adjusted. Make this silent // because these attributes are watched for changes and the viz is updated - // accordingly (set up in initialize). Because we are setting up, we don't want + // accordingly (set up in initialize). Because we are setting up, we don't want // the watch to trigger events here. track.get('config').set_value('min_value', self.data_bounds[0], {silent: true}); track.get('config').set_value('max_value', self.data_bounds[1], {silent: true}); @@ -660,7 +664,7 @@ var CircsterTrackView = Backbone.View.extend({ _get_path_function: function(chrom_arc, chrom_data) {}, /** - * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle + * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle * separated by gaps. */ _chroms_layout: function() { @@ -700,14 +704,14 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({ * Render labels. */ _render_data: function(svg) { - // -- Add chromosome label where it will fit; an alternative labeling mechanism + // -- Add chromosome label where it will fit; an alternative labeling mechanism // would be nice for small chromosomes. -- var self = this, chrom_arcs = svg.selectAll('g'); chrom_arcs.selectAll('path') .attr('id', function(d) { return 'label-' + d.data.chrom; }); - + chrom_arcs.append("svg:text") .filter(function(d) { return d.endAngle - d.startAngle > self.min_arc_len; @@ -857,12 +861,12 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({ return "rotate(90)"; }; - // FIXME: + // FIXME: // (1) using min_max class below is needed for _update_min_max, which could be improved. // (2) showing config on tick click should be replaced by proper track config icon. // Draw min, max on first chrom only. - var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], + var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], this._data_bounds_ticks_fn(), textTransform, true) .classed('min_max', true); @@ -872,7 +876,7 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({ var view = new config.ConfigSettingCollectionView({ collection: self.track.get('config') }); - view.render_in_modal('Configure Track'); + view.render_in_modal('Configure Track'); }); }); @@ -951,7 +955,7 @@ _.extend(CircsterQuantitativeTrackView.prototype, UsesTicks); var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({ get_data_bounds: function(data) { - // Set max across dataset by extracting all values, flattening them into a + // Set max across dataset by extracting all values, flattening them into a // single array, and getting third quartile. var values = _.flatten( _.map(data, function(d) { if (d) { @@ -965,8 +969,8 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({ return 0; } }) ); - - // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 + + // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 // for sparsely populated data, so use max in that case. return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ]; } @@ -1068,13 +1072,13 @@ var Circster = Backbone.View.extend( genome : genome, model : vis }); - + // Render vizualization viz_view.render(); - + // setup title $('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + " " + galaxy_config.app.viz_config.dbkey); - + // setup menu var menu = mod_icon_btn.create_icon_buttons_menu([ { @@ -1100,7 +1104,7 @@ var Circster = Backbone.View.extend( { // show saving dialog box Galaxy.modal.show({title: "Saving...", body: "progress" }); - + // send to server $.ajax({ url: galaxy_config.root + "visualization/save", @@ -1132,11 +1136,11 @@ var Circster = Backbone.View.extend( window.location = galaxy_config.root + "visualization/list"; } }], { tooltip_config: { placement: 'bottom' } }); - + // add menu menu.$el.attr("style", "float: right"); $("#center .unified-panel-header-inner").append(menu.$el); - + // manual tooltip config because default gravity is S and cannot be changed $(".menu-button").tooltip( { placement: 'bottom' } ); } diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample index 65bfb9ebdac..726f231384c 100644 --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -93,6 +93,7 @@ + diff --git a/config/plugins/interactive_environments/ipython/templates/ipython.mako b/config/plugins/interactive_environments/ipython/templates/ipython.mako index f4c169bcb60..8f3a3d6655a 100644 --- a/config/plugins/interactive_environments/ipython/templates/ipython.mako +++ b/config/plugins/interactive_environments/ipython/templates/ipython.mako @@ -35,6 +35,7 @@ notebook_access_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/note notebook_login_url = ie_request.url_template('${PROXY_URL}/ipython/${PORT}/login?next=%2Fipython%2F${PORT}%2Ftree') docker_cmd = ie_request.docker_cmd(temp_dir) +ie_request.log.info("Starting IPython docker container with command [%s]" % docker_cmd) subprocess.call(docker_cmd, shell=True) %> diff --git a/display_applications/igv/gff.xml b/display_applications/igv/gff.xml new file mode 100644 index 00000000000..57e60bbadc4 --- /dev/null +++ b/display_applications/igv/gff.xml @@ -0,0 +1,110 @@ + + + + + + + + + + + + + + + ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys} + + + ${redirect_url} + + + + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ] + #else: + $gff_file.dbkey + #end if + + + <?xml version="1.0" encoding="utf-8"?> +<jnlp + spec="1.0+" + codebase="${site_link}"> + <information> + <title>IGV 1.5</title> + <vendor>The Broad Institute</vendor> + <homepage href="http://www.broadinstitute.org/igv"/> + <description>IGV Software</description> + <description kind="short">IGV</description> + </information> + <security> + <all-permissions/> + </security> + <resources> + +<j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/> + <jar href="igv.jar" download="eager" main="true"/> + <jar href="batik-codec.jar" download="eager"/> + <property name="apple.laf.useScreenMenuBar" value="true"/> + <property name="com.apple.mrj.application.growbox.intrudes" value="false"/> + <property name="com.apple.mrj.application.live-resize" value="true"/> + <property name="com.apple.macos.smallTabs" value="true"/> + </resources> + + <resources os="Mac" arch="i386"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macintel.jar"/> + </resources> + + <resources os="Mac" arch="ppc"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Mac" arch="PowerPC"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Windows"> + <property name="sun.java2d.noddraw" value="true"/> + <nativelib href="hdfnative-win.jar"/> + </resources> + + <resources os="Linux"> + <nativelib href="hdfnative-linux64.jar"/> + </resources> + + <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> + <argument>-g</argument> + <argument>${site_organism}</argument> + <argument>${gff_file.url}</argument> + </application-desc> +</jnlp> + + + #if $site_id.startswith( 'local_' ) + ${site_link}?file=${gff_file.qp}&genome=${site_organism}&merge=true&name=${qp( $gff_file.name )} + #elif $site_id.startswith( 'web_link_' ): + ${site_link}?sessionURL=${gff_file.qp}&genome=${site_organism}&merge=true&name=${qp( $gff_file.name )} + #else: + ${jnlp.url} + #end if + + + + + + + + ${ $dataset.dbkey == $value } + + + http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&genome=${gff_file.dbkey}&merge=true&name=${qp( $gff_file.name )} + + + + + + + diff --git a/lib/galaxy/auth/providers/activedirectory.py b/lib/galaxy/auth/providers/activedirectory.py index 33c2e39aded..8f77a9703aa 100644 --- a/lib/galaxy/auth/providers/activedirectory.py +++ b/lib/galaxy/auth/providers/activedirectory.py @@ -52,7 +52,12 @@ class ActiveDirectory(AuthProvider): ldap.set_option(ldap.OPT_REFERRALS, 0) l = ldap.initialize(_get_subs(options, 'server', params)) l.protocol_version = 3 - l.simple_bind_s(_get_subs(options, 'search-user', params), _get_subs(options, 'search-password', params)) + + if 'search-user' in options: + l.simple_bind_s(_get_subs(options, 'search-user', params), _get_subs(options, 'search-password', params)) + else: + l.simple_bind_s() + scope = ldap.SCOPE_SUBTREE # setup search @@ -61,7 +66,8 @@ class ActiveDirectory(AuthProvider): # parse results _, suser = l.result(result, 60) - _, attrs = suser[0] + dn, attrs = suser[0] + log.debug(("AD dn: %s" % dn)) log.debug(("AD Search attributes: %s" % attrs)) if hasattr(attrs, 'has_key'): for attr in attributes: @@ -69,6 +75,7 @@ class ActiveDirectory(AuthProvider): params[attr] = str(attrs[attr][0]) else: params[attr] = "" + params['dn'] = dn except Exception: log.exception('ACTIVEDIRECTORY Search Exception for User: %s' % username) return (failure_mode, '') diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index e6f7c8556b7..a7f9863d0ad 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -476,7 +476,7 @@ class Configuration( object ): datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], job_config_file=[ 'config/job_conf.xml', 'job_conf.xml' ], - job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], + job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml', 'config/job_metrics_conf.xml.sample' ], dependency_resolvers_config_file=[ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], job_resource_params_file=[ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config=[ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 74d72c7bbc7..592f75850d4 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1138,6 +1138,7 @@ class JobWrapper( object ): # Update (non-library) job output datasets through the object store if dataset not in job.output_library_datasets: self.app.object_store.update_from_file(dataset.dataset, create=True) + self._collect_extra_files(dataset.dataset, self.working_directory) if job.states.ERROR == final_job_state: dataset.blurb = "error" dataset.mark_unhidden() @@ -1251,8 +1252,6 @@ class JobWrapper( object ): # instead of validated and transformed values during i.e. running workflows param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) param_dict = self.tool.params_from_strings( param_dict, self.app ) - # Check for and move associated_files - self.tool.collect_associated_files(out_data, self.working_directory) # Create generated output children and primary datasets and add to param_dict collected_datasets = { 'children': self.tool.collect_child_datasets(out_data, self.working_directory), @@ -1283,6 +1282,16 @@ class JobWrapper( object ): if job.user: job.user.total_disk_usage += bytes + # Empirically, we need to update job.user and + # job.workflow_invocation_step.workflow_invocation in separate + # transactions. Best guess as to why is that the workflow_invocation + # may or may not exist when the job is first loaded by the handler - + # and depending on whether it is or not sqlalchemy orders the updates + # differently and deadlocks can occur (one thread updates user and + # waits on invocation and the other updates invocation and waits on + # user). + self.sa_session.flush() + # fix permissions for path in [ dp.real_path for dp in self.get_mutable_output_fnames() ]: util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) @@ -1317,6 +1326,28 @@ class JobWrapper( object ): except: log.exception( "Unable to cleanup job %d" % self.job_id ) + def _collect_extra_files(self, dataset, job_working_directory): + temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( dataset.id ) ) + extra_dir = None + try: + # This skips creation of directories - object store + # automatically creates them. However, empty directories will + # not be created in the object store at all, which might be a + # problem. + for root, dirs, files in os.walk( temp_file_path ): + extra_dir = root.replace(job_working_directory, '', 1).lstrip(os.path.sep) + for f in files: + self.app.object_store.update_from_file( + dataset, + extra_dir=extra_dir, + alt_name=f, + file_name=os.path.join(root, f), + create=True, + preserve_symlinks=True + ) + except Exception, e: + log.debug( "Error in collect_associated_files: %s" % ( e ) ) + def _collect_metrics( self, has_metrics ): job = has_metrics.get_job() per_plugin_properties = self.app.job_metrics.collect_properties( job.destination_id, self.job_id, self.working_directory ) diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py index e66f7a27533..8c81223e6f9 100644 --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -700,8 +700,8 @@ class ModelDeserializer( object ): setattr( item, key, val ) return val - def deserialize_basestring( self, trans, item, key, val ): - val = self.validate.basestring( key, val ) + def deserialize_basestring( self, trans, item, key, val, convert_none_to_empty=False ): + val = '' if ( convert_none_to_empty and val is None ) else self.validate.basestring( key, val ) return self.default_deserializer( trans, item, key, val ) def deserialize_bool( self, trans, item, key, val ): diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py index 8cd1ae8eaf0..e99010feac6 100644 --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -426,7 +426,7 @@ class HDASerializer( datasets.DatasetAssociationSerializer, 'hda_ldda' : lambda *a: 'hda', # remapped - 'info' : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else i.info, + 'info' : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else '', 'misc_info' : lambda t, i, k: self.serializers[ 'info' ]( t, i, k ), 'misc_blurb' : lambda t, i, k: i.blurb, 'genome_build' : lambda t, i, k: i.dbkey, @@ -622,7 +622,8 @@ class HDADeserializer( datasets.DatasetAssociationDeserializer, # remapped 'genome_build' : lambda t, i, k, v: self.deserialize_genome_build( t, i, 'dbkey', v ), - 'misc_info' : lambda t, i, k, v: self.deserialize_basestring( t, i, 'info', v ), + 'misc_info' : lambda t, i, k, v: ( + self.deserialize_basestring( t, i, 'info', v, convert_none_to_empty=True ) ), # TODO: mixin: deletable 'deleted' : self.deserialize_bool, diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 11bf1cb6799..183346e37cf 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2148,39 +2148,6 @@ class Tool( object, Dictifiable ): """ pass - def collect_associated_files( self, output, job_working_directory ): - """ - Find extra files in the job working directory and move them into - the appropriate dataset's files directory - """ - for name, hda in output.items(): - temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) - extra_dir = None - try: - # This skips creation of directories - object store - # automatically creates them. However, empty directories will - # not be created in the object store at all, which might be a - # problem. - for root, dirs, files in os.walk( temp_file_path ): - extra_dir = root.replace(job_working_directory, '', 1).lstrip(os.path.sep) - for f in files: - self.app.object_store.update_from_file(hda.dataset, - extra_dir=extra_dir, - alt_name=f, - file_name=os.path.join(root, f), - create=True, - preserve_symlinks=True - ) - # Clean up after being handled by object store. - # FIXME: If the object (e.g., S3) becomes async, this will - # cause issues so add it to the object store functionality? - if extra_dir is not None: - # there was an extra_files_path dir, attempt to remove it - shutil.rmtree(temp_file_path) - except Exception, e: - log.debug( "Error in collect_associated_files: %s" % ( e ) ) - continue - def collect_child_datasets( self, output, job_working_directory ): """ Look for child dataset files, create HDA and attach to parent. @@ -2476,7 +2443,7 @@ class Tool( object, Dictifiable ): continue # state for subsection/group - group_state = state_inputs[input.name] + group_state = state_inputs.get(input.name, {}) # iterate and update values if input.type == 'repeat': @@ -2487,10 +2454,12 @@ class Tool( object, Dictifiable ): elif input.type == 'conditional': if 'test_param' in tool_dict: test_param = tool_dict['test_param'] - test_param['value'] = jsonify(group_state[test_param['name']]) - if '__current_case__' in group_state: - i = group_state['__current_case__'] - iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, group_state, other_values) + test_param['value'] = jsonify(group_state.get(test_param['name'], None)) + for i in range (len ( tool_dict['cases'] ) ): + current_state = {} + if i == group_state.get('__current_case__', None): + current_state = group_state + iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values) elif input.type == 'section': iterate( tool_dict['inputs'], input.inputs, group_state, other_values ) else: @@ -2504,11 +2473,15 @@ class Tool( object, Dictifiable ): input_name = tool_dict.get('name') if input_name: # backup default value - tool_dict['default_value'] = input.get_initial_value(trans, other_values) + try: + tool_dict['default_value'] = input.get_initial_value(trans, other_values) + except Exception: + # get initial value failed due to improper late validation + tool_dict['default_value'] = None + pass # update input value from tool state - if input_name in state_inputs: - tool_dict['value'] = state_inputs[input_name] + tool_dict['value'] = state_inputs.get(input_name, None) # sanitize values sanitize(tool_dict, 'value') diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 888019d0346..052f68d769d 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -15,6 +15,7 @@ from galaxy.util.bunch import Bunch from galaxy.util import string_as_bool, sanitize_param, unicodify from galaxy.util import listify from galaxy.util.odict import odict +from galaxy.util.expressions import ExpressionContext from sanitize import ToolParameterSanitizer import validation import dynamic_options @@ -802,8 +803,9 @@ class SelectToolParameter( ToolParameter ): self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) ) def _get_dynamic_options_call_other_values( self, trans, other_values ): - call_other_values = { "__trans__": trans } + call_other_values = ExpressionContext({ "__trans__": trans }) if other_values: + call_other_values.parent = other_values.parent call_other_values.update( other_values.dict ) return call_other_values @@ -1510,8 +1512,9 @@ class DrillDownSelectToolParameter( SelectToolParameter ): def _get_options_from_code( self, trans=None, value=None, other_values=None ): assert self.dynamic_options, Exception( "dynamic_options was not specifed" ) - call_other_values = { '__trans__': trans, '__value__': value } + call_other_values = ExpressionContext({ '__trans__': trans, '__value__': value }) if other_values: + call_other_values.parent = other_values.parent call_other_values.update( other_values.dict ) try: return eval( self.dynamic_options, self.tool.code_namespace, call_other_values ) diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index 4f5a98ffe86..63a8954ac4f 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -11,6 +11,9 @@ eggs.require("PyYAML") import yaml from galaxy.managers import api_keys +import logging +log = logging.getLogger(__name__) + class InteractiveEnviornmentRequest(object): @@ -18,6 +21,7 @@ class InteractiveEnviornmentRequest(object): plugin_config = plugin.config self.trans = trans + self.log = log self.attr = Bunch() self.attr.viz_id = plugin_config["name"].lower() @@ -161,5 +165,5 @@ class InteractiveEnviornmentRequest(object): """ return '%s run -d -u %s --sig-proxy=true -p %s:%s -v "%s:/import/" %s' % \ (self.attr.viz_config.get("docker", "command"), os.geteuid(), - self.attr.PORT, self.attr.docker_port, - temp_dir, self.attr.viz_config.get("docker", "image")) + self.attr.PORT, self.attr.docker_port, + temp_dir, self.attr.viz_config.get("docker", "image")) diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 780cf63e4a7..267880e9866 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,15 +1,12 @@ """ API operations on the contents of a library folder. """ -from galaxy import web from galaxy import util from galaxy import exceptions from galaxy import managers from galaxy.managers import folders from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from sqlalchemy.orm.exc import MultipleResultsFound -from sqlalchemy.orm.exc import NoResultFound from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems import logging @@ -130,7 +127,7 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary # Check whether user can modify the current folder can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) - + parent_library_id = None if folder.parent_library is not None: parent_library_id = trans.security.encode_id( folder.parent_library.id ) @@ -158,7 +155,7 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary if folder.parent_id is None: path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) else: - # We add the current folder and traverse up one folder. + # We add the current folder and traverse up one folder. path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) path_to_root.extend( self.build_path( trans, upper_folder ) ) @@ -187,11 +184,11 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary if subfolder.deleted: if include_deleted: if is_admin: - # Admins can see all deleted folders. + # Admins can see all deleted folders. subfolder.api_type = 'folder' content_items.append( subfolder ) else: - # Users with MODIFY permissions can see deleted folders. + # Users with MODIFY permissions can see deleted folders. can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, subfolder ) if can_modify: subfolder.api_type = 'folder' @@ -214,11 +211,11 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary if dataset.deleted: if include_deleted: if is_admin: - # Admins can see all deleted datasets. + # Admins can see all deleted datasets. dataset.api_type = 'file' content_items.append( dataset ) else: - # Users with MODIFY permissions on the item can see the deleted item. + # Users with MODIFY permissions on the item can see the deleted item. can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, dataset ) if can_modify: dataset.api_type = 'file' @@ -323,7 +320,7 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary raise exceptions.NotImplemented( 'Showing the library folder content is not implemented here.' ) @expose_api - def update( self, trans, id, library_id, payload, **kwd ): + def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/folders/{encoded_folder_id}/contents """ diff --git a/lib/galaxy/webapps/galaxy/api/lda_datasets.py b/lib/galaxy/webapps/galaxy/api/lda_datasets.py index 9bb7418ad9b..1af9d8d6c14 100644 --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -402,7 +402,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): """ load( self, trans, **kwd ): * POST /api/libraries/datasets - Load dataset from the given source into the library. + Load dataset from the given source into the library. Source can be: user directory - root folder specified in galaxy.ini as "$user_library_import_dir" example path: path/to/galaxy/$user_library_import_dir/user@example.com/{user can browse everything here} @@ -410,7 +410,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): (admin)import directory - root folder specified in galaxy ini as "$library_import_dir" example path: path/to/galaxy/$library_import_dir/{admin can browse everything here} (admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini - + :param encoded_folder_id: the encoded id of the folder to import dataset(s) to :type encoded_folder_id: an encoded id string :param source: source the datasets should be loaded form @@ -427,7 +427,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): :type dbkey: str :returns: dict containing information about the created upload job - :rtype: dictionary + :rtype: dictionary """ kwd[ 'space_to_tab' ] = 'False' @@ -572,7 +572,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): if format in [ 'zip', 'tgz', 'tbz' ]: # error = False killme = string.punctuation + string.whitespace - trantab = string.maketrans( killme, '_'*len( killme ) ) + trantab = string.maketrans( killme, '_' * len( killme ) ) try: outext = 'zip' if format == 'zip': diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py index aaf777707a1..bd3dfb90a71 100644 --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -232,7 +232,7 @@ class LibrariesController( BaseAPIController ): return_roles = [] for role in roles: - role_id = trans.security.encode_id ( role.id ) + role_id = trans.security.encode_id( role.id ) return_roles.append( dict( id=role_id, name=role.name, type=role.type ) ) return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) else: @@ -344,10 +344,10 @@ class LibrariesController( BaseAPIController ): if len( invalid_modify_roles_names ) > 0: log.warning( "The following roles could not be added to the modify library permission: " + str( invalid_modify_roles_names ) ) - permissions = { trans.app.security_agent.permitted_actions.LIBRARY_ACCESS : valid_access_roles } - permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_ADD : valid_add_roles } ) - permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MANAGE : valid_manage_roles } ) - permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } ) + permissions = { trans.app.security_agent.permitted_actions.LIBRARY_ACCESS: valid_access_roles } + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_ADD: valid_add_roles } ) + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MANAGE: valid_manage_roles } ) + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY: valid_modify_roles } ) trans.app.security_agent.set_all_library_permissions( trans, library, permissions ) trans.sa_session.refresh( library ) @@ -355,7 +355,7 @@ class LibrariesController( BaseAPIController ): trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) else: raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' - 'Allowed values are: "remove_restrictions", set_permissions"' ) + 'Allowed values are: "remove_restrictions", set_permissions"' ) roles = self.library_manager.get_current_roles( trans, library ) return roles @@ -376,6 +376,5 @@ class LibrariesController( BaseAPIController ): trans.sa_session.refresh( library ) # Copy the permissions to the root folder trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) - item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + item = library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) return item - diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py index 38c0d900536..638e6fb088b 100644 --- a/lib/galaxy/webapps/galaxy/api/remote_files.py +++ b/lib/galaxy/webapps/galaxy/api/remote_files.py @@ -4,16 +4,16 @@ API operations on remote files. import os import time import hashlib -from galaxy import web from galaxy import exceptions from galaxy.web import _future_expose_api as expose_api from galaxy.util import jstree -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web.base.controller import BaseAPIController from operator import itemgetter import logging log = logging.getLogger( __name__ ) + class RemoteFilesAPIController( BaseAPIController ): @expose_api @@ -109,9 +109,9 @@ class RemoteFilesAPIController( BaseAPIController ): for filename in filenames: path = os.path.relpath( os.path.join( dirpath, filename ), directory ) statinfo = os.lstat( os.path.join( dirpath, filename ) ) - response.append( dict( path = path, - size = statinfo.st_size, - ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) + response.append( dict( path=path, + size=statinfo.st_size, + ctime=time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) else: raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) # sort by path diff --git a/lib/galaxy/webapps/galaxy/api/search.py b/lib/galaxy/webapps/galaxy/api/search.py index da2aceb4746..444a620aad6 100644 --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/lib/galaxy/webapps/galaxy/api/search.py @@ -9,6 +9,7 @@ from galaxy.exceptions import ItemAccessibilityException log = logging.getLogger( __name__ ) + class SearchController( BaseAPIController, SharableItemSecurityMixin ): @web.expose_api @@ -24,14 +25,14 @@ class SearchController( BaseAPIController, SharableItemSecurityMixin ): try: query = se.query(query_txt) except Exception, e: - return {'error' : str(e)} + return {'error': str(e)} if query is not None: query.decode_query_ids(trans) current_user_roles = trans.get_current_user_roles() try: results = query.process(trans) except Exception, e: - return {'error' : str(e)} + return {'error': str(e)} for item in results: append = False if trans.user_is_admin(): @@ -49,7 +50,7 @@ class SearchController( BaseAPIController, SharableItemSecurityMixin ): append = True except ItemAccessibilityException: append = False - elif type ( item ) in [ trans.app.model.PageRevision ]: + elif type( item ) in [ trans.app.model.PageRevision ]: try: if self.security_check( trans, item.page, False, True): append = True @@ -62,4 +63,4 @@ class SearchController( BaseAPIController, SharableItemSecurityMixin ): if append: row = query.item_to_api_value(item) out.append( self.encode_all_ids( trans, row, True) ) - return { 'results' : out } + return { 'results': out } diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index a6687438040..6400188a76b 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -210,7 +210,6 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): if success: trans.response.set_content_type( 'application/x-gzip' ) download_file = open( tool_tarball ) - os.unlink( tool_tarball ) tarball_path, filename = os.path.split( tool_tarball ) trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.tgz"' % ( id ) return download_file @@ -397,7 +396,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ): # job's previous parameters and incoming parameters. Incoming parameters # have priority. # - original_job = self.hda_manager.creating_job( original_dataset ) + original_job = self.hda_manager.creating_job( trans, original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL diff --git a/lib/galaxy/webapps/galaxy/controllers/library_common.py b/lib/galaxy/webapps/galaxy/controllers/library_common.py index 2d000f10b8f..1a7bfd80f6a 100644 --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -1136,7 +1136,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ): link_data_only = params.get( 'link_data_only', 'copy_files' ) uuid_str = params.get( 'uuid', None ) - file_type = params.get( 'file_type' ) + file_type = params.get( 'file_type', None ) library_bunch.replace_dataset = None # not valid for these types of upload uploaded_dataset = util.bunch.Bunch() new_name = name @@ -1152,8 +1152,8 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet uploaded_dataset.type = type uploaded_dataset.ext = None uploaded_dataset.file_type = file_type - uploaded_dataset.dbkey = params.get( 'dbkey' ) - uploaded_dataset.space_to_tab = params.get( 'space_to_tab' ) + uploaded_dataset.dbkey = params.get( 'dbkey', None ) + uploaded_dataset.space_to_tab = params.get( 'space_to_tab', None ) if in_folder: uploaded_dataset.in_folder = in_folder uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch ) diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py index bbdf366bbf5..b12e7cd2789 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tag.py +++ b/lib/galaxy/webapps/galaxy/controllers/tag.py @@ -42,7 +42,7 @@ class TagsController ( BaseUIController, UsesTagsMixin ): # Apply tag. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).apply_item_tags( trans, user, item, new_tag.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).apply_item_tags( user, item, new_tag.encode( 'utf-8' ) ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=new_tag ) @@ -57,7 +57,7 @@ class TagsController ( BaseUIController, UsesTagsMixin ): # Remove tag. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).remove_item_tag( trans, user, item, tag_name.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).remove_item_tag( user, item, tag_name.encode( 'utf-8' ) ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=tag_name ) @@ -73,8 +73,8 @@ class TagsController ( BaseUIController, UsesTagsMixin ): # Apply tags. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).delete_item_tags( trans, user, item ) - self.get_tag_handler( trans ).apply_item_tags( trans, user, item, new_tags.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).delete_item_tags( user, item ) + self.get_tag_handler( trans ).apply_item_tags( user, item, new_tags.encode( 'utf-8' ) ) trans.sa_session.flush() @web.expose diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py index 990fb5882d3..d1c9868939d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -985,7 +985,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - job = self.hda_manager.creating_job( dataset ) + job = self.hda_manager.creating_job( trans, dataset ) viz_config = { 'dataset_id': dataset_id, 'tool_id': job.tool_id, @@ -1017,7 +1017,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio if dataset_id: decoded_id = self.decode_id( dataset_id ) hda = self.hda_manager.get_accessible( trans, decoded_id, trans.user ) - hda = self.hda_manager.error_if_uploading( hda ) + hda = self.hda_manager.error_if_uploading( trans, hda ) else: return trans.show_message( "Phyloviz couldn't find a dataset_id" ) diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py index f91f8331fcb..4af614f9cb0 100644 --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -876,7 +876,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix try: workflow_data = urllib2.urlopen( url ).read() except Exception, e: - message = "Failed to open URL: %s
Exception: %s" % ( url, str( e ) ) + message = "Failed to open URL: %s
Exception: %s" % ( url, escape( str( e ) ) ) status = 'error' elif workflow_text: # This case occurs when the workflow_text was sent via http from the tool shed. diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py index 5bbefe1ff3d..2f9e191b94b 100644 --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -144,8 +144,23 @@ def app_factory( global_conf, **kwargs ): # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - if asbool( kwargs.get( 'static_enabled', True ) ): - webapp = wrap_in_static( webapp, global_conf, **kwargs ) + # TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once. + is_uwsgi = False + try: + # The uwsgi module is automatically injected by the parent uwsgi + # process and only exists that way. If anything works, this is a + # uwsgi-managed process. + import uwsgi + is_uwsgi = uwsgi.numproc + is_uwsgi = True + except ImportError: + # This is not a uwsgi process, or something went horribly wrong. + pass + if asbool( kwargs.get( 'static_enabled', True) ): + if is_uwsgi: + log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.") + else: + webapp = wrap_in_static( webapp, global_conf, **kwargs ) # Close any pooled database connections before forking try: galaxy.webapps.tool_shed.model.mapping.metadata.engine.connection_provider._pool.dispose() diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py index 041044ae46a..7523d00e567 100644 --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -456,8 +456,8 @@ class MetadataGenerator( object ): try: exported_workflow_dict = json.loads( workflow_text ) except Exception, e: - log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" \ - % str( relative_path ), str( e ) ) + log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" + % ( str( relative_path ), str( e ) ) ) valid_exported_galaxy_workflow = False if valid_exported_galaxy_workflow and \ 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b.elements=a,b.length=a.length,b},a.SortedSet.prototype.add=function(){Array.prototype.slice.call(arguments).forEach(function(a){~this.indexOf(a)||this.elements.splice(this.locationFor(a),0,a)},this),this.length=this.elements.length},a.SortedSet.prototype.toArray=function(){return this.elements.slice()},a.SortedSet.prototype.map=function(a,b){return this.elements.map(a,b)},a.SortedSet.prototype.forEach=function(a,b){return this.elements.forEach(a,b)},a.SortedSet.prototype.indexOf=function(a,b,c){var b=b||0,c=c||this.elements.length,d=c-b,e=b+Math.floor(d/2),f=this.elements[e];return 1>=d?f===a?e:-1:a>f?this.indexOf(a,e,c):f>a?this.indexOf(a,b,e):f===a?e:void 0},a.SortedSet.prototype.locationFor=function(a,b,c){var b=b||0,c=c||this.elements.length,d=c-b,e=b+Math.floor(d/2),f=this.elements[e];if(1>=d){if(f>a)return e;if(a>f)return e+1}return a>f?this.locationFor(a,e,c):f>a?this.locationFor(a,b,e):void 0},a.SortedSet.prototype.intersect=function(b){for(var c=new a.SortedSet,d=0,e=0,f=this.length,g=b.length,h=this.elements,i=b.elements;;){if(d>f-1||e>g-1)break;h[d]!==i[e]?h[d]i[e]&&e++:(c.add(h[d]),d++,e++)}return c},a.SortedSet.prototype.clone=function(){var b=new a.SortedSet;return b.elements=this.toArray(),b.length=b.elements.length,b},a.SortedSet.prototype.union=function(a){var b,c,d;return this.length>=a.length?(b=this,c=a):(b=a,c=this),d=b.clone(),d.add.apply(d,c.toArray()),d},a.SortedSet.prototype.toJSON=function(){return this.toArray()},a.Index=function(){this._fields=[],this._ref="id",this.pipeline=new a.Pipeline,this.documentStore=new a.Store,this.tokenStore=new a.TokenStore,this.corpusTokens=new a.SortedSet,this.eventEmitter=new a.EventEmitter,this._idfCache={},this.on("add","remove","update",function(){this._idfCache={}}.bind(this))},a.Index.prototype.on=function(){var a=Array.prototype.slice.call(arguments);return this.eventEmitter.addListener.apply(this.eventEmitter,a)},a.Index.prototype.off=function(a,b){return this.eventEmitter.removeListener(a,b)},a.Index.load=function(b){b.version!==a.version&&a.utils.warn("version mismatch: current "+a.version+" importing "+b.version);var c=new this;return c._fields=b.fields,c._ref=b.ref,c.documentStore=a.Store.load(b.documentStore),c.tokenStore=a.TokenStore.load(b.tokenStore),c.corpusTokens=a.SortedSet.load(b.corpusTokens),c.pipeline=a.Pipeline.load(b.pipeline),c},a.Index.prototype.field=function(a,b){var b=b||{},c={name:a,boost:b.boost||1};return this._fields.push(c),this},a.Index.prototype.ref=function(a){return this._ref=a,this},a.Index.prototype.add=function(b,c){var d={},e=new a.SortedSet,f=b[this._ref],c=void 0===c?!0:c;this._fields.forEach(function(c){var f=this.pipeline.run(a.tokenizer(b[c.name]));d[c.name]=f,a.SortedSet.prototype.add.apply(e,f)},this),this.documentStore.set(f,e),a.SortedSet.prototype.add.apply(this.corpusTokens,e.toArray());for(var g=0;g0&&(d=1+Math.log(this.tokenStore.length/c)),this._idfCache[b]=d},a.Index.prototype.search=function(b){var c=this.pipeline.run(a.tokenizer(b)),d=new a.Vector,e=[],f=this._fields.reduce(function(a,b){return a+b.boost},0),g=c.some(function(a){return this.tokenStore.has(a)},this);if(!g)return[];c.forEach(function(b,c,g){var h=1/g.length*this._fields.length*f,i=this,j=this.tokenStore.expand(b).reduce(function(c,e){var f=i.corpusTokens.indexOf(e),g=i.idf(e),j=1,k=new a.SortedSet;if(e!==b){var l=Math.max(3,e.length-b.length);j=1/Math.log(l)}return f>-1&&d.insert(f,h*g*j),Object.keys(i.tokenStore.get(e)).forEach(function(a){k.add(a)}),c.union(k)},new a.SortedSet);e.push(j)},this);var h=e.reduce(function(a,b){return a.intersect(b)});return h.map(function(a){return{ref:a,score:d.similarity(this.documentVector(a))}},this).sort(function(a,b){return b.score-a.score})},a.Index.prototype.documentVector=function(b){for(var c=this.documentStore.get(b),d=c.length,e=new a.Vector,f=0;d>f;f++){var g=c.elements[f],h=this.tokenStore.get(g)[b].tf,i=this.idf(g);e.insert(this.corpusTokens.indexOf(g),h*i)}return e},a.Index.prototype.toJSON=function(){return{version:a.version,fields:this._fields,ref:this._ref,documentStore:this.documentStore.toJSON(),tokenStore:this.tokenStore.toJSON(),corpusTokens:this.corpusTokens.toJSON(),pipeline:this.pipeline.toJSON()}},a.Index.prototype.use=function(a){var b=Array.prototype.slice.call(arguments,1);b.unshift(this),a.apply(this,b)},a.Store=function(){this.store={},this.length=0},a.Store.load=function(b){var c=new this;return c.length=b.length,c.store=Object.keys(b.store).reduce(function(c,d){return c[d]=a.SortedSet.load(b.store[d]),c},{}),c},a.Store.prototype.set=function(a,b){this.has(a)||this.length++,this.store[a]=b},a.Store.prototype.get=function(a){return this.store[a]},a.Store.prototype.has=function(a){return a in this.store},a.Store.prototype.remove=function(a){this.has(a)&&(delete this.store[a],this.length--)},a.Store.prototype.toJSON=function(){return{store:this.store,length:this.length}},a.stemmer=function(){var a={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"},b={icate:"ic",ative:"",alize:"al",iciti:"ic",ical:"ic",ful:"",ness:""},c="[^aeiou]",d="[aeiouy]",e=c+"[^aeiouy]*",f=d+"[aeiou]*",g="^("+e+")?"+f+e,h="^("+e+")?"+f+e+"("+f+")?$",i="^("+e+")?"+f+e+f+e,j="^("+e+")?"+d,k=new RegExp(g),l=new RegExp(i),m=new RegExp(h),n=new RegExp(j),o=/^(.+?)(ss|i)es$/,p=/^(.+?)([^s])s$/,q=/^(.+?)eed$/,r=/^(.+?)(ed|ing)$/,s=/.$/,t=/(at|bl|iz)$/,u=new RegExp("([^aeiouylsz])\\1$"),v=new RegExp("^"+e+d+"[^aeiouwxy]$"),w=/^(.+?[^aeiou])y$/,x=/^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/,y=/^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/,z=/^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/,A=/^(.+?)(s|t)(ion)$/,B=/^(.+?)e$/,C=/ll$/,D=new RegExp("^"+e+d+"[^aeiouwxy]$"),E=function(c){var d,e,f,g,h,i,j;if(c.length<3)return c;if(f=c.substr(0,1),"y"==f&&(c=f.toUpperCase()+c.substr(1)),g=o,h=p,g.test(c)?c=c.replace(g,"$1$2"):h.test(c)&&(c=c.replace(h,"$1$2")),g=q,h=r,g.test(c)){var E=g.exec(c);g=k,g.test(E[1])&&(g=s,c=c.replace(g,""))}else if(h.test(c)){var E=h.exec(c);d=E[1],h=n,h.test(d)&&(c=d,h=t,i=u,j=v,h.test(c)?c+="e":i.test(c)?(g=s,c=c.replace(g,"")):j.test(c)&&(c+="e"))}if(g=w,g.test(c)){var E=g.exec(c);d=E[1],c=d+"i"}if(g=x,g.test(c)){var E=g.exec(c);d=E[1],e=E[2],g=k,g.test(d)&&(c=d+a[e])}if(g=y,g.test(c)){var E=g.exec(c);d=E[1],e=E[2],g=k,g.test(d)&&(c=d+b[e])}if(g=z,h=A,g.test(c)){var E=g.exec(c);d=E[1],g=l,g.test(d)&&(c=d)}else if(h.test(c)){var E=h.exec(c);d=E[1]+E[2],h=l,h.test(d)&&(c=d)}if(g=B,g.test(c)){var E=g.exec(c);d=E[1],g=l,h=m,i=D,(g.test(d)||h.test(d)&&!i.test(d))&&(c=d)}return g=C,h=l,g.test(c)&&h.test(c)&&(g=s,c=c.replace(g,"")),"y"==f&&(c=f.toLowerCase()+c.substr(1)),c};return E}(),a.Pipeline.registerFunction(a.stemmer,"stemmer"),a.stopWordFilter=function(b){return-1===a.stopWordFilter.stopWords.indexOf(b)?b:void 0},a.stopWordFilter.stopWords=new a.SortedSet,a.stopWordFilter.stopWords.length=119,a.stopWordFilter.stopWords.elements=["","a","able","about","across","after","all","almost","also","am","among","an","and","any","are","as","at","be","because","been","but","by","can","cannot","could","dear","did","do","does","either","else","ever","every","for","from","get","got","had","has","have","he","her","hers","him","his","how","however","i","if","in","into","is","it","its","just","least","let","like","likely","may","me","might","most","must","my","neither","no","nor","not","of","off","often","on","only","or","other","our","own","rather","said","say","says","she","should","since","so","some","than","that","the","their","them","then","there","these","they","this","tis","to","too","twas","us","wants","was","we","were","what","when","where","which","while","who","whom","why","will","with","would","yet","you","your"],a.Pipeline.registerFunction(a.stopWordFilter,"stopWordFilter"),a.trimmer=function(a){return a.replace(/^\W+/,"").replace(/\W+$/,"")},a.Pipeline.registerFunction(a.trimmer,"trimmer"),a.TokenStore=function(){this.root={docs:{}},this.length=0},a.TokenStore.load=function(a){var b=new this;return b.root=a.root,b.length=a.length,b},a.TokenStore.prototype.add=function(a,b,c){var c=c||this.root,d=a[0],e=a.slice(1);return d in c||(c[d]={docs:{}}),0===e.length?(c[d].docs[b.ref]=b,void(this.length+=1)):this.add(e,b,c[d])},a.TokenStore.prototype.has=function(a){if(!a)return!1;for(var b=this.root,c=0;c");return a.append(Handlebars.templates.tool_link(this.model.toJSON())),"upload1"===this.model.id&&a.find("a").on("click",function(a){a.preventDefault(),Galaxy.upload.show()}),this.$el.append(a),this}}),s=q.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append($("").text(this.model.attributes.text)),this}}),t=q.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){q.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var b=this.$el.find(".toolSectionBody");return a.each(this.model.attributes.elems,function(a){if(a instanceof k){var c=new r({model:a,className:"toolTitle"});c.render(),b.append(c.$el)}else if(a instanceof m){var d=new s({model:a});d.render(),b.append(d.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),u=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(Handlebars.templates.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(a){return this.model.attributes.clear_key&&this.model.attributes.clear_key===a.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),v=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var a=this,b=new u({model:this.model.get("tool_search")});return b.render(),a.$el.append(b.$el),this.model.get("layout").each(function(b){if(b instanceof n){var c=new t({model:b});c.render(),a.$el.append(c.$el)}else if(b instanceof k){var d=new r({model:b,className:"toolTitleNoSection"});d.render(),a.$el.append(d.$el)}else if(b instanceof m){var e=new s({model:b});e.render(),a.$el.append(e.$el)}}),a.$el.find("a.tool-link").click(function(b){var c=$(this).attr("class").split(/\s+/)[0],d=a.model.get("tools").get(c);a.trigger("tool_link_click",b,d)}),this},handle_search_results:function(){var a=this.model.get("tool_search").get("results");a&&0===a.length?$("#search-no-results").show():$("#search-no-results").hide()}}),w=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new v({collection:this.collection}),this.tool_form_view=new w},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$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.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(b,c){b.preventDefault(),a.show_tool(c)})},show_tool:function(a){var b=this;a.fetch().done(function(){b.tool_form_view.model=a,b.tool_form_view.render(),b.tool_form_view.$el.show(),$("#left").width("650px")})}})}return{ToolParameter:e,IntegerToolParameter:h,SelectToolParameter:j,Tool:k,ToolCollection:l,ToolSearch:o,ToolPanel:p,ToolPanelView:v,ToolFormView:w}}); +define(["libs/underscore","viz/trackster/util","mvc/data"],function(a,b,c){var d={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(a){this.set("value",a||"")}}),f=Backbone.Collection.extend({model:e}),g=e.extend({}),h=e.extend({set_value:function(a){this.set("value",parseInt(a,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),i=h.extend({set_value:function(a){this.set("value",parseFloat(a))}}),j=e.extend({get_samples:function(){return a.map(this.get("options"),function(a){return a[0]})}});e.subModelTypes={integer:h,"float":i,data:g,select:j};var k=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(b){this.set("inputs",new f(a.map(b.inputs,function(a){var b=e.subModelTypes[a.type]||e;return new b(a)})))},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);return a.inputs=this.get("inputs").map(function(a){return a.toJSON()}),a},remove_inputs:function(a){var b=this,c=b.get("inputs").filter(function(b){return-1!==a.indexOf(b.get("type"))});b.get("inputs").remove(c)},copy:function(a){var b=new k(this.toJSON());if(a){var c=new Backbone.Collection;b.get("inputs").each(function(a){a.get_samples()&&c.push(a)}),b.set("inputs",c)}return b},apply_search_results:function(b){return-1!==a.indexOf(b,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(b){return b.get("name")===a}).set("value",b)},set_input_values:function(b){var c=this;a.each(a.keys(b),function(a){c.set_input_value(a,b[a])})},run:function(){return this._run()},rerun:function(a,b){return this._run({action:"rerun",target_dataset_id:a.id,regions:b})},get_inputs_dict:function(){var a={};return this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")}),a},_run:function(d){var e=a.extend({tool_id:this.id,inputs:this.get_inputs_dict()},d),f=$.Deferred(),g=new b.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(e),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(a){return"pending"!==a}});return $.when(g.go()).then(function(a){f.resolve((new c.DatasetCollection).reset(a))}),f}});a.extend(k.prototype,d);var l=(Backbone.View.extend({}),Backbone.Collection.extend({model:k})),m=Backbone.Model.extend(d),n=Backbone.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){a.each(this.attributes.elems,function(a){a.show()}),this.show(),this.set("open",!1)},apply_search_results:function(b){var c,d=!0;a.each(this.attributes.elems,function(a){a instanceof m?(c=a,c.hide()):a instanceof k&&a.apply_search_results(b)&&(d=!1,c&&c.show())}),d?this.hide():(this.show(),this.set("open",!0))}});a.extend(n.prototype,d);var o=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:galaxy_config.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var a=this.attributes.query;if(a.length");return a.append(Handlebars.templates.tool_link(this.model.toJSON())),"upload1"===this.model.id&&a.find("a").on("click",function(a){a.preventDefault(),Galaxy.upload.show()}),this.$el.append(a),this}}),s=q.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append($("").text(this.model.attributes.text)),this}}),t=q.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){q.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var b=this.$el.find(".toolSectionBody");return a.each(this.model.attributes.elems,function(a){if(a instanceof k){var c=new r({model:a,className:"toolTitle"});c.render(),b.append(c.$el)}else if(a instanceof m){var d=new s({model:a});d.render(),b.append(d.$el)}}),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")}}),u=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(){return this.$el.append(Handlebars.templates.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(a){return this.model.attributes.clear_key&&this.model.attributes.clear_key===a.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),v=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 a=this,b=new u({model:this.model.get("tool_search")});return b.render(),a.$el.append(b.$el),this.model.get("layout").each(function(b){if(b instanceof n){var c=new t({model:b});c.render(),a.$el.append(c.$el)}else if(b instanceof k){var d=new r({model:b,className:"toolTitleNoSection"});d.render(),a.$el.append(d.$el)}else if(b instanceof m){var e=new s({model:b});e.render(),a.$el.append(e.$el)}}),a.$el.find("a.tool-link").click(function(b){var c=$(this).attr("class").split(/\s+/)[0],d=a.model.get("tools").get(c);a.trigger("tool_link_click",b,d)}),this},handle_search_results:function(){var a=this.model.get("tool_search").get("results");a&&0===a.length?$("#search-no-results").show():$("#search-no-results").hide()}}),w=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new v({collection:this.collection}),this.tool_form_view=new w},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 a=this;this.tool_panel_view.on("tool_link_click",function(b,c){b.preventDefault(),a.show_tool(c)})},show_tool:function(a){var b=this;a.fetch().done(function(){b.tool_form_view.model=a,b.tool_form_view.render(),b.tool_form_view.$el.show(),$("#left").width("650px")})}})}return{ToolParameter:e,IntegerToolParameter:h,SelectToolParameter:j,Tool:k,ToolCollection:l,ToolSearch:o,ToolPanel:p,ToolPanelView:v,ToolFormView:w}}); //# sourceMappingURL=../../maps/mvc/tools.js.map \ No newline at end of file diff --git a/static/scripts/viz/circster.js b/static/scripts/viz/circster.js index 9ee68c2fb8b..0d1c77225b7 100644 --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,2 +1,2 @@ -require(["utils/utils","mvc/ui/icon-button","libs/farbtastic"],function(a){a.cssLoadFile("static/style/circster.css")}),define(["libs/underscore","libs/d3","viz/visualization","utils/config"],function(a,b,c,d){var e=Backbone.Model.extend({is_visible:function(a){var b=a.getBoundingClientRect(),c=$("svg")[0].getBoundingClientRect();return b.right<0||b.left>c.right||b.bottom<0||b.top>c.bottom?!1:!0}}),f={drawTicks:function(a,b,c,d,e){var f=a.append("g").selectAll("g").data(b).enter().append("g").selectAll("g").data(c).enter().append("g").attr("class","tick").attr("transform",function(a){return"rotate("+(180*a.angle/Math.PI-90)+")translate("+a.radius+",0)"}),g=[],h=[],i=function(a){return a.angle>Math.PI?"end":null};return e?(g=[0,0,0,-4],h=[4,0,"",".35em"],i=null):(g=[1,0,4,0],h=[0,4,".35em",""]),f.append("line").attr("x1",g[0]).attr("y1",g[1]).attr("x2",g[2]).attr("y1",g[3]).style("stroke","#000"),f.append("text").attr("x",h[0]).attr("y",h[1]).attr("dx",h[2]).attr("dy",h[3]).attr("text-anchor",i).attr("transform",d).text(function(a){return a.label})},formatNum:function(a,b){if(void 0===b&&(b=2),null===a)return null;var c=null;if(Math.abs(a)<1)c=a.toPrecision(b);else{var d=Math.round(a.toPrecision(b));a=Math.abs(a),1e3>a?c=d:1e6>a?c=Math.round((d/1e3).toPrecision(3)).toFixed(0)+"K":1e9>a&&(c=Math.round((d/1e6).toPrecision(3)).toFixed(0)+"M")}return c}},g=Backbone.Model.extend({}),h=Backbone.View.extend({className:"circster",initialize:function(a){this.genome=a.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var b=this.model.get("config");b.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),b.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(a){return"DiagonalHeatmapTrack"!==a.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(a){return"DiagonalHeatmapTrack"===a.get("track_type")})},get_tracks_bounds:function(){var c=this.get_circular_tracks(),d=this.model.get("config").get_value("arc_dataset_height"),e=this.model.get("config").get_value("track_gap"),f=Math.min(this.$el.width(),this.$el.height())-20,g=f/2-c.length*(d+e)+e-this.label_arc_height,h=b.range(g,f/2,d+e);return a.map(h,function(a){return[a,a+d]})},render:function(){var a=this,c=a.$el.width(),d=a.$el.height(),e=this.get_circular_tracks(),f=this.get_chord_tracks(),h=a.model.get("config").get_value("total_gap"),i=this.get_tracks_bounds(),k=b.select(a.$el[0]).append("svg").attr("width",c).attr("height",d).attr("pointer-events","all").append("svg:g").call(b.behavior.zoom().on("zoom",function(){var c=b.event.scale;k.attr("transform","translate("+b.event.translate+") scale("+c+")"),a.scale!==c&&(a.zoom_drag_timeout&&clearTimeout(a.zoom_drag_timeout),a.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+c/2+","+d/2+")").append("svg:g").attr("class","tracks");this.circular_views=e.map(function(b,c){var d=new l({el:k.append("g")[0],track:b,radius_bounds:i[c],genome:a.genome,total_gap:h});return d.render(),d}),this.chords_views=f.map(function(b){var c=new m({el:k.append("g")[0],track:b,radius_bounds:i[0],genome:a.genome,total_gap:h});return c.render(),c});var n=this.circular_views[this.circular_views.length-1].radius_bounds[1],o=[n,n+this.label_arc_height];this.label_track_view=new j({el:k.append("g")[0],track:new g,radius_bounds:o,genome:a.genome,total_gap:h}),this.label_track_view.render()},add_track:function(c){var d=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===c.get("track_type")){var e=this.circular_views[0].radius_bounds,f=new m({el:b.select("g.tracks").append("g")[0],track:c,radius_bounds:e,genome:this.genome,total_gap:d});f.render(),this.chords_views.push(f)}else{var g=this.get_tracks_bounds();a.each(this.circular_views,function(a,b){a.update_radius_bounds(g[b])}),a.each(this.chords_views,function(a){a.update_radius_bounds(g[0])});var h=this.circular_views.length,i=new l({el:b.select("g.tracks").append("g")[0],track:c,radius_bounds:g[h],genome:this.genome,total_gap:d});i.render(),this.circular_views.push(i)}},remove_track:function(b,c,d){var e=this.circular_views[d.index];this.circular_views.splice(d.index,1),e.$el.remove();var f=this.get_tracks_bounds();a.each(this.circular_views,function(a,b){a.update_radius_bounds(f[b])})},update_track_bounds:function(){var b=this.get_tracks_bounds();a.each(this.circular_views,function(a,c){a.update_radius_bounds(b[c])}),a.each(this.chords_views,function(a){a.update_radius_bounds(b[0])})}}),i=Backbone.View.extend({tagName:"g",initialize:function(a){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=a.total_gap,this.track=a.track,this.radius_bounds=a.radius_bounds,this.genome=a.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=b.select(this.$el[0])},get_fill_color:function(){var a=this.track.get("config").get_value("block_color");return a||(a=this.track.get("config").get_value("color")),a},render:function(){var a=this.parent_elt,c=this.chroms_layout,d=b.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),e=a.selectAll("g").data(c).enter().append("svg:g"),f=e.append("path").attr("d",d).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);f.append("title").text(function(a){return a.data.chrom});var g=this,h=g.track.get("data_manager"),i=h?h.data_is_ready():!0;$.when(i).then(function(){$.when(g._render_data(a)).then(function(){f.style("fill",g.bg_fill),g.render_labels()})})},render_labels:function(){},update_radius_bounds:function(a){this.radius_bounds=a;var c=b.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",c),this._transition_chrom_data(),this._transition_labels()},update_scale:function(c){var d=this.scale;if(this.scale=c,!(d>=c)){var f=this,g=new e;return this.parent_elt.selectAll("path.chrom-data").filter(function(){return g.is_visible(this)}).each(function(){var d,e=b.select(this),g=e.attr("chrom"),h=f.genome.get_chrom_region(g),i=f.track.get("data_manager");i.can_get_more_detailed_data(h)&&(d=f.track.get("data_manager").get_more_detailed_data(h,"Coverage",0,c),$.when(d).then(function(b){e.remove(),f._update_data_bounds();var c=a.find(f.chroms_layout,function(a){return a.data.chrom===g}),d=f.get_fill_color();f._render_chrom_data(f.parent_elt,c,b).style("stroke",d).style("fill",d)}))}),f}},_transition_chrom_data:function(){var c=this.track,d=this.chroms_layout,e=this.parent_elt.selectAll("g>path.chrom-data"),f=e[0].length;if(f>0){var g=this;$.when(c.get("data_manager").get_genome_wide_data(this.genome)).then(function(f){var h=a.reject(a.map(f,function(a,b){var c=null,e=g._get_path_function(d[b],a);return e&&(c=e(a.data)),c}),function(a){return null===a}),i=c.get("config").get_value("color");e.each(function(a,c){b.select(this).transition().duration(1e3).style("stroke",i).style("fill",i).attr("d",h[c])})})}},_transition_labels:function(){},_update_data_bounds:function(a){this.data_bounds;this.data_bounds=a||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(b){var c=this,d=this.chroms_layout,e=this.track,f=$.Deferred();return $.when(e.get("data_manager").get_genome_wide_data(this.genome)).then(function(g){c.data_bounds=c.get_data_bounds(g),e.get("config").set_value("min_value",c.data_bounds[0],{silent:!0}),e.get("config").set_value("max_value",c.data_bounds[1],{silent:!0}),layout_and_data=a.zip(d,g),chroms_data_layout=a.map(layout_and_data,function(a){var d=a[0],e=a[1];return c._render_chrom_data(b,d,e)});var h=c.get_fill_color();c.parent_elt.selectAll("path.chrom-data").style("stroke",h).style("fill",h),f.resolve(b)}),f},_render_chrom_data:function(){},_get_path_function:function(){},_chroms_layout:function(){var c=this.genome.get_chroms_info(),d=b.layout.pie().value(function(a){return a.len}).sort(null),e=d(c),f=2*Math.PI*this.total_gap/c.length,g=a.map(e,function(a){var b=a.endAngle-f;return a.endAngle=b>a.startAngle?b:a.startAngle,a});return g}}),j=i.extend({initialize:function(a){i.prototype.initialize.call(this,a),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(c){var d=this,e=c.selectAll("g");e.selectAll("path").attr("id",function(a){return"label-"+a.data.chrom}),e.append("svg:text").filter(function(a){return a.endAngle-a.startAngle>d.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(a){return"#label-"+a.data.chrom}).attr("startOffset","25%").text(function(a){return a.data.chrom});var f=function(a){var c=(a.endAngle-a.startAngle)/a.value,e=b.range(0,a.value,25e6).map(function(b,e){return{radius:d.innerRadius,angle:b*c+a.startAngle,label:0===e?0:e%3?null:d.formatNum(b)}});return e.length<4&&(e[e.length-1].label=d.formatNum(Math.round((e[e.length-1].angle-a.startAngle)/c))),e},g=function(a){return a.angle>Math.PI?"rotate(180)translate(-16)":null},h=a.filter(this.chroms_layout,function(a){return a.endAngle-a.startAngle>d.min_arc_len});this.drawTicks(this.parent_elt,h,f,g)}});a.extend(j.prototype,f);var k=i.extend({initialize:function(a){i.prototype.initialize.call(this,a);var b=this.track.get("config");b.get("min_value").on("change:value",this._update_min_max,this),b.get("max_value").on("change:value",this._update_min_max,this),b.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var a=this.track.get("config"),b=[a.get_value("min_value"),a.get_value("max_value")];this._update_data_bounds(b),this.parent_elt.selectAll(".min_max").text(function(a,c){return b[c]})},_quantile:function(a,c){return a.sort(b.ascending),b.quantile(a,c)},_render_chrom_data:function(a,b,c){var d=this._get_path_function(b,c);if(!d)return null;var e=a.datum(c.data),f=e.append("path").attr("class","chrom-data").attr("chrom",b.data.chrom).attr("d",d);return f},_get_path_function:function(a,c){if("string"==typeof c||!c.data||0===c.data.length)return null;var d=b.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),e=b.scale.linear().domain([0,c.data.length]).range([a.startAngle,a.endAngle]),f=b.svg.line.radial().interpolate("linear").radius(function(a){return d(a[1])}).angle(function(a,b){return e(b)});return b.svg.area.radial().interpolate(f.interpolate()).innerRadius(d(0)).outerRadius(f.radius()).angle(f.angle())},render_labels:function(){var b=this,c=function(){return"rotate(90)"},e=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),c,!0).classed("min_max",!0);a.each(e,function(a){$(a).click(function(){var a=new d.ConfigSettingCollectionView({collection:b.track.get("config")});a.render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var b=this,c=a.filter(this.chroms_layout,function(a){return a.endAngle-a.startAngle>.08}),d=a.filter(c,function(a,b){return b%3===0}),e=a.flatten(a.map(d,function(a){return b._data_bounds_ticks_fn()(a)}));this.parent_elt.selectAll("g.tick").data(e).transition().attr("transform",function(a){return"rotate("+(180*a.angle/Math.PI-90)+")translate("+a.radius+",0)"})}},_data_bounds_ticks_fn:function(){var a=this;return visibleChroms=0,function(b){return[{radius:a.radius_bounds[0],angle:b.startAngle,label:a.formatNum(a.data_bounds[0])},{radius:a.radius_bounds[1],angle:b.startAngle,label:a.formatNum(a.data_bounds[1])}]}},get_data_bounds:function(){}});a.extend(k.prototype,f);var l=k.extend({get_data_bounds:function(b){var c=a.flatten(a.map(b,function(b){return b?a.map(b.data,function(a){return parseInt(a[1],10)||0}):0}));return[a.min(c),this._quantile(c,.98)||a.max(c)]}}),m=i.extend({render:function(){var c=this;$.when(c.track.get("data_manager").data_is_ready()).then(function(){$.when(c.track.get("data_manager").get_genome_wide_data(c.genome)).then(function(d){var e=[],f=c.genome.get_chroms_info();a.each(d,function(b,d){var g=f[d].chrom,h=a.map(b.data,function(a){var b=c._get_region_angle(g,a[1]),d=c._get_region_angle(a[3],a[4]);return{source:{startAngle:b,endAngle:b+.01},target:{startAngle:d,endAngle:d+.01}}});e=e.concat(h)}),c.parent_elt.append("g").attr("class","chord").selectAll("path").data(e).enter().append("path").style("fill",c.get_fill_color()).attr("d",b.svg.chord().radius(c.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(a){this.radius_bounds=a,this.parent_elt.selectAll("path").transition().attr("d",b.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(b,c){var d=a.find(this.chroms_layout,function(a){return a.data.chrom===b});return d.endAngle-(d.endAngle-d.startAngle)*(d.data.len-c)/d.data.len}}),n=Backbone.View.extend({initialize:function(){var a=new c.Genome(galaxy_config.app.genome),b=new c.GenomeVisualization(galaxy_config.app.viz_config);b.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"track_gap",label:"Gap Between Tracks",type:"int",value:5,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:.4,view:"circster",hidden:!0}]);var e=new h({el:$("#center .unified-panel-body"),genome:a,model:b});e.render(),$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var f=mod_icon_btn.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",b.get("dbkey"),function(a){b.add_tracks(a)})}},{icon_class:"gear",title:"Settings",on_click:function(){var a=new d.ConfigSettingCollectionView({collection:b.get("config")});a.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"}),$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.get("vis_id"),title:b.get("title"),dbkey:b.get("dbkey"),type:"trackster",vis_json:JSON.stringify(b)}}).success(function(a){Galaxy.modal.hide(),b.set("vis_id",a.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});f.$el.attr("style","float: right"),$("#center .unified-panel-header-inner").append(f.$el),$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:n}}); +require(["utils/utils"],function(a){a.cssLoadFile("static/style/circster.css")}),define(["libs/underscore","libs/d3","viz/visualization","utils/config","mvc/ui/icon-button","libs/farbtastic"],function(a,b,c,d,e){var f=Backbone.Model.extend({is_visible:function(a){var b=a.getBoundingClientRect(),c=$("svg")[0].getBoundingClientRect();return b.right<0||b.left>c.right||b.bottom<0||b.top>c.bottom?!1:!0}}),g={drawTicks:function(a,b,c,d,e){var f=a.append("g").selectAll("g").data(b).enter().append("g").selectAll("g").data(c).enter().append("g").attr("class","tick").attr("transform",function(a){return"rotate("+(180*a.angle/Math.PI-90)+")translate("+a.radius+",0)"}),g=[],h=[],i=function(a){return a.angle>Math.PI?"end":null};return e?(g=[0,0,0,-4],h=[4,0,"",".35em"],i=null):(g=[1,0,4,0],h=[0,4,".35em",""]),f.append("line").attr("x1",g[0]).attr("y1",g[1]).attr("x2",g[2]).attr("y1",g[3]).style("stroke","#000"),f.append("text").attr("x",h[0]).attr("y",h[1]).attr("dx",h[2]).attr("dy",h[3]).attr("text-anchor",i).attr("transform",d).text(function(a){return a.label})},formatNum:function(a,b){if(void 0===b&&(b=2),null===a)return null;var c=null;if(Math.abs(a)<1)c=a.toPrecision(b);else{var d=Math.round(a.toPrecision(b));a=Math.abs(a),1e3>a?c=d:1e6>a?c=Math.round((d/1e3).toPrecision(3)).toFixed(0)+"K":1e9>a&&(c=Math.round((d/1e6).toPrecision(3)).toFixed(0)+"M")}return c}},h=Backbone.Model.extend({}),i=Backbone.View.extend({className:"circster",initialize:function(a){this.genome=a.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var b=this.model.get("config");b.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),b.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(a){return"DiagonalHeatmapTrack"!==a.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(a){return"DiagonalHeatmapTrack"===a.get("track_type")})},get_tracks_bounds:function(){var c=this.get_circular_tracks(),d=this.model.get("config").get_value("arc_dataset_height"),e=this.model.get("config").get_value("track_gap"),f=Math.min(this.$el.width(),this.$el.height())-20,g=f/2-c.length*(d+e)+e-this.label_arc_height,h=b.range(g,f/2,d+e);return a.map(h,function(a){return[a,a+d]})},render:function(){var a=this,c=a.$el.width(),d=a.$el.height(),e=this.get_circular_tracks(),f=this.get_chord_tracks(),g=a.model.get("config").get_value("total_gap"),i=this.get_tracks_bounds(),j=b.select(a.$el[0]).append("svg").attr("width",c).attr("height",d).attr("pointer-events","all").append("svg:g").call(b.behavior.zoom().on("zoom",function(){var c=b.event.scale;j.attr("transform","translate("+b.event.translate+") scale("+c+")"),a.scale!==c&&(a.zoom_drag_timeout&&clearTimeout(a.zoom_drag_timeout),a.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+c/2+","+d/2+")").append("svg:g").attr("class","tracks");this.circular_views=e.map(function(b,c){var d=new m({el:j.append("g")[0],track:b,radius_bounds:i[c],genome:a.genome,total_gap:g});return d.render(),d}),this.chords_views=f.map(function(b){var c=new n({el:j.append("g")[0],track:b,radius_bounds:i[0],genome:a.genome,total_gap:g});return c.render(),c});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],o=[l,l+this.label_arc_height];this.label_track_view=new k({el:j.append("g")[0],track:new h,radius_bounds:o,genome:a.genome,total_gap:g}),this.label_track_view.render()},add_track:function(c){var d=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===c.get("track_type")){var e=this.circular_views[0].radius_bounds,f=new n({el:b.select("g.tracks").append("g")[0],track:c,radius_bounds:e,genome:this.genome,total_gap:d});f.render(),this.chords_views.push(f)}else{var g=this.get_tracks_bounds();a.each(this.circular_views,function(a,b){a.update_radius_bounds(g[b])}),a.each(this.chords_views,function(a){a.update_radius_bounds(g[0])});var h=this.circular_views.length,i=new m({el:b.select("g.tracks").append("g")[0],track:c,radius_bounds:g[h],genome:this.genome,total_gap:d});i.render(),this.circular_views.push(i)}},remove_track:function(b,c,d){var e=this.circular_views[d.index];this.circular_views.splice(d.index,1),e.$el.remove();var f=this.get_tracks_bounds();a.each(this.circular_views,function(a,b){a.update_radius_bounds(f[b])})},update_track_bounds:function(){var b=this.get_tracks_bounds();a.each(this.circular_views,function(a,c){a.update_radius_bounds(b[c])}),a.each(this.chords_views,function(a){a.update_radius_bounds(b[0])})}}),j=Backbone.View.extend({tagName:"g",initialize:function(a){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=a.total_gap,this.track=a.track,this.radius_bounds=a.radius_bounds,this.genome=a.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=b.select(this.$el[0])},get_fill_color:function(){var a=this.track.get("config").get_value("block_color");return a||(a=this.track.get("config").get_value("color")),a},render:function(){var a=this.parent_elt,c=this.chroms_layout,d=b.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),e=a.selectAll("g").data(c).enter().append("svg:g"),f=e.append("path").attr("d",d).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);f.append("title").text(function(a){return a.data.chrom});var g=this,h=g.track.get("data_manager"),i=h?h.data_is_ready():!0;$.when(i).then(function(){$.when(g._render_data(a)).then(function(){f.style("fill",g.bg_fill),g.render_labels()})})},render_labels:function(){},update_radius_bounds:function(a){this.radius_bounds=a;var c=b.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",c),this._transition_chrom_data(),this._transition_labels()},update_scale:function(c){var d=this.scale;if(this.scale=c,!(d>=c)){var e=this,g=new f;return this.parent_elt.selectAll("path.chrom-data").filter(function(){return g.is_visible(this)}).each(function(){var d,f=b.select(this),g=f.attr("chrom"),h=e.genome.get_chrom_region(g),i=e.track.get("data_manager");i.can_get_more_detailed_data(h)&&(d=e.track.get("data_manager").get_more_detailed_data(h,"Coverage",0,c),$.when(d).then(function(b){f.remove(),e._update_data_bounds();var c=a.find(e.chroms_layout,function(a){return a.data.chrom===g}),d=e.get_fill_color();e._render_chrom_data(e.parent_elt,c,b).style("stroke",d).style("fill",d)}))}),e}},_transition_chrom_data:function(){var c=this.track,d=this.chroms_layout,e=this.parent_elt.selectAll("g>path.chrom-data"),f=e[0].length;if(f>0){var g=this;$.when(c.get("data_manager").get_genome_wide_data(this.genome)).then(function(f){var h=a.reject(a.map(f,function(a,b){var c=null,e=g._get_path_function(d[b],a);return e&&(c=e(a.data)),c}),function(a){return null===a}),i=c.get("config").get_value("color");e.each(function(a,c){b.select(this).transition().duration(1e3).style("stroke",i).style("fill",i).attr("d",h[c])})})}},_transition_labels:function(){},_update_data_bounds:function(a){this.data_bounds;this.data_bounds=a||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(b){var c=this,d=this.chroms_layout,e=this.track,f=$.Deferred();return $.when(e.get("data_manager").get_genome_wide_data(this.genome)).then(function(g){c.data_bounds=c.get_data_bounds(g),e.get("config").set_value("min_value",c.data_bounds[0],{silent:!0}),e.get("config").set_value("max_value",c.data_bounds[1],{silent:!0}),layout_and_data=a.zip(d,g),chroms_data_layout=a.map(layout_and_data,function(a){var d=a[0],e=a[1];return c._render_chrom_data(b,d,e)});var h=c.get_fill_color();c.parent_elt.selectAll("path.chrom-data").style("stroke",h).style("fill",h),f.resolve(b)}),f},_render_chrom_data:function(){},_get_path_function:function(){},_chroms_layout:function(){var c=this.genome.get_chroms_info(),d=b.layout.pie().value(function(a){return a.len}).sort(null),e=d(c),f=2*Math.PI*this.total_gap/c.length,g=a.map(e,function(a){var b=a.endAngle-f;return a.endAngle=b>a.startAngle?b:a.startAngle,a});return g}}),k=j.extend({initialize:function(a){j.prototype.initialize.call(this,a),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(c){var d=this,e=c.selectAll("g");e.selectAll("path").attr("id",function(a){return"label-"+a.data.chrom}),e.append("svg:text").filter(function(a){return a.endAngle-a.startAngle>d.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(a){return"#label-"+a.data.chrom}).attr("startOffset","25%").text(function(a){return a.data.chrom});var f=function(a){var c=(a.endAngle-a.startAngle)/a.value,e=b.range(0,a.value,25e6).map(function(b,e){return{radius:d.innerRadius,angle:b*c+a.startAngle,label:0===e?0:e%3?null:d.formatNum(b)}});return e.length<4&&(e[e.length-1].label=d.formatNum(Math.round((e[e.length-1].angle-a.startAngle)/c))),e},g=function(a){return a.angle>Math.PI?"rotate(180)translate(-16)":null},h=a.filter(this.chroms_layout,function(a){return a.endAngle-a.startAngle>d.min_arc_len});this.drawTicks(this.parent_elt,h,f,g)}});a.extend(k.prototype,g);var l=j.extend({initialize:function(a){j.prototype.initialize.call(this,a);var b=this.track.get("config");b.get("min_value").on("change:value",this._update_min_max,this),b.get("max_value").on("change:value",this._update_min_max,this),b.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var a=this.track.get("config"),b=[a.get_value("min_value"),a.get_value("max_value")];this._update_data_bounds(b),this.parent_elt.selectAll(".min_max").text(function(a,c){return b[c]})},_quantile:function(a,c){return a.sort(b.ascending),b.quantile(a,c)},_render_chrom_data:function(a,b,c){var d=this._get_path_function(b,c);if(!d)return null;var e=a.datum(c.data),f=e.append("path").attr("class","chrom-data").attr("chrom",b.data.chrom).attr("d",d);return f},_get_path_function:function(a,c){if("string"==typeof c||!c.data||0===c.data.length)return null;var d=b.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),e=b.scale.linear().domain([0,c.data.length]).range([a.startAngle,a.endAngle]),f=b.svg.line.radial().interpolate("linear").radius(function(a){return d(a[1])}).angle(function(a,b){return e(b)});return b.svg.area.radial().interpolate(f.interpolate()).innerRadius(d(0)).outerRadius(f.radius()).angle(f.angle())},render_labels:function(){var b=this,c=function(){return"rotate(90)"},e=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),c,!0).classed("min_max",!0);a.each(e,function(a){$(a).click(function(){var a=new d.ConfigSettingCollectionView({collection:b.track.get("config")});a.render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var b=this,c=a.filter(this.chroms_layout,function(a){return a.endAngle-a.startAngle>.08}),d=a.filter(c,function(a,b){return b%3===0}),e=a.flatten(a.map(d,function(a){return b._data_bounds_ticks_fn()(a)}));this.parent_elt.selectAll("g.tick").data(e).transition().attr("transform",function(a){return"rotate("+(180*a.angle/Math.PI-90)+")translate("+a.radius+",0)"})}},_data_bounds_ticks_fn:function(){var a=this;return visibleChroms=0,function(b){return[{radius:a.radius_bounds[0],angle:b.startAngle,label:a.formatNum(a.data_bounds[0])},{radius:a.radius_bounds[1],angle:b.startAngle,label:a.formatNum(a.data_bounds[1])}]}},get_data_bounds:function(){}});a.extend(l.prototype,g);var m=l.extend({get_data_bounds:function(b){var c=a.flatten(a.map(b,function(b){return b?a.map(b.data,function(a){return parseInt(a[1],10)||0}):0}));return[a.min(c),this._quantile(c,.98)||a.max(c)]}}),n=j.extend({render:function(){var c=this;$.when(c.track.get("data_manager").data_is_ready()).then(function(){$.when(c.track.get("data_manager").get_genome_wide_data(c.genome)).then(function(d){var e=[],f=c.genome.get_chroms_info();a.each(d,function(b,d){var g=f[d].chrom,h=a.map(b.data,function(a){var b=c._get_region_angle(g,a[1]),d=c._get_region_angle(a[3],a[4]);return{source:{startAngle:b,endAngle:b+.01},target:{startAngle:d,endAngle:d+.01}}});e=e.concat(h)}),c.parent_elt.append("g").attr("class","chord").selectAll("path").data(e).enter().append("path").style("fill",c.get_fill_color()).attr("d",b.svg.chord().radius(c.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(a){this.radius_bounds=a,this.parent_elt.selectAll("path").transition().attr("d",b.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(b,c){var d=a.find(this.chroms_layout,function(a){return a.data.chrom===b});return d.endAngle-(d.endAngle-d.startAngle)*(d.data.len-c)/d.data.len}}),o=Backbone.View.extend({initialize:function(){var a=new c.Genome(galaxy_config.app.genome),b=new c.GenomeVisualization(galaxy_config.app.viz_config);b.get("config").add([{key:"arc_dataset_height",label:"Arc Dataset Height",type:"int",value:25,view:"circster"},{key:"track_gap",label:"Gap Between Tracks",type:"int",value:5,view:"circster"},{key:"total_gap",label:"Gap [0-1]",type:"float",value:.4,view:"circster",hidden:!0}]);var f=new i({el:$("#center .unified-panel-body"),genome:a,model:b});f.render(),$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var g=e.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",b.get("dbkey"),function(a){b.add_tracks(a)})}},{icon_class:"gear",title:"Settings",on_click:function(){var a=new d.ConfigSettingCollectionView({collection:b.get("config")});a.render_in_modal("Configure Visualization")}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"}),$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:b.get("vis_id"),title:b.get("title"),dbkey:b.get("dbkey"),type:"trackster",vis_json:JSON.stringify(b)}}).success(function(a){Galaxy.modal.hide(),b.set("vis_id",a.vis_id)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});g.$el.attr("style","float: right"),$("#center .unified-panel-header-inner").append(g.$el),$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:o}}); //# sourceMappingURL=../../maps/viz/circster.js.map \ No newline at end of file diff --git a/test/api/test_tools.py b/test/api/test_tools.py index e1b5485ce5b..a0510b751fe 100644 --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -539,6 +539,59 @@ class ToolsTestCase( api.ApiTestCase ): } self._run_and_check_simple_collection_mapping( history_id, inputs ) + @skip_without_tool( "output_action_change_format" ) + def test_map_over_with_output_format_actions( self ): + for use_action in ["do", "dont"]: + history_id = self.dataset_populator.new_history() + hdca_id = self.__build_pair( history_id, [ "123", "456" ] ) + inputs = { + "input_cond|dispatch": use_action, + "input_cond|input": { 'batch': True, 'values': [ { 'src': 'hdca', 'id': hdca_id } ] }, + } + create = self._run( 'output_action_change_format', history_id, inputs ).json() + outputs = create[ 'outputs' ] + jobs = create[ 'jobs' ] + implicit_collections = create[ 'implicit_collections' ] + self.assertEquals( len( jobs ), 2 ) + self.assertEquals( len( outputs ), 2 ) + self.assertEquals( len( implicit_collections ), 1 ) + output1 = outputs[ 0 ] + output2 = outputs[ 1 ] + output1_details = self.dataset_populator.get_history_dataset_details( history_id, dataset=output1 ) + output2_details = self.dataset_populator.get_history_dataset_details( history_id, dataset=output2 ) + assert output1_details[ "file_ext" ] == "txt" if (use_action == "do") else "data" + assert output2_details[ "file_ext" ] == "txt" if (use_action == "do") else "data" + + @skip_without_tool( "Cut1" ) + def test_map_over_with_complex_output_actions( self ): + history_id = self.dataset_populator.new_history() + hdca_id = self._bed_list(history_id) + inputs = { + "columnList": "c1,c2,c3,c4,c5", + "delimiter": "T", + "input": { 'batch': True, 'values': [ { 'src': 'hdca', 'id': hdca_id } ] }, + } + create = self._run( 'Cut1', history_id, inputs ).json() + outputs = create[ 'outputs' ] + jobs = create[ 'jobs' ] + implicit_collections = create[ 'implicit_collections' ] + self.assertEquals( len( jobs ), 2 ) + self.assertEquals( len( outputs ), 2 ) + self.assertEquals( len( implicit_collections ), 1 ) + output1 = outputs[ 0 ] + output2 = outputs[ 1 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) + assert output1_content.startswith("chr1") + assert output2_content.startswith("chr1") + + def _bed_list(self, history_id): + bed1_contents = open(self.get_filename("1.bed"), "r").read() + bed2_contents = open(self.get_filename("2.bed"), "r").read() + contents = [bed1_contents, bed2_contents] + hdca = self.dataset_collection_populator.create_list_in_history( history_id, contents=contents ).json() + return hdca["id"] + def _run_and_check_simple_collection_mapping( self, history_id, inputs ): create = self._run_cat1( history_id, inputs=inputs, assert_ok=True ) outputs = create[ 'outputs' ] diff --git a/test/functional/tools/output_action_change_format.xml b/test/functional/tools/output_action_change_format.xml new file mode 100644 index 00000000000..c9a59cc70e8 --- /dev/null +++ b/test/functional/tools/output_action_change_format.xml @@ -0,0 +1,52 @@ + + + echo "1\t2" > out1; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml index 52d9d75ccbe..801c2d371b3 100644 --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -36,6 +36,7 @@ + diff --git a/tools/genomespace/genomespace_exporter.py b/tools/genomespace/genomespace_exporter.py index a5bd30dfa09..ec88fa26af6 100644 --- a/tools/genomespace/genomespace_exporter.py +++ b/tools/genomespace/genomespace_exporter.py @@ -1,3 +1,4 @@ +#!/usr/bin/env python #Dan Blankenberg import base64 @@ -10,17 +11,37 @@ import json import logging import optparse import os +import tempfile import urllib import urllib2 from urlparse import urljoin log = logging.getLogger( "tools.genomespace.genomespace_exporter" )#( __name__ ) +try: + from galaxy import eggs + eggs.require('boto') +except ImportError: + pass + +try: + import boto + from boto.s3.connection import S3Connection +except ImportError: + boto = None + GENOMESPACE_API_VERSION_STRING = "v1.0" GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING ) CHUNK_SIZE = 2**20 #1mb +# TODO: TARGET_SPLIT_SIZE and TARGET_SIMPLE_PUT_UPLOAD_SIZE are arbitrarily defined +# we should programmatically determine these, based upon the current environment +TARGET_SPLIT_SIZE = 250 * 1024 * 1024 # 250 mb +MIN_MULTIPART_UPLOAD_SIZE = 5 * 1024 * 1024 # 5mb +MAX_SIMPLE_PUT_UPLOAD_SIZE = 5 * 1024 * 1024 * 1024 # 5gb +TARGET_SIMPLE_PUT_UPLOAD_SIZE = MAX_SIMPLE_PUT_UPLOAD_SIZE / 2 + # Some basic Caching, so we don't have to reload and download everything every time, # especially now that we are calling the parameter's get options method 5 times # (6 on reload) when a user loads the tool interface @@ -203,28 +224,69 @@ def send_file_to_genomespace( genomespace_site, username, token, source_filename directory_dict = get_personal_directory( url_opener, dm_url )['directory'] #this is the base for the auto-generated galaxy export directories #what directory to stuff this in target_directory_dict = create_directory( url_opener, directory_dict, target_directory, dm_url ) - #get upload url - upload_url = "uploadurl" content_length = os.path.getsize( source_filename ) input_file = open( source_filename, 'rb' ) - content_md5 = hashlib.md5() - chunk_write( input_file, content_md5, target_method="update" ) - input_file.seek( 0 ) #back to start, for uploading - - upload_params = { 'Content-Length': content_length, 'Content-MD5': base64.standard_b64encode( content_md5.digest() ), 'Content-Type': content_type } - upload_url = "%s/%s/%s%s/%s?%s" % ( dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], urllib.quote( target_filename, safe='' ), urllib.urlencode( upload_params ) ) - new_file_request = urllib2.Request( upload_url )#, headers = { 'Content-Type': 'application/json', 'Accept': 'application/text' } ) #apparently http://www.genomespace.org/team/specs/updated-dm-rest-api:"Every HTTP request to the Data Manager should include the Accept header with a preference for the media types application/json and application/text." is not correct - new_file_request.get_method = lambda: 'GET' - #get url to upload to - target_upload_url = url_opener.open( new_file_request ).read() - #upload file to determined url - upload_headers = dict( upload_params ) - #upload_headers[ 'x-amz-meta-md5-hash' ] = content_md5.hexdigest() - upload_headers[ 'Accept' ] = 'application/json' - upload_file_request = urllib2.Request( target_upload_url, headers = upload_headers, data = input_file ) - upload_file_request.get_method = lambda: 'PUT' - upload_result = urllib2.urlopen( upload_file_request ).read() + if content_length > TARGET_SIMPLE_PUT_UPLOAD_SIZE: + # Determine sizes of each part. + split_count = content_length / TARGET_SPLIT_SIZE + last_size = content_length - ( split_count * TARGET_SPLIT_SIZE ) + sizes = [ TARGET_SPLIT_SIZE ] * split_count + if last_size: + if last_size < MIN_MULTIPART_UPLOAD_SIZE: + if sizes: + sizes[-1] = sizes[-1] + last_size + else: + sizes = [ last_size ] + else: + sizes.append( last_size ) + print "Performing multi-part upload in %i parts." % ( len( sizes ) ) + #get upload url + upload_url = "uploadinfo" + upload_url = "%s/%s/%s%s/%s" % ( dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], urllib.quote( target_filename, safe='' ) ) + upload_request = urllib2.Request( upload_url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } ) + upload_request.get_method = lambda: 'GET' + upload_info = json.loads( url_opener.open( upload_request ).read() ) + conn = S3Connection( aws_access_key_id=upload_info['amazonCredentials']['accessKey'], + aws_secret_access_key=upload_info['amazonCredentials']['secretKey'], + security_token=upload_info['amazonCredentials']['sessionToken'] ) + # Cannot use conn.get_bucket due to permissions, manually create bucket object + bucket = boto.s3.bucket.Bucket( connection=conn, name=upload_info['s3BucketName'] ) + mp = bucket.initiate_multipart_upload( upload_info['s3ObjectKey'] ) + for i,part_size in enumerate( sizes, start=1 ): + fh = tempfile.TemporaryFile( 'wb+' ) + while part_size: + if CHUNK_SIZE > part_size: + read_size = part_size + else: + read_size = CHUNK_SIZE + chunk = input_file.read( read_size ) + fh.write( chunk ) + part_size = part_size - read_size + fh.flush() + fh.seek(0) + mp.upload_part_from_file( fh, i ) + fh.close() + upload_result = mp.complete_upload() + else: + print 'Performing simple put upload.' + upload_url = "uploadurl" + content_md5 = hashlib.md5() + chunk_write( input_file, content_md5, target_method="update" ) + input_file.seek( 0 ) #back to start, for uploading + upload_params = { 'Content-Length': content_length, 'Content-MD5': base64.standard_b64encode( content_md5.digest() ), 'Content-Type': content_type } + upload_url = "%s/%s/%s%s/%s?%s" % ( dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], urllib.quote( target_filename, safe='' ), urllib.urlencode( upload_params ) ) + new_file_request = urllib2.Request( upload_url )#, headers = { 'Content-Type': 'application/json', 'Accept': 'application/text' } ) #apparently http://www.genomespace.org/team/specs/updated-dm-rest-api:"Every HTTP request to the Data Manager should include the Accept header with a preference for the media types application/json and application/text." is not correct + new_file_request.get_method = lambda: 'GET' + #get url to upload to + target_upload_url = url_opener.open( new_file_request ).read() + #upload file to determined url + upload_headers = dict( upload_params ) + #upload_headers[ 'x-amz-meta-md5-hash' ] = content_md5.hexdigest() + upload_headers[ 'Accept' ] = 'application/json' + upload_file_request = urllib2.Request( target_upload_url, headers = upload_headers, data = input_file ) + upload_file_request.get_method = lambda: 'PUT' + upload_result = urllib2.urlopen( upload_file_request ).read() result_url = "%s/%s" % ( target_directory_dict['url'], urllib.quote( target_filename, safe='' ) ) #determine available gs launch apps web_tools = get_genome_space_launch_apps( genomespace_site_dict['atmServer'], url_opener, result_url, file_type ) diff --git a/tools/genomespace/genomespace_exporter.xml b/tools/genomespace/genomespace_exporter.xml index 344698e2baa..1f9561e11dc 100644 --- a/tools/genomespace/genomespace_exporter.xml +++ b/tools/genomespace/genomespace_exporter.xml @@ -1,5 +1,5 @@ - + - send data to GenomeSpace genomespace_exporter.py --genomespace_site "prod" @@ -36,7 +36,7 @@ - +