- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2581: Merge.
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3353b15d0fb5 changeset: 2581:3353b15d0fb5 user: James Taylor <james(a)jamestaylor.org> date: Wed Aug 19 17:51:46 2009 -0400 description: Merge. 0 file(s) affected in this change: diffs (2275 lines): diff -r 7d48dc7e60b4 -r 3353b15d0fb5 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Wed Aug 19 11:08:58 2009 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Aug 19 17:51:46 2009 -0400 @@ -3,6 +3,7 @@ """ import logging,sys +from cgi import escape log = logging.getLogger(__name__) class BaseField(object): @@ -28,7 +29,7 @@ self.value = value or "" def get_html( self, prefix="" ): return '<input type="text" name="%s%s" size="%d" value="%s">' \ - % ( prefix, self.name, self.size, self.value ) + % ( prefix, self.name, self.size, escape(str(self.value), quote=True) ) def set_size(self, size): self.size = int( size ) @@ -49,7 +50,7 @@ self.value = value or "" def get_html( self, prefix="" ): return '<textarea name="%s%s" rows="%d" cols="%d">%s</textarea>' \ - % ( prefix, self.name, self.rows, self.cols, self.value ) + % ( prefix, self.name, self.rows, self.cols, escape(str(self.value), quote=True) ) def set_size(self, rows, cols): self.rows = rows self.cols = cols @@ -113,7 +114,7 @@ self.name = name self.value = value or "" def get_html( self, prefix="" ): - return '<input type="hidden" name="%s%s" value="%s">' % ( prefix, self.name, self.value ) + return '<input type="hidden" name="%s%s" value="%s">' % ( prefix, self.name, escape(str(self.value), quote=True) ) class SelectField(BaseField): """ @@ -190,9 +191,9 @@ if len(self.options) > 2 and ctr % 2 == 1: style = " class=\"odd_row\"" if selected: - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" checked>%s</div>' % ( style, prefix, self.name, value, text) ) + rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s" checked>%s</div>' % ( style, prefix, self.name, escape(str(value), quote=True), text) ) else: - rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s">%s</div>' % ( style, prefix, self.name, value, text) ) + rval.append( '<div%s><input type="checkbox" name="%s%s" value="%s">%s</div>' % ( style, prefix, self.name, escape(str(value), quote=True), text) ) ctr += 1 return "\n".join( rval ) def get_html_radio( self, prefix="" ): @@ -204,7 +205,7 @@ style = " class=\"odd_row\"" if selected: selected_text = " checked" else: selected_text = "" - rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s"%s>%s</div>' % ( style, prefix, self.name, self.refresh_on_change_text, value, selected_text, text ) ) + rval.append( '<div%s><input type="radio" name="%s%s"%s value="%s"%s>%s</div>' % ( style, prefix, self.name, self.refresh_on_change_text, escape(str(value), quote=True), selected_text, text ) ) ctr += 1 return "\n".join( rval ) def get_html_default( self, prefix="" ): @@ -217,9 +218,9 @@ selected_text = " selected" last_selected_value = value else: selected_text = "" - rval.append( '<option value="%s"%s>%s</option>' % ( value, selected_text, text ) ) + rval.append( '<option value="%s"%s>%s</option>' % ( escape(str(value), quote=True), selected_text, text ) ) if last_selected_value: - last_selected_value = ' last_selected_value="%s"' % last_selected_value + last_selected_value = ' last_selected_value="%s"' % escape(str(last_selected_value), quote=True) rval.insert( 0, '<select name="%s%s"%s%s%s>' % ( prefix, self.name, multiple, self.refresh_on_change_text, last_selected_value ) ) rval.append( '</select>' ) return "\n".join( rval ) @@ -326,12 +327,12 @@ if option['value'] in expanded_options: default_state = 'expanded' default_icon = '[-]' - html.append( '<li><span class="toolParameterExpandableCollapsable">%s</span><input type="%s" name="%s%s" value="%s"%s">%s' % ( default_icon, self.display, prefix, self.name, option['value'], selected, option['name']) ) + html.append( '<li><span class="toolParameterExpandableCollapsable">%s</span><input type="%s" name="%s%s" value="%s"%s">%s' % ( default_icon, self.display, prefix, self.name, escape(str(option['value']), quote=True), selected, option['name']) ) html.append( '<ul class="toolParameterExpandableCollapsable" default_state="%s">' % default_state ) recurse_options( html, option['options'], expanded_options ) html.append( '</ul>') else: - html.append( '<li><input type="%s" name="%s%s" value="%s"%s">%s' % ( self.display, prefix, self.name, option['value'], selected, option['name']) ) + html.append( '<li><input type="%s" name="%s%s" value="%s"%s">%s' % ( self.display, prefix, self.name, escape(str(option['value']), quote=True), selected, option['name']) ) html.append( '</li>' ) rval = [] rval.append( '<div><ul class="toolParameterExpandableCollapsable">' ) diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/jStore.Flash.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/jStore.Flash.html Wed Aug 19 17:51:46 2009 -0400 @@ -0,0 +1,19 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"> + <head> + <title>Flash External Object</title> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <script type="text/javascript"> + /** + * This function captures the flash_ready event. We need to relay this + * back to the parent so it knows flash is ready. + */ + function flash_ready(){ + parent.flash_ready(); + } + </script> + </head> + <body> + <object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#versi…" width="1" height="1" id="jStoreFlash"><param name="allowScriptAccess" value="always" /><param name="movie" value="jStore.swf" /><param name="quality" value="high" /><param name="bgcolor" value="#ffcc00" /><embed src="jStore.swf" quality="high" bgcolor="#ffcc00" width="1" height="1" name="jStoreFlash" align="middle" allowScriptAccess="always" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" /></object> + </body> +</html> \ No newline at end of file diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/jStore.swf Binary file static/jStore.swf has changed diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 19 11:08:58 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 19 17:51:46 2009 -0400 @@ -359,6 +359,7 @@ this.nodes = {}; this.name = null; this.has_changes = false; + this.active_form_has_changes = false; } $.extend( Workflow.prototype, { add_node : function( node ) { @@ -438,6 +439,28 @@ }); }); }, + enable_auto_save : function() { + // Implements auto-saving based on whether the inputs change. We consider + // "changed" to be when a field is accessed and not necessarily modified + // because of an issue where "onchange" is not triggered when activating + // another node, or saving the workflow. + outer_this = this; + $(".toolFormBody").find("input,textarea,select").each( function() { + $(this).focus( function() { + outer_this.active_form_has_changes = true; + }); + }); + }, + check_changes_in_active_form : function() { + // If active form has changed, save it + if (this.active_form_has_changes) { + this.has_changes = true; + $(".toolFormBody").find("form").each( function() { + $(this).submit(); + }); + this.active_form_has_changes = false; + } + }, clear_active_node : function() { if ( this.active_node ) { this.active_node.make_inactive(); @@ -447,6 +470,7 @@ }, activate_node : function( node ) { if ( this.active_node != node ) { + this.check_changes_in_active_form(); this.clear_active_node(); parent.show_form_for_tool( node.form_html, node ); node.make_active(); @@ -461,6 +485,7 @@ } }, layout : function () { + this.check_changes_in_active_form(); // Prepare predecessor / successor tracking var n_pred = {}; var successors = {}; @@ -502,7 +527,7 @@ var v = level_parents[k]; delete n_pred[v]; for ( var sk in successors[v] ) { - n_pred[ sucessors[v][sk] ] -= 1; + n_pred[ successors[v][sk] ] -= 1; } } } @@ -805,6 +830,10 @@ self.draw_overview(); }); + /* Disable dragging for child element of the panel so that resizing can + only be done by dragging the borders */ + $("#overview-border div").bind("drag", function(e) { }); + }, update_viewport_overlay: function() { var cc = this.cc, diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/scripts/jquery.jstore-all.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/jquery.jstore-all.js Wed Aug 19 17:51:46 2009 -0400 @@ -0,0 +1,748 @@ +/*! + * jStore - Persistent Client-Side Storage + * + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * + * Dual licensed under: + * MIT: http://www.opensource.org/licenses/mit-license.php + * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html + *//** + * Javascript Class Framework + * + * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) + * Inspired by base2 and Prototype + */ +(function(){ + var initializing = false, fnTest = /xyz/.test(function(){xyz;}) ? /\b_super\b/ : /.*/; + + // The base Class implementation (does nothing) + this.Class = function(){}; + + // Create a new Class that inherits from this class + Class.extend = function(prop) { + var _super = this.prototype; + + // Instantiate a base class (but only create the instance, + // don't run the init constructor) + initializing = true; + var prototype = new this(); + initializing = false; + + // Copy the properties over onto the new prototype + for (var name in prop) { + // Check if we're overwriting an existing function + prototype[name] = typeof prop[name] == "function" && + typeof _super[name] == "function" && fnTest.test(prop[name]) ? + (function(name, fn){ + return function() { + var tmp = this._super; + + // Add a new ._super() method that is the same method + // but on the super-class + this._super = _super[name]; + + // The method only need to be bound temporarily, so we + // remove it when we're done executing + var ret = fn.apply(this, arguments); + this._super = tmp; + + return ret; + }; + })(name, prop[name]) : + prop[name]; + } + + // The dummy class constructor + function Class() { + // All construction is actually done in the init method + if ( !initializing && this.init ) + this.init.apply(this, arguments); + } + + // Populate our constructed prototype object + Class.prototype = prototype; + + // Enforce the constructor to be what we expect + Class.constructor = Class; + + // And make this class extendable + Class.extend = arguments.callee; + + return Class; + }; +})(); +/*! + * jStore Delegate Framework + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + this.jStoreDelegate = Class.extend({ + init: function(parent){ + // The Object this delgate operates for + this.parent = parent; + // Container for callbacks to dispatch. + // eventType => [ callback, callback, ... ] + this.callbacks = {}; + }, + bind: function(event, callback){ + if ( !$.isFunction(callback) ) return this; + if ( !this.callbacks[ event ] ) this.callbacks[ event ] = []; + + this.callbacks[ event ].push(callback); + + return this; + }, + trigger: function(){ + var parent = this.parent, + args = [].slice.call(arguments), + event = args.shift(), + handlers = this.callbacks[ event ]; + + if ( !handlers ) return false; + + $.each(handlers, function(){ this.apply(parent, args) }); + return this; + } + }); + +})(jQuery);/** + * jStore-jQuery Interface + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Setup the jStore namespace in jQuery for options storage + $.jStore = {}; + + // Seed the options in + $.extend($.jStore, { + EngineOrder: [], + // Engines should put their availability tests within jStore.Availability + Availability: {}, + // Defined engines should enter themselves into the jStore.Engines + Engines: {}, + // Instanciated engines should exist within jStore.Instances + Instances: {}, + // The current engine to use for storage + CurrentEngine: null, + // Provide global settings for overwriting + defaults: { + project: null, + engine: null, + autoload: true, + flash: 'jStore.Flash.html' + }, + // Boolean for ready state handling + isReady: false, + // Boolean for flash ready state handling + isFlashReady: false, + // An event delegate + delegate: new jStoreDelegate($.jStore) + .bind('jStore-ready', function(engine){ + $.jStore.isReady = true; + if ($.jStore.defaults.autoload) engine.connect(); + }) + .bind('flash-ready', function(){ + $.jStore.isFlashReady = true; + }) + }); + + // Enable ready callback for jStore + $.jStore.ready = function(callback){ + if ($.jStore.isReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); + else $.jStore.delegate.bind('jStore-ready', callback); + } + + // Enable failure callback registration for jStore + $.jStore.fail = function(callback){ + $.jStore.delegate.bind('jStore-failure', callback); + } + + // Enable ready callback for Flash + $.jStore.flashReady = function(callback){ + if ($.jStore.isFlashReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); + else $.jStore.delegate.bind('flash-ready', callback); + } + + // Enable and test an engine + $.jStore.use = function(engine, project, identifier){ + project = project || $.jStore.defaults.project || location.hostname.replace(/\./g, '-') || 'unknown'; + + var e = $.jStore.Engines[engine.toLowerCase()] || null, + name = (identifier ? identifier + '.' : '') + project + '.' + engine; + + if ( !e ) throw 'JSTORE_ENGINE_UNDEFINED'; + + // Instanciate the engine + e = new e(project, name); + + // Prevent against naming conflicts + if ($.jStore.Instances[name]) throw 'JSTORE_JRI_CONFLICT'; + + // Test the engine + if (e.isAvailable()){ + $.jStore.Instances[name] = e; // The Easy Way + if (!$.jStore.CurrentEngine){ + $.jStore.CurrentEngine = e; + } + $.jStore.delegate.trigger('jStore-ready', e); + } else { + if (!e.autoload) // Not available + throw 'JSTORE_ENGINE_UNAVILABLE'; + else { // The hard way + e.included(function(){ + if (this.isAvailable()) { // Worked out + $.jStore.Instances[name] = this; + // If there is no current engine, use this one + if (!$.jStore.CurrentEngine){ + $.jStore.CurrentEngine = this; + } + $.jStore.delegate.trigger('jStore-ready', this); + } + else $.jStore.delegate.trigger('jStore-failure', this); + }).include(); + } + } + } + + // Set the current storage engine + $.jStore.setCurrentEngine = function(name){ + if (!$.jStore.Instances.length ) // If no instances exist, attempt to load one + return $.jStore.FindEngine(); + + if (!name && $.jStore.Instances.length >= 1) { // If no name is specified, use the first engine + $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[0]); + return $.jStore.CurrentEngine = $.jStore.Instances[0]; + } + + if (name && $.jStore.Instances[name]) { // If a name is specified and exists, use it + $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[name]); + return $.jStore.CurrentEngine = $.jStore.Instances[name]; + } + + throw 'JSTORE_JRI_NO_MATCH'; + } + + // Test all possible engines for straightforward useability + $.jStore.FindEngine = function(){ + $.each($.jStore.EngineOrder, function(k){ + if ($.jStore.Availability[this]()){ // Find the first, easiest option and use it. + $.jStore.use(this, $.jStore.defaults.project, 'default'); + return false; + } + }) + } + + // Provide a simple interface for storing/getting values + $.jStore.store = function(key, value){ + if (!$.jStore.CurrentEngine) return false; + + if ( !value ) // Executing a get command + return $.jStore.CurrentEngine.get(key); + // Executing a set command + return $.jStore.CurrentEngine.set(key, value); + } + // Provide a simple interface for storing/getting values + $.jStore.remove = function(key){ + if (!$.jStore.CurrentEngine) return false; + + return $.jStore.CurrentEngine.rem(key); + } + + // Provide a chainable interface for storing values/getting a value at the end of a chain + $.fn.store = function(key, value){ + if (!$.jStore.CurrentEngine) return this; + + var result = $.jStore.store(key, value); + + return !value ? result : this; + } + + // Provide a chainable interface for removing values + $.fn.removeStore = function(key){ + $.jStore.remove(key); + + return this; + } + + // Provide a way for users to call for auto-loading + $.jStore.load = function(){ + if ($.jStore.defaults.engine) + return $.jStore.use($.jStore.defaults.engine, $.jStore.defaults.project, 'default'); + + // Attempt to find a valid engine, and catch any exceptions if we can't + try { + $.jStore.FindEngine(); + } catch (e) {} + } + +})(jQuery); +/** + * jStore Engine Core + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + this.StorageEngine = Class.extend({ + init: function(project, name){ + // Configure the project name + this.project = project; + // The JRI name given by the manager + this.jri = name; + // Cache the data so we can work synchronously + this.data = {}; + // The maximum limit of the storage engine + this.limit = -1; + // Third party script includes + this.includes = []; + // Create an event delegate for users to subscribe to event triggers + this.delegate = new jStoreDelegate(this) + .bind('engine-ready', function(){ + this.isReady = true; + }) + .bind('engine-included', function(){ + this.hasIncluded = true; + }); + // If enabled, the manager will check availability, then run include(), then check again + this.autoload = false; // This should be changed by the engines, if they have required includes + // When set, we're ready to transact data + this.isReady = false; + // When the includer is finished, it will set this to true + this.hasIncluded = false; + }, + // Performs all necessary script includes + include: function(){ + var self = this, + total = this.includes.length, + count = 0; + + $.each(this.includes, function(){ + $.ajax({type: 'get', url: this, dataType: 'script', cache: true, + success: function(){ + count++; + if (count == total) self.delegate.trigger('engine-included'); + } + }) + }); + }, + // This should be overloaded with an actual functionality presence check + isAvailable: function(){ + return false; + }, + /** Event Subscription Shortcuts **/ + ready: function(callback){ + if (this.isReady) callback.apply(this); + else this.delegate.bind('engine-ready', callback); + return this; + }, + included: function(callback){ + if (this.hasIncluded) callback.apply(this); + else this.delegate.bind('engine-included', callback); + return this; + }, + /** Cache Data Access **/ + get: function(key){ + return this.data[key] || null; + }, + set: function(key, value){ + this.data[key] = value; + return value; + }, + rem: function(key){ + var beforeDelete = this.data[key]; + this.data[key] = null; + return beforeDelete; + } + }); + +})(jQuery); +/*! + * jStore DOM Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var sessionAvailability = $.jStore.Availability.session = function(){ + return !!window.sessionStorage; + }, + localAvailability = $.jStore.Availability.local = function(){ + return !!(window.localStorage || window.globalStorage); + }; + + this.jStoreDom = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'DOM'; + + // Set the Database limit + this.limit = 5 * 1024 * 1024; + }, + connect: function(){ + // Fire our delegate to indicate we're ready for data transactions + this.delegate.trigger('engine-ready'); + }, + get: function(key){ + var out = this.db.getItem(key); + // Gecko's getItem returns {value: 'the value'}, WebKit returns 'the value' + return out && out.value ? out.value : out + }, + set: function(key, value){ + this.db.setItem(key,value); + return value; + }, + rem: function(key){ + var out = this.get(key); + this.db.removeItem(key); + return out + } + }) + + this.jStoreLocal = jStoreDom.extend({ + connect: function(){ + // Gecko uses a non-standard globalStorage[ www.example.com ] DOM access object for persistant storage. + this.db = !window.globalStorage ? window.localStorage : window.globalStorage[location.hostname]; + this._super(); + }, + isAvailable: localAvailability + }) + + this.jStoreSession = jStoreDom.extend({ + connect: function(){ + this.db = sessionStorage; + this._super(); + }, + isAvailable: sessionAvailability + }) + + $.jStore.Engines.local = jStoreLocal; + $.jStore.Engines.session = jStoreSession; + + // Store the ordering preference + $.jStore.EngineOrder[ 1 ] = 'local'; + +})(jQuery); +/*! + * jStore Flash Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.flash = function(){ + return !!($.jStore.hasFlash('8.0.0')); + } + + this.jStoreFlash = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'Flash'; + + // Bind our flashReady function to the jStore Delegate + var self = this; + $.jStore.flashReady(function(){ self.flashReady() }); + }, + connect: function(){ + var name = 'jstore-flash-embed-' + this.project; + + // To make Flash Storage work on IE, we have to load up an iFrame + // which contains an HTML page that embeds the object using an + // object tag wrapping an embed tag. Of course, this is unnecessary for + // all browsers except for IE, which, to my knowledge, is the only browser + // in existance where you need to complicate your code to fix bugs. Goddamnit. :( + $(document.body) + .append('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" ' + + 'id="jStoreFlashFrame" src="' +$.jStore.defaults.flash + '"></iframe>'); + }, + flashReady: function(e){ + var iFrame = $('#jStoreFlashFrame')[0]; + + // IE + if (iFrame.Document && $.isFunction(iFrame.Document['jStoreFlash'].f_get_cookie)) this.db = iFrame.Document['jStoreFlash']; + // Safari && Firefox + else if (iFrame.contentWindow && iFrame.contentWindow.document){ + var doc = iFrame.contentWindow.document; + // Safari + if ($.isFunction($('object', $(doc))[0].f_get_cookie)) this.db = $('object', $(doc))[0]; + // Firefox + else if ($.isFunction($('embed', $(doc))[0].f_get_cookie)) this.db = $('embed', $(doc))[0]; + } + + // We're ready to process data + if (this.db) this.delegate.trigger('engine-ready'); + }, + isAvailable: avilability, + get: function(key){ + var out = this.db.f_get_cookie(key); + return out == 'null' ? null : out; + }, + set: function(key, value){ + this.db.f_set_cookie(key, value); + return value; + }, + rem: function(key){ + var beforeDelete = this.get(key); + this.db.f_delete_cookie(key); + return beforeDelete; + } + }) + + $.jStore.Engines.flash = jStoreFlash; + + // Store the ordering preference + $.jStore.EngineOrder[ 2 ] = 'flash'; + + /** + * Flash Detection functions copied from the jQuery Flash Plugin + * Copyright (c) 2006 Luke Lutman (http://jquery.lukelutman.com/plugins/flash) + * Dual licensed under the MIT and GPL licenses. + * http://www.opensource.org/licenses/mit-license.php + * http://www.opensource.org/licenses/gpl-license.php + */ + $.jStore.hasFlash = function(version){ + var pv = $.jStore.flashVersion().match(/\d+/g), + rv = version.match(/\d+/g); + + for(var i = 0; i < 3; i++) { + pv[i] = parseInt(pv[i] || 0); + rv[i] = parseInt(rv[i] || 0); + // player is less than required + if(pv[i] < rv[i]) return false; + // player is greater than required + if(pv[i] > rv[i]) return true; + } + // major version, minor version and revision match exactly + return true; + } + + $.jStore.flashVersion = function(){ + // ie + try { + try { + // avoid fp6 minor version lookup issues + // see: http://blog.deconcept.com/2006/01/11/getvariable-setvariable-crash-internet… + var axo = new ActiveXObject('ShockwaveFlash.ShockwaveFlash.6'); + try { axo.AllowScriptAccess = 'always'; } + catch(e) { return '6,0,0'; } + } catch(e) {} + return new ActiveXObject('ShockwaveFlash.ShockwaveFlash').GetVariable('$version').replace(/\D+/g, ',').match(/^,?(.+),?$/)[1]; + // other browsers + } catch(e) { + try { + if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){ + return (navigator.plugins["Shockwave Flash 2.0"] || navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g, ",").match(/^,?(.+),?$/)[1]; + } + } catch(e) {} + } + return '0,0,0'; + } + +})(jQuery); + +// Callback fired when ExternalInterface is established +function flash_ready(){ + $.jStore.delegate.trigger('flash-ready'); +} +/*! + * jStore Google Gears Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.gears = function(){ + return !!(window.google && window.google.gears) + } + + this.jStoreGears = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'Google Gears'; + + // Add required third-party scripts + this.includes.push('http://code.google.com/apis/gears/gears_init.js'); + + // Allow Autoloading on fail + this.autoload = true; + }, + connect: function(){ + // Create our database connection + var db = this.db = google.gears.factory.create('beta.database'); + db.open( 'jstore-' + this.project ); + db.execute( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); + + // Cache the data from the table + this.updateCache(); + }, + updateCache: function(){ + // Read the database into our cache object + var result = this.db.execute( 'SELECT k,v FROM jstore' ); + while (result.isValidRow()){ + this.data[result.field(0)] = result.field(1); + result.next(); + } result.close(); + + // Fire our delegate to indicate we're ready for data transactions + this.delegate.trigger('engine-ready'); + }, + isAvailable: avilability, + set: function(key, value){ + // Update the database + var db = this.db; + db.execute( 'BEGIN' ); + db.execute( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value] ); + db.execute( 'COMMIT' ); + return this._super(key, value); + }, + rem: function(key){ + // Update the database + var db = this.db; + db.execute( 'BEGIN' ); + db.execute( 'DELETE FROM jstore WHERE k = ?', [key] ); + db.execute( 'COMMIT' ); + return this._super(key); + } + }) + + $.jStore.Engines.gears = jStoreGears; + + // Store the ordering preference + $.jStore.EngineOrder[ 3 ] = 'gears'; + +})(jQuery); +/*! + * jStore HTML5 Specification Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.html5 = function(){ + return !!window.openDatabase + } + + this.jStoreHtml5 = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'HTML5'; + + // Set the Database limit + this.limit = 1024 * 200; + }, + connect: function(){ + // Create our database connection + var db = this.db = openDatabase('jstore-' + this.project, '1.0', this.project, this.limit); + if (!db) throw 'JSTORE_ENGINE_HTML5_NODB'; + db.transaction(function(db){ + db.executeSql( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); + }); + + // Cache the data from the table + this.updateCache(); + }, + updateCache: function(){ + var self = this; + // Read the database into our cache object + this.db.transaction(function(db){ + db.executeSql( 'SELECT k,v FROM jstore', [], function(db, result){ + var rows = result.rows, i = 0, row; + for (; i < rows.length; ++i){ + row = rows.item(i); + self.data[row.k] = row.v; + } + + // Fire our delegate to indicate we're ready for data transactions + self.delegate.trigger('engine-ready'); + }); + }); + }, + isAvailable: avilability, + set: function(key, value){ + // Update the database + this.db.transaction(function(db){ + db.executeSql( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value]); + }); + return this._super(key, value); + }, + rem: function(key){ + // Update the database + this.db.transaction(function(db){ + db.executeSql( 'DELETE FROM jstore WHERE k = ?', [key] ) + }) + return this._super(key); + } + }) + + $.jStore.Engines.html5 = jStoreHtml5; + + // Store the ordering preference + $.jStore.EngineOrder[ 0 ] = 'html5'; + +})(jQuery); +/*!* + * jStore IE Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.ie = function(){ + return !!window.ActiveXObject; + } + + this.jStoreIE = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'IE'; + + // Allow Autoloading on fail + this.limit = 64 * 1024; + }, + connect: function(){ + // Create a hidden div to store attributes in + this.db = $('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-' + this.project + '"></div>') + .appendTo(document.body).get(0); + // Fire our delegate to indicate we're ready for data transactions + this.delegate.trigger('engine-ready'); + }, + isAvailable: avilability, + get: function(key){ + this.db.load(this.project); + return this.db.getAttribute(key); + }, + set: function(key, value){ + this.db.setAttribute(key, value); + this.db.save(this.project); + return value; + }, + rem: function(key){ + var beforeDelete = this.get(key); + this.db.removeAttribute(key); + this.db.save(this.project); + return beforeDelete; + } + }) + + $.jStore.Engines.ie = jStoreIE; + + // Store the ordering preference + $.jStore.EngineOrder[ 4 ] = 'ie'; + +})(jQuery); \ No newline at end of file diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/scripts/json2.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/json2.js Wed Aug 19 17:51:46 2009 -0400 @@ -0,0 +1,476 @@ +/* + http://www.JSON.org/json2.js + 2009-06-29 + + Public Domain. + + NO WARRANTY EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK. + + See http://www.JSON.org/js.html + + This file creates a global JSON object containing two methods: stringify + and parse. + + JSON.stringify(value, replacer, space) + value any JavaScript value, usually an object or array. + + replacer an optional parameter that determines how object + values are stringified for objects. It can be a + function or an array of strings. + + space an optional parameter that specifies the indentation + of nested structures. If it is omitted, the text will + be packed without extra whitespace. If it is a number, + it will specify the number of spaces to indent at each + level. If it is a string (such as '\t' or ' '), + it contains the characters used to indent at each level. + + This method produces a JSON text from a JavaScript value. + + When an object value is found, if the object contains a toJSON + method, its toJSON method will be called and the result will be + stringified. A toJSON method does not serialize: it returns the + value represented by the name/value pair that should be serialized, + or undefined if nothing should be serialized. The toJSON method + will be passed the key associated with the value, and this will be + bound to the object holding the key. + + For example, this would serialize Dates as ISO strings. + + Date.prototype.toJSON = function (key) { + function f(n) { + // Format integers to have at least two digits. + return n < 10 ? '0' + n : n; + } + + return this.getUTCFullYear() + '-' + + f(this.getUTCMonth() + 1) + '-' + + f(this.getUTCDate()) + 'T' + + f(this.getUTCHours()) + ':' + + f(this.getUTCMinutes()) + ':' + + f(this.getUTCSeconds()) + 'Z'; + }; + + You can provide an optional replacer method. It will be passed the + key and value of each member, with this bound to the containing + object. The value that is returned from your method will be + serialized. If your method returns undefined, then the member will + be excluded from the serialization. + + If the replacer parameter is an array of strings, then it will be + used to select the members to be serialized. It filters the results + such that only members with keys listed in the replacer array are + stringified. + + Values that do not have JSON representations, such as undefined or + functions, will not be serialized. Such values in objects will be + dropped; in arrays they will be replaced with null. You can use + a replacer function to replace those with JSON values. + JSON.stringify(undefined) returns undefined. + + The optional space parameter produces a stringification of the + value that is filled with line breaks and indentation to make it + easier to read. + + If the space parameter is a non-empty string, then that string will + be used for indentation. If the space parameter is a number, then + the indentation will be that many spaces. + + Example: + + text = JSON.stringify(['e', {pluribus: 'unum'}]); + // text is '["e",{"pluribus":"unum"}]' + + + text = JSON.stringify(['e', {pluribus: 'unum'}], null, '\t'); + // text is '[\n\t"e",\n\t{\n\t\t"pluribus": "unum"\n\t}\n]' + + text = JSON.stringify([new Date()], function (key, value) { + return this[key] instanceof Date ? + 'Date(' + this[key] + ')' : value; + }); + // text is '["Date(---current time---)"]' + + + JSON.parse(text, reviver) + This method parses a JSON text to produce an object or array. + It can throw a SyntaxError exception. + + The optional reviver parameter is a function that can filter and + transform the results. It receives each of the keys and values, + and its return value is used instead of the original value. + If it returns what it received, then the structure is not modified. + If it returns undefined then the member is deleted. + + Example: + + // Parse the text. Values that look like ISO date strings will + // be converted to Date objects. + + myData = JSON.parse(text, function (key, value) { + var a; + if (typeof value === 'string') { + a = +/^(\d{4})-(\d{2})-(\d{2})T(\d{2}):(\d{2}):(\d{2}(?:\.\d*)?)Z$/.exec(value); + if (a) { + return new Date(Date.UTC(+a[1], +a[2] - 1, +a[3], +a[4], + +a[5], +a[6])); + } + } + return value; + }); + + myData = JSON.parse('["Date(09/09/2001)"]', function (key, value) { + var d; + if (typeof value === 'string' && + value.slice(0, 5) === 'Date(' && + value.slice(-1) === ')') { + d = new Date(value.slice(5, -1)); + if (d) { + return d; + } + } + return value; + }); + + + This is a reference implementation. You are free to copy, modify, or + redistribute. + + This code should be minified before deployment. + See http://javascript.crockford.com/jsmin.html + + USE YOUR OWN COPY. IT IS EXTREMELY UNWISE TO LOAD CODE FROM SERVERS YOU DO + NOT CONTROL. +*/ + +/*jslint evil: true */ + +/*members "", "\b", "\t", "\n", "\f", "\r", "\"", JSON, "\\", apply, + call, charCodeAt, getUTCDate, getUTCFullYear, getUTCHours, + getUTCMinutes, getUTCMonth, getUTCSeconds, hasOwnProperty, join, + lastIndex, length, parse, prototype, push, replace, slice, stringify, + test, toJSON, toString, valueOf +*/ + +// Create a JSON object only if one does not already exist. We create the +// methods in a closure to avoid creating global variables. + +var JSON = JSON || {}; + +(function () { + + function f(n) { + // Format integers to have at least two digits. + return n < 10 ? '0' + n : n; + } + + if (typeof Date.prototype.toJSON !== 'function') { + + Date.prototype.toJSON = function (key) { + + return isFinite(this.valueOf()) ? + this.getUTCFullYear() + '-' + + f(this.getUTCMonth() + 1) + '-' + + f(this.getUTCDate()) + 'T' + + f(this.getUTCHours()) + ':' + + f(this.getUTCMinutes()) + ':' + + f(this.getUTCSeconds()) + 'Z' : null; + }; + + String.prototype.toJSON = + Number.prototype.toJSON = + Boolean.prototype.toJSON = function (key) { + return this.valueOf(); + }; + } + + var cx = /[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g, + escapable = /[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g, + gap, + indent, + meta = { // table of character substitutions + '\b': '\\b', + '\t': '\\t', + '\n': '\\n', + '\f': '\\f', + '\r': '\\r', + '"' : '\\"', + '\\': '\\\\' + }, + rep; + + + function quote(string) { + +// If the string contains no control characters, no quote characters, and no +// backslash characters, then we can safely slap some quotes around it. +// Otherwise we must also replace the offending characters with safe escape +// sequences. + + escapable.lastIndex = 0; + return escapable.test(string) ? + '"' + string.replace(escapable, function (a) { + var c = meta[a]; + return typeof c === 'string' ? c : + '\\u' + ('0000' + a.charCodeAt(0).toString(16)).slice(-4); + }) + '"' : + '"' + string + '"'; + } + + + function str(key, holder) { + +// Produce a string from holder[key]. + + var i, // The loop counter. + k, // The member key. + v, // The member value. + length, + mind = gap, + partial, + value = holder[key]; + +// If the value has a toJSON method, call it to obtain a replacement value. + + if (value && typeof value === 'object' && + typeof value.toJSON === 'function') { + value = value.toJSON(key); + } + +// If we were called with a replacer function, then call the replacer to +// obtain a replacement value. + + if (typeof rep === 'function') { + value = rep.call(holder, key, value); + } + +// What happens next depends on the value's type. + + switch (typeof value) { + case 'string': + return quote(value); + + case 'number': + +// JSON numbers must be finite. Encode non-finite numbers as null. + + return isFinite(value) ? String(value) : 'null'; + + case 'boolean': + case 'null': + +// If the value is a boolean or null, convert it to a string. Note: +// typeof null does not produce 'null'. The case is included here in +// the remote chance that this gets fixed someday. + + return String(value); + +// If the type is 'object', we might be dealing with an object or an array or +// null. + + case 'object': + +// Due to a specification blunder in ECMAScript, typeof null is 'object', +// so watch out for that case. + + if (!value) { + return 'null'; + } + +// Make an array to hold the partial results of stringifying this object value. + + gap += indent; + partial = []; + +// Is the value an array? + + if (Object.prototype.toString.apply(value) === '[object Array]') { + +// The value is an array. Stringify every element. Use null as a placeholder +// for non-JSON values. + + length = value.length; + for (i = 0; i < length; i += 1) { + partial[i] = str(i, value) || 'null'; + } + +// Join all of the elements together, separated with commas, and wrap them in +// brackets. + + v = partial.length === 0 ? '[]' : + gap ? '[\n' + gap + + partial.join(',\n' + gap) + '\n' + + mind + ']' : + '[' + partial.join(',') + ']'; + gap = mind; + return v; + } + +// If the replacer is an array, use it to select the members to be stringified. + + if (rep && typeof rep === 'object') { + length = rep.length; + for (i = 0; i < length; i += 1) { + k = rep[i]; + if (typeof k === 'string') { + v = str(k, value); + if (v) { + partial.push(quote(k) + (gap ? ': ' : ':') + v); + } + } + } + } else { + +// Otherwise, iterate through all of the keys in the object. + + for (k in value) { + if (Object.hasOwnProperty.call(value, k)) { + v = str(k, value); + if (v) { + partial.push(quote(k) + (gap ? ': ' : ':') + v); + } + } + } + } + +// Join all of the member texts together, separated with commas, +// and wrap them in braces. + + v = partial.length === 0 ? '{}' : + gap ? '{\n' + gap + partial.join(',\n' + gap) + '\n' + + mind + '}' : '{' + partial.join(',') + '}'; + gap = mind; + return v; + } + } + +// If the JSON object does not yet have a stringify method, give it one. + + if (typeof JSON.stringify !== 'function') { + JSON.stringify = function (value, replacer, space) { + +// The stringify method takes a value and an optional replacer, and an optional +// space parameter, and returns a JSON text. The replacer can be a function +// that can replace values, or an array of strings that will select the keys. +// A default replacer method can be provided. Use of the space parameter can +// produce text that is more easily readable. + + var i; + gap = ''; + indent = ''; + +// If the space parameter is a number, make an indent string containing that +// many spaces. + + if (typeof space === 'number') { + for (i = 0; i < space; i += 1) { + indent += ' '; + } + +// If the space parameter is a string, it will be used as the indent string. + + } else if (typeof space === 'string') { + indent = space; + } + +// If there is a replacer, it must be a function or an array. +// Otherwise, throw an error. + + rep = replacer; + if (replacer && typeof replacer !== 'function' && + (typeof replacer !== 'object' || + typeof replacer.length !== 'number')) { + throw new Error('JSON.stringify'); + } + +// Make a fake root object containing our value under the key of ''. +// Return the result of stringifying the value. + + return str('', {'': value}); + }; + } + + +// If the JSON object does not yet have a parse method, give it one. + + if (typeof JSON.parse !== 'function') { + JSON.parse = function (text, reviver) { + +// The parse method takes a text and an optional reviver function, and returns +// a JavaScript value if the text is a valid JSON text. + + var j; + + function walk(holder, key) { + +// The walk method is used to recursively walk the resulting structure so +// that modifications can be made. + + var k, v, value = holder[key]; + if (value && typeof value === 'object') { + for (k in value) { + if (Object.hasOwnProperty.call(value, k)) { + v = walk(value, k); + if (v !== undefined) { + value[k] = v; + } else { + delete value[k]; + } + } + } + } + return reviver.call(holder, key, value); + } + + +// Parsing happens in four stages. In the first stage, we replace certain +// Unicode characters with escape sequences. JavaScript handles many characters +// incorrectly, either silently deleting them, or treating them as line endings. + + cx.lastIndex = 0; + if (cx.test(text)) { + text = text.replace(cx, function (a) { + return '\\u' + + ('0000' + a.charCodeAt(0).toString(16)).slice(-4); + }); + } + +// In the second stage, we run the text against regular expressions that look +// for non-JSON patterns. We are especially concerned with '()' and 'new' +// because they can cause invocation, and '=' because it can cause mutation. +// But just to be safe, we want to reject all unexpected forms. + +// We split the second stage into 4 regexp operations in order to work around +// crippling inefficiencies in IE's and Safari's regexp engines. First we +// replace the JSON backslash pairs with '@' (a non-JSON character). Second, we +// replace all simple value tokens with ']' characters. Third, we delete all +// open brackets that follow a colon or comma or that begin the text. Finally, +// we look to see that the remaining characters are only whitespace or ']' or +// ',' or ':' or '{' or '}'. If that is so, then the text is safe for eval. + + if (/^[\],:{}\s]*$/. +test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g, '@'). +replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g, ']'). +replace(/(?:^|:|,)(?:\s*\[)+/g, ''))) { + +// In the third stage we use the eval function to compile the text into a +// JavaScript structure. The '{' operator is subject to a syntactic ambiguity +// in JavaScript: it can begin a block or an object literal. We wrap the text +// in parens to eliminate the ambiguity. + + j = eval('(' + text + ')'); + +// In the optional fourth stage, we recursively walk the new structure, passing +// each name/value pair to a reviver function for possible transformation. + + return typeof reviver === 'function' ? + walk({'': j}, '') : j; + } + +// If the text is not JSON parseable, then a SyntaxError is thrown. + + throw new SyntaxError('JSON.parse'); + }; + } +}()); diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/scripts/json_cookie.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/json_cookie.js Wed Aug 19 17:51:46 2009 -0400 @@ -0,0 +1,61 @@ +/* + JSONCookie: Uses JSON to allow the settings of multiple preferences in one cookie. + Kanwei Li, 2009 + + cookie = new JSONCookie("cookie_name"); // Pass in the name of the cookie + + // Gets the value of a preference, returns optional second argument if pref not found + cookie.get("pref", "val_if_not_found"); + + cookie.set("pref", "val"); // Sets a value for the preference and saves cookie + cookie.unset("pref"); // Unsets the preference and saves cookie + cookie.clear() // Deletes the cookie + +*/ + +function JSONCookie(name) { + this.cookie_name = name; + +} + +JSONCookie.prototype = { + json_data : function() { + cookie = $.cookie(this.cookie_name); + return cookie ? JSON.parse(cookie) : null; + }, + + save : function(data) { + $.cookie(this.cookie_name, JSON.stringify(data)); + }, + + get : function(attr, else_val) { + data = this.json_data(); + if (data && data[attr]) { return data[attr]; + } else if (else_val) { return else_val; + } else { return null; + } + }, + + set : function(attr, val) { + data = this.json_data(); + if (data) { + data[attr] = val; + } else { + data = { attr : val } + } + this.save(data); + }, + + unset : function(attr) { + data = this.json_data(); + if (data) { + delete data[attr]; + } + this.save(data); + }, + + clear : function() { + this.save(null); + } + +}; \ No newline at end of file diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Aug 19 11:08:58 2009 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Aug 19 17:51:46 2009 -0400 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.ha ndle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_ form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[sucessors[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$( this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prot otype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this; var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({wi dth:f,height:f});b.draw_overview()})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewp ort_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connecto rs,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},enable_auto_save:function(){outer_this=this;$(".toolFormBody").find("input,textarea,select").each(function(){$(this).focus(function(){outer_this.active_form_has_changes=true})})},check_changes_in_active_form:functio n(){if(this.active_form_has_changes){this.has_changes=true;$(".toolFormBody").find("form").each(function(){$(this).submit()});this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){l evel_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this .canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></d iv>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this). offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.c ss("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_n odes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/scripts/packed/jquery.jstore-all.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/jquery.jstore-all.js Wed Aug 19 17:51:46 2009 -0400 @@ -0,0 +1,41 @@ +/* + * jStore - Persistent Client-Side Storage + * + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * + * Dual licensed under: + * MIT: http://www.opensource.org/licenses/mit-license.php + * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html + */ +(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=typeof g[d]=="function"&&typeof f[d]=="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}})(d,g[d]):g[d]}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}})(); +/* + * jStore Delegate Framework + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(a){this.jStoreDelegate=Class.extend({init:function(b){this.parent=b;this.callbacks={}},bind:function(b,c){if(!a.isFunction(c)){return this}if(!this.callbacks[b]){this.callbacks[b]=[]}this.callbacks[b].push(c);return this},trigger:function(){var d=this.parent,c=[].slice.call(arguments),e=c.shift(),b=this.callbacks[e];if(!b){return false}a.each(b,function(){this.apply(d,c)});return this}})})(jQuery);(function(a){a.jStore={};a.extend(a.jStore,{EngineOrder:[],Availability:{},Engines:{},Instances:{},CurrentEngine:null,defaults:{project:null,engine:null,autoload:true,flash:"jStore.Flash.html"},isReady:false,isFlashReady:false,delegate:new jStoreDelegate(a.jStore).bind("jStore-ready",function(b){a.jStore.isReady=true;if(a.jStore.defaults.autoload){b.connect()}}).bind("flash-ready",function(){a.jStore.isFlashReady=true})});a.jStore.ready=function(b){if(a.jStore.isReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("jStore-ready",b)}};a.jStore.fail =function(b){a.jStore.delegate.bind("jStore-failure",b)};a.jStore.flashReady=function(b){if(a.jStore.isFlashReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("flash-ready",b)}};a.jStore.use=function(d,g,c){g=g||a.jStore.defaults.project||location.hostname.replace(/\./g,"-")||"unknown";var f=a.jStore.Engines[d.toLowerCase()]||null,b=(c?c+".":"")+g+"."+d;if(!f){throw"JSTORE_ENGINE_UNDEFINED"}f=new f(g,b);if(a.jStore.Instances[b]){throw"JSTORE_JRI_CONFLICT"}if(f.isAvailable()){a.jStore.Instances[b]=f;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=f}a.jStore.delegate.trigger("jStore-ready",f)}else{if(!f.autoload){throw"JSTORE_ENGINE_UNAVILABLE"}else{f.included(function(){if(this.isAvailable()){a.jStore.Instances[b]=this;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=this}a.jStore.delegate.trigger("jStore-ready",this)}else{a.jStore.delegate.trigger("jStore-failure",this)}}).include()}}};a.jStore.setCurrentEngine=function(b){if(!a.jStore.Instanc es.length){return a.jStore.FindEngine()}if(!b&&a.jStore.Instances.length>=1){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[0]);return a.jStore.CurrentEngine=a.jStore.Instances[0]}if(b&&a.jStore.Instances[b]){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[b]);return a.jStore.CurrentEngine=a.jStore.Instances[b]}throw"JSTORE_JRI_NO_MATCH"};a.jStore.FindEngine=function(){a.each(a.jStore.EngineOrder,function(b){if(a.jStore.Availability[this]()){a.jStore.use(this,a.jStore.defaults.project,"default");return false}})};a.jStore.store=function(b,c){if(!a.jStore.CurrentEngine){return false}if(!c){return a.jStore.CurrentEngine.get(b)}return a.jStore.CurrentEngine.set(b,c)};a.jStore.remove=function(b){if(!a.jStore.CurrentEngine){return false}return a.jStore.CurrentEngine.rem(b)};a.fn.store=function(c,d){if(!a.jStore.CurrentEngine){return this}var b=a.jStore.store(c,d);return !d?b:this};a.fn.removeStore=function(b){a.jStore.remove(b);return this};a.jStore.load=f unction(){if(a.jStore.defaults.engine){return a.jStore.use(a.jStore.defaults.engine,a.jStore.defaults.project,"default")}try{a.jStore.FindEngine()}catch(b){}}})(jQuery);(function(a){this.StorageEngine=Class.extend({init:function(c,b){this.project=c;this.jri=b;this.data={};this.limit=-1;this.includes=[];this.delegate=new jStoreDelegate(this).bind("engine-ready",function(){this.isReady=true}).bind("engine-included",function(){this.hasIncluded=true});this.autoload=false;this.isReady=false;this.hasIncluded=false},include:function(){var b=this,d=this.includes.length,c=0;a.each(this.includes,function(){a.ajax({type:"get",url:this,dataType:"script",cache:true,success:function(){c++;if(c==d){b.delegate.trigger("engine-included")}}})})},isAvailable:function(){return false},ready:function(b){if(this.isReady){b.apply(this)}else{this.delegate.bind("engine-ready",b)}return this},included:function(b){if(this.hasIncluded){b.apply(this)}else{this.delegate.bind("engine-included",b)}return th is},get:function(b){return this.data[b]||null},set:function(b,c){this.data[b]=c;return c},rem:function(b){var c=this.data[b];this.data[b]=null;return c}})})(jQuery); +/* + * jStore DOM Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(c){var b=c.jStore.Availability.session=function(){return !!window.sessionStorage},a=c.jStore.Availability.local=function(){return !!(window.localStorage||window.globalStorage)};this.jStoreDom=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="DOM";this.limit=5*1024*1024},connect:function(){this.delegate.trigger("engine-ready")},get:function(e){var d=this.db.getItem(e);return d&&d.value?d.value:d},set:function(d,e){this.db.setItem(d,e);return e},rem:function(e){var d=this.get(e);this.db.removeItem(e);return d}});this.jStoreLocal=jStoreDom.extend({connect:function(){this.db=!window.globalStorage?window.localStorage:window.globalStorage[location.hostname];this._super()},isAvailable:a});this.jStoreSession=jStoreDom.extend({connect:function(){this.db=sessionStorage;this._super()},isAvailable:b});c.jStore.Engines.local=jStoreLocal;c.jStore.Engines.session=jStoreSession;c.jStore.EngineOrder[1]="local"})(jQuery); +/* + * jStore Flash Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) + */ +(function(b){var a=b.jStore.Availability.flash=function(){return !!(b.jStore.hasFlash("8.0.0"))};this.jStoreFlash=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="Flash";var c=this;b.jStore.flashReady(function(){c.flashReady()})},connect:function(){var c="jstore-flash-embed-"+this.project;b(document.body).append('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" id="jStoreFlashFrame" src="'+b.jStore.defaults.flash+'"></iframe>')},flashReady:function(f){var c=b("#jStoreFlashFrame")[0];if(c.Document&&b.isFunction(c.Document.jStoreFlash.f_get_cookie)){this.db=c.Document.jStoreFlash}else{if(c.contentWindow&&c.contentWindow.document){var d=c.contentWindow.document;if(b.isFunction(b("object",b(d))[0].f_get_cookie)){this.db=b("object",b(d))[0]}else{if(b.isFunction(b("embed",b(d))[0].f_get_cookie)){this.db=b("embed",b(d))[0]}}}}if(this.db){this.delegate.trigger("engine-ready")}},isAvailable:a,get:function(d){var c=this.db.f_g et_cookie(d);return c=="null"?null:c},set:function(c,d){this.db.f_set_cookie(c,d);return d},rem:function(c){var d=this.get(c);this.db.f_delete_cookie(c);return d}});b.jStore.Engines.flash=jStoreFlash;b.jStore.EngineOrder[2]="flash";b.jStore.hasFlash=function(c){var e=b.jStore.flashVersion().match(/\d+/g),f=c.match(/\d+/g);for(var d=0;d<3;d++){e[d]=parseInt(e[d]||0);f[d]=parseInt(f[d]||0);if(e[d]<f[d]){return false}if(e[d]>f[d]){return true}}return true};b.jStore.flashVersion=function(){try{try{var c=new ActiveXObject("ShockwaveFlash.ShockwaveFlash.6");try{c.AllowScriptAccess="always"}catch(d){return"6,0,0"}}catch(d){}return new ActiveXObject("ShockwaveFlash.ShockwaveFlash").GetVariable("$version").replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}catch(d){try{if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){return(navigator.plugins["Shockwave Flash 2.0"]||navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}}catch(d){}}r eturn"0,0,0"}})(jQuery);function flash_ready(){$.jStore.delegate.trigger("flash-ready")} +/* + * jStore Google Gears Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(b){var a=b.jStore.Availability.gears=function(){return !!(window.google&&window.google.gears)};this.jStoreGears=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="Google Gears";this.includes.push("http://code.google.com/apis/gears/gears_init.js");this.autoload=true},connect:function(){var c=this.db=google.gears.factory.create("beta.database");c.open("jstore-"+this.project);c.execute("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)");this.updateCache()},updateCache:function(){var c=this.db.execute("SELECT k,v FROM jstore");while(c.isValidRow()){this.data[c.field(0)]=c.field(1);c.next()}c.close();this.delegate.trigger("engine-ready")},isAvailable:a,set:function(d,e){var c=this.db;c.execute("BEGIN");c.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[d,e]);c.execute("COMMIT");return this._super(d,e)},rem:function(d){var c=this.db;c.execute("BEGIN");c.execute("DELETE FROM jstore WHERE k = ?",[d]);c.ex ecute("COMMIT");return this._super(d)}});b.jStore.Engines.gears=jStoreGears;b.jStore.EngineOrder[3]="gears"})(jQuery); +/* + * jStore HTML5 Specification Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(b){var a=b.jStore.Availability.html5=function(){return !!window.openDatabase};this.jStoreHtml5=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="HTML5";this.limit=1024*200},connect:function(){var c=this.db=openDatabase("jstore-"+this.project,"1.0",this.project,this.limit);if(!c){throw"JSTORE_ENGINE_HTML5_NODB"}c.transaction(function(d){d.executeSql("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)")});this.updateCache()},updateCache:function(){var c=this;this.db.transaction(function(d){d.executeSql("SELECT k,v FROM jstore",[],function(f,e){var h=e.rows,g=0,j;for(;g<h.length;++g){j=h.item(g);c.data[j.k]=j.v}c.delegate.trigger("engine-ready")})})},isAvailable:a,set:function(c,d){this.db.transaction(function(e){e.executeSql("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[c,d])});return this._super(c,d)},rem:function(c){this.db.transaction(function(d){d.executeSql("DELETE FROM jstore WHERE k = ?",[c])});ret urn this._super(c)}});b.jStore.Engines.html5=jStoreHtml5;b.jStore.EngineOrder[0]="html5"})(jQuery); +/** + * jStore IE Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(b){var a=b.jStore.Availability.ie=function(){return !!window.ActiveXObject};this.jStoreIE=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="IE";this.limit=64*1024},connect:function(){this.db=b('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+this.project+'"></div>').appendTo(document.body).get(0);this.delegate.trigger("engine-ready")},isAvailable:a,get:function(c){this.db.load(this.project);return this.db.getAttribute(c)},set:function(c,d){this.db.setAttribute(c,d);this.db.save(this.project);return d},rem:function(c){var d=this.get(c);this.db.removeAttribute(c);this.db.save(this.project);return d}});b.jStore.Engines.ie=jStoreIE;b.jStore.EngineOrder[4]="ie"})(jQuery); \ No newline at end of file diff -r 7d48dc7e60b4 -r 3353b15d0fb5 static/scripts/packed/json2.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/json2.js Wed Aug 19 17:51:46 2009 -0400 @@ -0,0 +1,1 @@ +var JSON=JSON||{};(function(){function f(n){return n<10?"0"+n:n}if(typeof Date.prototype.toJSON!=="function"){Date.prototype.toJSON=function(key){return isFinite(this.valueOf())?this.getUTCFullYear()+"-"+f(this.getUTCMonth()+1)+"-"+f(this.getUTCDate())+"T"+f(this.getUTCHours())+":"+f(this.getUTCMinutes())+":"+f(this.getUTCSeconds())+"Z":null};String.prototype.toJSON=Number.prototype.toJSON=Boolean.prototype.toJSON=function(key){return this.valueOf()}}var cx=/[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,escapable=/[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,gap,indent,meta={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},rep;function quote(string){escapable.lastIndex=0;return escapable.test(string)?'"'+string.replace(escapable,function(a){var c=meta[a];return typeof c==="string"?c:"\\u"+("0000"+a.charCodeAt(0) .toString(16)).slice(-4)})+'"':'"'+string+'"'}function str(key,holder){var i,k,v,length,mind=gap,partial,value=holder[key];if(value&&typeof value==="object"&&typeof value.toJSON==="function"){value=value.toJSON(key)}if(typeof rep==="function"){value=rep.call(holder,key,value)}switch(typeof value){case"string":return quote(value);case"number":return isFinite(value)?String(value):"null";case"boolean":case"null":return String(value);case"object":if(!value){return"null"}gap+=indent;partial=[];if(Object.prototype.toString.apply(value)==="[object Array]"){length=value.length;for(i=0;i<length;i+=1){partial[i]=str(i,value)||"null"}v=partial.length===0?"[]":gap?"[\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"]":"["+partial.join(",")+"]";gap=mind;return v}if(rep&&typeof rep==="object"){length=rep.length;for(i=0;i<length;i+=1){k=rep[i];if(typeof k==="string"){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}else{for(k in value){if(Object.hasOwnProperty.call(value,k)){v=str( k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}v=partial.length===0?"{}":gap?"{\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"}":"{"+partial.join(",")+"}";gap=mind;return v}}if(typeof JSON.stringify!=="function"){JSON.stringify=function(value,replacer,space){var i;gap="";indent="";if(typeof space==="number"){for(i=0;i<space;i+=1){indent+=" "}}else{if(typeof space==="string"){indent=space}}rep=replacer;if(replacer&&typeof replacer!=="function"&&(typeof replacer!=="object"||typeof replacer.length!=="number")){throw new Error("JSON.stringify")}return str("",{"":value})}}if(typeof JSON.parse!=="function"){JSON.parse=function(text,reviver){var j;function walk(holder,key){var k,v,value=holder[key];if(value&&typeof value==="object"){for(k in value){if(Object.hasOwnProperty.call(value,k)){v=walk(value,k);if(v!==undefined){value[k]=v}else{delete value[k]}}}}return reviver.call(holder,key,value)}cx.lastIndex=0;if(cx.test(text)){text=text.replace(cx,function(a){return"\\u"+("000 0"+a.charCodeAt(0).toString(16)).slice(-4)})}if(/^[\],:{}\s]*$/.test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))){j=eval("("+text+")");return typeof reviver==="function"?walk({"":j},""):j}throw new SyntaxError("JSON.parse")}}}()); \ No newline at end of file diff -r 7d48dc7e60b4 -r 3353b15d0fb5 templates/root/history.mako --- a/templates/root/history.mako Wed Aug 19 11:08:58 2009 -0400 +++ b/templates/root/history.mako Wed Aug 19 17:51:46 2009 -0400 @@ -15,219 +15,242 @@ <meta http-equiv="Pragma" content="no-cache"> ${h.css( "base", "history" )} -${h.js( "jquery", "jquery.cookie", "cookie_set" )} - +${h.js( "jquery", "json2", "jquery.jstore-all" )} + <script type="text/javascript"> - $( document ).ready( function() { - initShowHide(); - setupHistoryItem( $("div.historyItemWrapper") ); - // Collapse all - $("#top-links").append( "| " ).append( $("<a href='#'>${_('collapse all')}</a>").click( function() { - $( "div.historyItemBody:visible" ).each( function() { - if ( $.browser.mozilla ) - { - $(this).find( "pre.peek" ).css( "overflow", "hidden" ); +$(function() { + // Load jStore for local storage + $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) + $.jStore.load(); // Auto-select best storage + + $.jStore.ready(function(engine) { + engine.ready(function() { + // Init stuff that requires the local storage to be running + initShowHide(); + setupHistoryItem( $("div.historyItemWrapper") ); + }); + }); + + // Generate 'collapse all' link + $("#top-links").append( "| " ).append( $("<a href='#'>${_('collapse all')}</a>").click( function() { + $( "div.historyItemBody:visible" ).each( function() { + if ( $.browser.mozilla ) { + $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + } + $(this).slideUp( "fast" ); + }); + $.jStore.remove("history_expand_state"); + })); + + $("#history-rename").click( function() { + var old_name = $("#history-name").text() + var t = $("<input type='text' value='" + old_name + "'></input>" ); + t.blur( function() { + $(this).remove(); + $("#history-name").show(); + }); + t.keyup( function( e ) { + if ( e.keyCode == 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( e.keyCode == 13 ) { + // Enter key + new_value = this.value; + $(this).trigger( "blur" ); + $.ajax({ + url: "${h.url_for( controller='history', action='rename_async', id=history.id )}", + data: { "_": true, new_name: new_value }, + error: function() { alert( "Rename failed" ) }, + success: function() { + $("#history-name").text( new_value ); + } + }); + } + }); + $("#history-name").hide(); + $("#history-name-area").append( t ); + t.focus(); + return false; + }); + // Updater + updater({ + %for i, data in enumerate( reversed( datasets ) ): + %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: + %if i > 0: + , + %endif + "${data.id}": "${data.state}" + %endif + %endfor + }); +}); +// Functionized so AJAX'd datasets can call them +// Get shown/hidden state from cookie +function initShowHide() { + + // Load saved state and show as neccesary + try { + var stored = $.jStore.store("history_expand_state"); + if (stored) { + var st = JSON.parse(stored); + for (var id in st) { + $("#" + id + " div.historyItemBody" ).show(); + } + } + } catch(err) { + // Something was wrong with values in storage, so clear storage + $.jStore.remove("history_expand_state"); + } + + // If Mozilla, hide scrollbars in hidden items since they cause animation bugs + if ( $.browser.mozilla ) { + $( "div.historyItemBody" ).each( function() { + if ( ! $(this).is( ":visible" ) ) $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + }) + } +} +// Add show/hide link and delete link to a history item +function setupHistoryItem( query ) { + query.each( function() { + var id = this.id; + var body = $(this).children( "div.historyItemBody" ); + var peek = body.find( "pre.peek" ) + $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { + if ( body.is(":visible") ) { + // Hiding stuff here + if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } + body.slideUp( "fast" ); + + // Save setting + var stored = $.jStore.store("history_expand_state") + var prefs = stored ? JSON.parse(stored) : null + if (prefs) { + delete prefs[id]; + $.jStore.store("history_expand_state", JSON.stringify(prefs)); } - $(this).slideUp( "fast" ); - }) - var state = new CookieSet( "galaxy.history.expand_state" ); - state.removeAll().save(); - return false; - })); - $("#history-rename").click( function() { - var old_name = $("#history-name").text() - var t = $("<input type='text' value='" + old_name + "'></input>" ); - t.blur( function() { - $(this).remove(); - $("#history-name").show(); - }); - t.keyup( function( e ) { - if ( e.keyCode == 27 ) { - // Escape key - $(this).trigger( "blur" ); - } else if ( e.keyCode == 13 ) { - // Enter key - new_value = this.value; - $(this).trigger( "blur" ); - $.ajax({ - url: "${h.url_for( controller='history', action='rename_async', id=history.id )}", - data: { "_": true, new_name: new_value }, - error: function() { alert( "Rename failed" ) }, - success: function() { - $("#history-name").text( new_value ); - } - }); - } - }); - $("#history-name").hide(); - $("#history-name-area").append( t ); - t.focus(); - return false; - }); - // Updater - updater({ - %for i, data in enumerate( reversed( datasets ) ): - %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: - %if i > 0: - , - %endif - "${data.id}": "${data.state}" - %endif - %endfor + } + else { + // Showing stuff here + body.slideDown( "fast", function() { + if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } + }); + + // Save setting + var stored = $.jStore.store("history_expand_state") + var prefs = stored ? JSON.parse(stored) : new Object; + prefs[id] = true; + $.jStore.store("history_expand_state", JSON.stringify(prefs)); + } + return false; }); - }) - //' Functionized so AJAX'd datasets can call them - // Get shown/hidden state from cookie - function initShowHide() { - // $( "div.historyItemBody" ).hide(); - // Load saved state and show as neccesary - var state = new CookieSet( "galaxy.history.expand_state" ); - for ( id in state.store ) { - if ( id ) { - $( "#" + id + " div.historyItemBody" ).show(); - } - } - // If Mozilla, hide scrollbars in hidden items since they cause animation bugs - if ( $.browser.mozilla ) { - $( "div.historyItemBody" ).each( function() { - if ( ! $(this).is( ":visible" ) ) $(this).find( "pre.peek" ).css( "overflow", "hidden" ); - }) - } - delete state; - } - // Add show/hide link and delete link to a history item - function setupHistoryItem( query ) { - query.each( function() { - var id = this.id; - var body = $(this).children( "div.historyItemBody" ); - var peek = body.find( "pre.peek" ) - $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { - if ( body.is(":visible") ) { - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } - body.slideUp( "fast" ); - ## other instances of this could be editing the cookie, refetch - var state = new CookieSet( "galaxy.history.expand_state" ); - state.remove( id ); state.save(); - delete state; - } - else { - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - var state = new CookieSet( "galaxy.history.expand_state" ); - state.add( id ); state.save(); - delete state; - } + // Delete link + $(this).find( "div.historyItemButtons > .delete" ).each( function() { + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#historyItem-' + data_id + "> div.historyItemTitleBar" ).addClass( "spinner" ); + $.ajax({ + url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Delete failed" ) }, + success: function() { + %if show_deleted: + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + %else: + $( "#historyItem-" + data_id ).fadeOut( "fast", function() { + $( "#historyItemContainer-" + data_id ).remove(); + if ( $( "div.historyItemContainer" ).length < 1 ) { + $( "#emptyHistoryMessage" ).show(); + } + }); + %endif + } + }); return false; }); - // Delete link - $(this).find( "div.historyItemButtons > .delete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#historyItem-' + data_id + "> div.historyItemTitleBar" ).addClass( "spinner" ); - $.ajax({ - url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Delete failed" ) }, - success: function() { - %if show_deleted: - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - %else: - $( "#historyItem-" + data_id ).fadeOut( "fast", function() { - $( "#historyItemContainer-" + data_id ).remove(); - if ( $( "div.historyItemContainer" ).length < 1 ) { - $( "#emptyHistoryMessage" ).show(); - } - }); - %endif - } - }); - return false; + }); + // Undelete link + $(this).find( "a.historyItemUndelete" ).each( function() { + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#historyItem-' + data_id + " > div.historyItemTitleBar" ).addClass( "spinner" ); + $.ajax({ + url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Undelete failed" ) }, + success: function() { + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + } }); - }); - // Undelete link - $(this).find( "a.historyItemUndelete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#historyItem-' + data_id + " > div.historyItemTitleBar" ).addClass( "spinner" ); - $.ajax({ - url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Undelete failed" ) }, - success: function() { - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - } - }); - return false; - }); + return false; }); }); - }; - // Looks for changes in dataset state using an async request. Keeps - // calling itself (via setTimeout) until all datasets are in a terminal - // state. - var updater = function ( tracked_datasets ) { - // Check if there are any items left to track - var empty = true; - for ( i in tracked_datasets ) { - empty = false; - break; + }); +}; +// Looks for changes in dataset state using an async request. Keeps +// calling itself (via setTimeout) until all datasets are in a terminal +// state. +var updater = function ( tracked_datasets ) { + // Check if there are any items left to track + var empty = true; + for ( i in tracked_datasets ) { + empty = false; + break; + } + if ( ! empty ) { + // console.log( "Updater running in 3 seconds" ); + setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); + } else { + // console.log( "Updater finished" ); + } +}; +var updater_callback = function ( tracked_datasets ) { + // Build request data + var ids = [] + var states = [] + var force_history_refresh = false + $.each( tracked_datasets, function ( id, state ) { + ids.push( id ); + states.push( state ); + }); + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='root', action='history_item_updates' )}", + dataType: "json", + data: { ids: ids.join( "," ), states: states.join( "," ) }, + success : function ( data ) { + $.each( data, function( id, val ) { + // Replace HTML + var container = $("#historyItemContainer-" + id); + container.html( val.html ); + setupHistoryItem( container.children( ".historyItemWrapper" ) ); + initShowHide(); + // If new state was terminal, stop tracking + if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { + if ( val.force_history_refresh ){ + force_history_refresh = true; + } + delete tracked_datasets[ parseInt(id) ]; + } else { + tracked_datasets[ parseInt(id) ] = val.state; + } + }); + if ( force_history_refresh ) { + parent.frames.galaxy_history.location.reload(); + } + else { + // Keep going (if there are still any items to track) + updater( tracked_datasets ); + } + }, + error: function() { + // Just retry, like the old method, should try to be smarter + updater( tracked_datasets ); } - if ( ! empty ) { - // console.log( "Updater running in 3 seconds" ); - setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); - } else { - // console.log( "Updater finished" ); - } - }; - var updater_callback = function ( tracked_datasets ) { - // Build request data - var ids = [] - var states = [] - var force_history_refresh = false - $.each( tracked_datasets, function ( id, state ) { - ids.push( id ); - states.push( state ); - }); - // Make ajax call - $.ajax( { - type: "POST", - url: "${h.url_for( controller='root', action='history_item_updates' )}", - dataType: "json", - data: { ids: ids.join( "," ), states: states.join( "," ) }, - success : function ( data ) { - $.each( data, function( id, val ) { - // Replace HTML - var container = $("#historyItemContainer-" + id); - container.html( val.html ); - setupHistoryItem( container.children( ".historyItemWrapper" ) ); - initShowHide(); - // If new state was terminal, stop tracking - if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { - if ( val.force_history_refresh ){ - force_history_refresh = true; - } - delete tracked_datasets[ parseInt(id) ]; - } else { - tracked_datasets[ parseInt(id) ] = val.state; - } - }); - if ( force_history_refresh ) { - parent.frames.galaxy_history.location.reload(); - } - else { - // Keep going (if there are still any items to track) - updater( tracked_datasets ); - } - }, - error: function() { - // Just retry, like the old method, should try to be smarter - updater( tracked_datasets ); - } - }); - }; + }); +}; </script> <style> diff -r 7d48dc7e60b4 -r 3353b15d0fb5 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Wed Aug 19 11:08:58 2009 -0400 +++ b/templates/workflow/editor.mako Wed Aug 19 17:51:46 2009 -0400 @@ -31,6 +31,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.hover.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.form.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.json.js')}"> </script> + <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.jstore-all.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.base.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.workflow_editor.canvas.js')}"> </script> @@ -47,6 +48,7 @@ canvas_manager = null; // jQuery onReady $( function() { + if ( window.lt_ie_7 ) { show_modal( "Browser not supported", @@ -54,8 +56,14 @@ ); return; } + + // Load jStore for local storage + $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) + $.jStore.load(); // Auto-select best storage + // Canvas overview management canvas_manager = new CanvasManager( $("#canvas-viewport"), $("#overview") ); + // Initialize workflow state reset(); // Load the datatype info @@ -121,17 +129,46 @@ canvas_manager.draw_overview(); }); - /* Lets the viewport be toggled visible and invisible, adjusting the arrows accordingly */ + $.jStore.ready(function(engine) { + engine.ready(function() { + // On load, set the size to the pref stored in local storage if it exists + overview_size = $.jStore.store("overview-size"); + if (overview_size) { + $("#overview-border").css( { + width: overview_size, + height: overview_size + }); + } + + // Show viewport on load unless pref says it's off + $.jStore.store("overview-off") ? hide_overview() : show_overview() + }); + }); + + // Stores the size of the overview into local storage when it's resized + $("#overview-border").bind( "dragend", function( e ) { + var op = $(this).offsetParent(); + var opo = op.offset(); + var new_size = Math.max( op.width() - ( e.offsetX - opo.left ), + op.height() - ( e.offsetY - opo.top ) ); + $.jStore.store("overview-size", new_size + "px"); + }); + + function show_overview() { + $.jStore.remove("overview-off"); + $("#overview-border").css("right", "0px"); + $("#close-viewport").css("background-position", "0px 0px"); + } + + function hide_overview() { + $.jStore.store("overview-off", true); + $("#overview-border").css("right", "20000px"); + $("#close-viewport").css("background-position", "12px 0px"); + } + + // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly $("#close-viewport").click( function() { - if ( $("#overview-border").css("right") == "0px" ) { - $("#overview-border").css("right", "20000px"); - $("#close-viewport").css("background-position", "12px 0px"); - - } else { - $("#overview-border").css("right", "0px"); - $("#close-viewport").css("background-position", "0px 0px"); - } - + $("#overview-border").css("right") == "0px" ? hide_overview() : show_overview(); }); // Unload handler @@ -245,10 +282,6 @@ beforeSubmit: function( data ) { data.push( { name: 'tool_state', value: node.tool_state } ); data.push( { name: '_', value: "true" } ); - $("#tool-form-save-button").each( function() { - this.value = "Saving..."; - this.disabled = true; - }); } }).each( function() { form = this; @@ -275,6 +308,7 @@ var close_editor = function() { <% next_url = h.url_for( controller='workflow', action='index' ) %> + workflow.check_changes_in_active_form(); if ( workflow && workflow.has_changes ) { do_close = function() { window.onbeforeunload = undefined; @@ -297,39 +331,46 @@ var save_current_workflow = function ( success_callback ) { show_modal( "Saving workflow", "progress" ); - $.ajax( { - url: "${h.url_for( action='save_workflow' )}", - type: "POST", - data: { - id: "${trans.security.encode_id( workflow_id )}", - workflow_data: $.toJSON( workflow.to_simple() ), - "_": "true" - }, - dataType: 'json', - success: function( data ) { - var body = $("<div></div>").text( data.message ); - if ( data.errors ) { - body.addClass( "warningmark" ) - var errlist = $( "<ul/>" ); - $.each( data.errors, function( i, v ) { - $("<li></li>").text( v ).appendTo( errlist ); - }); - body.append( errlist ); - } else { - body.addClass( "donemark" ); + workflow.check_changes_in_active_form(); + // We bind to ajaxStop because of auto-saving, since the form submission ajax + // call needs to be completed so that the new data is saved + $(document).bind('ajaxStop.save_workflow', function() { + $(document).unbind('ajaxStop.save_workflow'); + $.ajax( { + url: "${h.url_for( action='save_workflow' )}", + type: "POST", + data: { + id: "${trans.security.encode_id( workflow_id )}", + workflow_data: function() { return $.toJSON( workflow.to_simple() ) }, + "_": "true" + }, + dataType: 'json', + success: function( data ) { + var body = $("<div></div>").text( data.message ); + if ( data.errors ) { + body.addClass( "warningmark" ) + var errlist = $( "<ul/>" ); + $.each( data.errors, function( i, v ) { + $("<li></li>").text( v ).appendTo( errlist ); + }); + body.append( errlist ); + } else { + body.addClass( "donemark" ); + } + workflow.name = data.name; + workflow.has_changes = false; + workflow.stored = true; + if ( success_callback ) { + success_callback(); + } + if ( data.errors ) { + show_modal( "Saving workflow", body, { "Ok" : hide_modal } ); + } else { + hide_modal(); + } } - workflow.name = data.name; - workflow.has_changes = false; - workflow.stored = true; - if ( success_callback ) { - success_callback(); - } - if ( data.errors ) { - show_modal( "Saving workflow", body, { "Ok" : hide_modal } ); - } else { - hide_modal(); - } - } + }); + $(document).unbind('ajaxStop.save_workflow'); // IE7 needs it here }); } @@ -642,7 +683,7 @@ <div id="canvas-viewport" style="width: 100%; height: 100%; position: absolute; overflow: hidden; background: #EEEEEE; background: white url(${h.url_for('/static/images/light_gray_grid.gif')}) repeat;"> <div id="canvas-container" style="position: absolute; width: 100%; height: 100%;"></div> </div> - <div id="overview-border" style="position: absolute; width: 150px; height: 150px; right: 0px; bottom: 0px; border-top: solid gray 1px; border-left: solid grey 1px; padding: 7px 0 0 7px; background: #EEEEEE no-repeat url(${h.url_for('/static/images/resizable.png')}); z-index: 20000; overflow: hidden; max-width: 300px; max-height: 300px; min-width: 50px; min-height: 50px"> + <div id="overview-border" style="position: absolute; width: 150px; height: 150px; right: 20000px; bottom: 0px; border-top: solid gray 1px; border-left: solid grey 1px; padding: 7px 0 0 7px; background: #EEEEEE no-repeat url(${h.url_for('/static/images/resizable.png')}); z-index: 20000; overflow: hidden; max-width: 300px; max-height: 300px; min-width: 50px; min-height: 50px"> <div style="position: relative; overflow: hidden; width: 100%; height: 100%; border-top: solid gray 1px; border-left: solid grey 1px;"> <div id="overview" style="position: absolute;"> <canvas width="0" height="0" style="background: white; width: 100%; height: 100%;" id="overview-canvas"></canvas> @@ -650,7 +691,7 @@ </div> </div> </div> - <div id="close-viewport" style="border-left: 1px solid #999; border-top: 1px solid #999; background: #ddd url(${h.url_for('/static/images/overview_arrows.png')}); position: absolute; right: 0px; bottom: 0px; width: 12px; height: 12px; z-index: 25000;"></div> + <div id="close-viewport" style="border-left: 1px solid #999; border-top: 1px solid #999; background: #ddd url(${h.url_for('/static/images/overview_arrows.png')}) 12px 0px; position: absolute; right: 0px; bottom: 0px; width: 12px; height: 12px; z-index: 25000;"></div> </div> </%def> diff -r 7d48dc7e60b4 -r 3353b15d0fb5 templates/workflow/editor_generic_form.mako --- a/templates/workflow/editor_generic_form.mako Wed Aug 19 11:08:58 2009 -0400 +++ b/templates/workflow/editor_generic_form.mako Wed Aug 19 17:51:46 2009 -0400 @@ -15,7 +15,7 @@ ${input.label}: </label> <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="${input.type}" name="${input.name}" value="${input.value}" size="40"> + <input type="${input.type}" name="${input.name | h}" value="${input.value | h}" size="30"> </div> %if input.error: <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;"> @@ -33,11 +33,14 @@ </div> %endfor - <div class="form-row"><input type="submit" value="${form.submit_text}"></div> %else: <div class="form-row"><i>No options</i></div> %endif </table> </form> </div> -</div> \ No newline at end of file +</div> + +<script type="text/javascript"> + workflow.enable_auto_save(); +</script> diff -r 7d48dc7e60b4 -r 3353b15d0fb5 templates/workflow/editor_tool_form.mako --- a/templates/workflow/editor_tool_form.mako Wed Aug 19 11:08:58 2009 -0400 +++ b/templates/workflow/editor_tool_form.mako Wed Aug 19 17:51:46 2009 -0400 @@ -93,7 +93,7 @@ <div style="clear: both"></div> </div> </%def> - + <div class="toolForm"> <div class="toolFormTitle">Tool: ${tool.name}</div> <div class="toolFormBody"> @@ -105,9 +105,11 @@ %endif ${do_inputs( inputs, values, errors, "" )} %endfor - <div class="form-row"> - <input type="submit" id="tool-form-save-button" value="Save"></input> - </div> </form> </div> -</div> \ No newline at end of file +</div> + +<script type="text/javascript"> + workflow.enable_auto_save(); +</script> + diff -r 7d48dc7e60b4 -r 3353b15d0fb5 tools/new_operations/cluster.xml --- a/tools/new_operations/cluster.xml Wed Aug 19 11:08:58 2009 -0400 +++ b/tools/new_operations/cluster.xml Wed Aug 19 17:51:46 2009 -0400 @@ -74,7 +74,7 @@ **Syntax** - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered "clustered". **Negative** values for distance are allowed, and are useful for clustering intervals that overlap. -- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the ouput. +- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the output. - **Merge clusters into single intervals** outputs intervals that span the entire cluster. - **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file. - **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost.

1 0

[hg] galaxy 2578: Fix workflow layout
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e9d70dca2ff5 changeset: 2578:e9d70dca2ff5 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Aug 19 11:33:48 2009 -0400 description: Fix workflow layout 1 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js diffs (12 lines): diff -r 5b6146705e80 -r e9d70dca2ff5 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Aug 13 13:44:04 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 19 11:33:48 2009 -0400 @@ -502,7 +502,7 @@ var v = level_parents[k]; delete n_pred[v]; for ( var sk in successors[v] ) { - n_pred[ sucessors[v][sk] ] -= 1; + n_pred[ successors[v][sk] ] -= 1; } } }

1 0

[hg] galaxy 2579: Typo
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c5968ee9399b changeset: 2579:c5968ee9399b user: Kanwei Li <kanwei(a)gmail.com> date: Wed Aug 19 11:33:58 2009 -0400 description: Typo 1 file(s) affected in this change: tools/new_operations/cluster.xml diffs (12 lines): diff -r e9d70dca2ff5 -r c5968ee9399b tools/new_operations/cluster.xml --- a/tools/new_operations/cluster.xml Wed Aug 19 11:33:48 2009 -0400 +++ b/tools/new_operations/cluster.xml Wed Aug 19 11:33:58 2009 -0400 @@ -74,7 +74,7 @@ **Syntax** - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered "clustered". **Negative** values for distance are allowed, and are useful for clustering intervals that overlap. -- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the ouput. +- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the output. - **Merge clusters into single intervals** outputs intervals that span the entire cluster. - **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file. - **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost.

1 0

[hg] galaxy 2580: Auto-save for workflow forms
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ea6708c96cd1 changeset: 2580:ea6708c96cd1 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Aug 19 17:27:00 2009 -0400 description: Auto-save for workflow forms 5 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js static/scripts/packed/galaxy.workflow_editor.canvas.js templates/workflow/editor.mako templates/workflow/editor_generic_form.mako templates/workflow/editor_tool_form.mako diffs (215 lines): diff -r c5968ee9399b -r ea6708c96cd1 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 19 11:33:58 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 19 17:27:00 2009 -0400 @@ -359,6 +359,7 @@ this.nodes = {}; this.name = null; this.has_changes = false; + this.active_form_has_changes = false; } $.extend( Workflow.prototype, { add_node : function( node ) { @@ -438,6 +439,28 @@ }); }); }, + enable_auto_save : function() { + // Implements auto-saving based on whether the inputs change. We consider + // "changed" to be when a field is accessed and not necessarily modified + // because of an issue where "onchange" is not triggered when activating + // another node, or saving the workflow. + outer_this = this; + $(".toolFormBody").find("input,textarea,select").each( function() { + $(this).focus( function() { + outer_this.active_form_has_changes = true; + }); + }); + }, + check_changes_in_active_form : function() { + // If active form has changed, save it + if (this.active_form_has_changes) { + this.has_changes = true; + $(".toolFormBody").find("form").each( function() { + $(this).submit(); + }); + this.active_form_has_changes = false; + } + }, clear_active_node : function() { if ( this.active_node ) { this.active_node.make_inactive(); @@ -447,6 +470,7 @@ }, activate_node : function( node ) { if ( this.active_node != node ) { + this.check_changes_in_active_form(); this.clear_active_node(); parent.show_form_for_tool( node.form_html, node ); node.make_active(); @@ -461,6 +485,7 @@ } }, layout : function () { + this.check_changes_in_active_form(); // Prepare predecessor / successor tracking var n_pred = {}; var successors = {}; diff -r c5968ee9399b -r ea6708c96cd1 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Aug 19 11:33:58 2009 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Wed Aug 19 17:27:00 2009 -0400 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.ha ndle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_ form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[sucessors[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$( this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prot otype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this; var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({wi dth:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRe ct(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connecto rs,function(j,k){f[h.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},enable_auto_save:function(){outer_this=this;$(".toolFormBody").find("input,textarea,select").each(function(){$(this).focus(function(){outer_this.active_form_has_changes=true})})},check_changes_in_active_form:functio n(){if(this.active_form_has_changes){this.has_changes=true;$(".toolFormBody").find("form").each(function(){$(this).submit()});this.active_form_has_changes=false}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){this.check_changes_in_active_form();var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){l evel_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this .canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></d iv>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this). offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.c ss("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_n odes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r c5968ee9399b -r ea6708c96cd1 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Wed Aug 19 11:33:58 2009 -0400 +++ b/templates/workflow/editor.mako Wed Aug 19 17:27:00 2009 -0400 @@ -282,10 +282,6 @@ beforeSubmit: function( data ) { data.push( { name: 'tool_state', value: node.tool_state } ); data.push( { name: '_', value: "true" } ); - $("#tool-form-save-button").each( function() { - this.value = "Saving..."; - this.disabled = true; - }); } }).each( function() { form = this; @@ -312,6 +308,7 @@ var close_editor = function() { <% next_url = h.url_for( controller='workflow', action='index' ) %> + workflow.check_changes_in_active_form(); if ( workflow && workflow.has_changes ) { do_close = function() { window.onbeforeunload = undefined; @@ -334,39 +331,46 @@ var save_current_workflow = function ( success_callback ) { show_modal( "Saving workflow", "progress" ); - $.ajax( { - url: "${h.url_for( action='save_workflow' )}", - type: "POST", - data: { - id: "${trans.security.encode_id( workflow_id )}", - workflow_data: $.toJSON( workflow.to_simple() ), - "_": "true" - }, - dataType: 'json', - success: function( data ) { - var body = $("<div></div>").text( data.message ); - if ( data.errors ) { - body.addClass( "warningmark" ) - var errlist = $( "<ul/>" ); - $.each( data.errors, function( i, v ) { - $("<li></li>").text( v ).appendTo( errlist ); - }); - body.append( errlist ); - } else { - body.addClass( "donemark" ); + workflow.check_changes_in_active_form(); + // We bind to ajaxStop because of auto-saving, since the form submission ajax + // call needs to be completed so that the new data is saved + $(document).bind('ajaxStop.save_workflow', function() { + $(document).unbind('ajaxStop.save_workflow'); + $.ajax( { + url: "${h.url_for( action='save_workflow' )}", + type: "POST", + data: { + id: "${trans.security.encode_id( workflow_id )}", + workflow_data: function() { return $.toJSON( workflow.to_simple() ) }, + "_": "true" + }, + dataType: 'json', + success: function( data ) { + var body = $("<div></div>").text( data.message ); + if ( data.errors ) { + body.addClass( "warningmark" ) + var errlist = $( "<ul/>" ); + $.each( data.errors, function( i, v ) { + $("<li></li>").text( v ).appendTo( errlist ); + }); + body.append( errlist ); + } else { + body.addClass( "donemark" ); + } + workflow.name = data.name; + workflow.has_changes = false; + workflow.stored = true; + if ( success_callback ) { + success_callback(); + } + if ( data.errors ) { + show_modal( "Saving workflow", body, { "Ok" : hide_modal } ); + } else { + hide_modal(); + } } - workflow.name = data.name; - workflow.has_changes = false; - workflow.stored = true; - if ( success_callback ) { - success_callback(); - } - if ( data.errors ) { - show_modal( "Saving workflow", body, { "Ok" : hide_modal } ); - } else { - hide_modal(); - } - } + }); + $(document).unbind('ajaxStop.save_workflow'); // IE7 needs it here }); } diff -r c5968ee9399b -r ea6708c96cd1 templates/workflow/editor_generic_form.mako --- a/templates/workflow/editor_generic_form.mako Wed Aug 19 11:33:58 2009 -0400 +++ b/templates/workflow/editor_generic_form.mako Wed Aug 19 17:27:00 2009 -0400 @@ -33,11 +33,14 @@ </div> %endfor - <div class="form-row"><input type="submit" value="${form.submit_text}"></div> %else: <div class="form-row"><i>No options</i></div> %endif </table> </form> </div> -</div> \ No newline at end of file +</div> + +<script type="text/javascript"> + workflow.enable_auto_save(); +</script> diff -r c5968ee9399b -r ea6708c96cd1 templates/workflow/editor_tool_form.mako --- a/templates/workflow/editor_tool_form.mako Wed Aug 19 11:33:58 2009 -0400 +++ b/templates/workflow/editor_tool_form.mako Wed Aug 19 17:27:00 2009 -0400 @@ -93,7 +93,7 @@ <div style="clear: both"></div> </div> </%def> - + <div class="toolForm"> <div class="toolFormTitle">Tool: ${tool.name}</div> <div class="toolFormBody"> @@ -105,9 +105,11 @@ %endif ${do_inputs( inputs, values, errors, "" )} %endfor - <div class="form-row"> - <input type="submit" id="tool-form-save-button" value="Save"></input> - </div> </form> </div> -</div> \ No newline at end of file +</div> + +<script type="text/javascript"> + workflow.enable_auto_save(); +</script> +

1 0

[hg] galaxy 2577: Merge trunk
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5b6146705e80 changeset: 2577:5b6146705e80 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Aug 13 13:44:04 2009 -0400 description: Merge trunk 14 file(s) affected in this change: templates/admin/library/create_info_template.mako templates/admin/library/edit_info_template.mako templates/admin/library/info_permissions.mako templates/admin/library/info_template_permissions.mako templates/admin/library/new_info.mako templates/admin/library/new_info_template.mako templates/history/grid.mako templates/history/list_shared.mako templates/library/create_info_template.mako templates/library/edit_info_template.mako templates/library/info_permissions.mako templates/library/info_template_permissions.mako templates/library/new_info.mako templates/library/new_info_template.mako diffs (truncated from 7699 to 3000 lines): diff -r f1f2d1de5f3e -r 5b6146705e80 cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample Thu Aug 13 13:43:25 2009 -0400 +++ b/cron/updateucsc.sh.sample Thu Aug 13 13:44:04 2009 -0400 @@ -9,8 +9,20 @@ export PYTHONPATH=${GALAXY}/lib # setup directories -mkdir ${GALAXY}/tool-data/shared/ucsc/new -mkdir ${GALAXY}/tool-data/shared/ucsc/chrom/new +echo "Creating required directories." +DIRS=" +${GALAXY}/tool-data/shared/ucsc/new +${GALAXY}/tool-data/shared/ucsc/chrom +${GALAXY}/tool-data/shared/ucsc/chrom/new +" +for dir in $DIRS; do + if [ ! -d $dir ]; then + echo "Creating $dir" + mkdir $dir + else + echo "$dir already exists, continuing." + fi +done date echo "Updating UCSC shared data tables." diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/app.py --- a/lib/galaxy/app.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/app.py Thu Aug 13 13:44:04 2009 -0400 @@ -37,6 +37,8 @@ self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self ) # Load datatype converters self.datatypes_registry.load_datatype_converters( self.toolbox ) + #load external metadata tool + self.datatypes_registry.load_external_metadata_tool( self.toolbox ) # Load datatype indexers self.datatypes_registry.load_datatype_indexers( self.toolbox ) #Load security policy diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,7 +1,7 @@ """ Provides mapping between extensions and datatypes, mime-types, etc. """ -import os +import os, tempfile import logging import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo import galaxy.util @@ -18,6 +18,7 @@ self.datatype_converters = odict() self.datatype_indexers = odict() self.converters = [] + self.set_external_metadata_tool = None self.indexers = [] self.sniff_order = [] self.upload_file_formats = [] @@ -251,6 +252,31 @@ self.datatype_converters[source_datatype][target_datatype] = converter self.log.debug( "Loaded converter: %s", converter.id ) + def load_external_metadata_tool( self, toolbox ): + """Adds a tool which is used to set external metadata""" + #we need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated tool. + #We'll create a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective + #Properly building a tool without relying on parsing an XML file is near impossible...so we'll create a temporary file + tool_xml_text = """ + <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.0" tool_type="set_metadata"> + <type class="SetMetadataTool" module="galaxy.tools"/> + <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/> + <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command> + <inputs> + <param format="data" name="input1" type="data" label="File to set metadata on."/> + <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/> + <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/> + </inputs> + </tool> + """ + tmp_name = tempfile.NamedTemporaryFile() + tmp_name.write( tool_xml_text ) + tmp_name.flush() + set_meta_tool = toolbox.load_tool( tmp_name.name ) + toolbox.tools_by_id[ set_meta_tool.id ] = set_meta_tool + self.set_external_metadata_tool = set_meta_tool + self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id ) + def load_datatype_indexers( self, toolbox ): """Adds indexers from self.indexers to the toolbox from app""" for elem in self.indexers: diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/datatypes/sequence.py Thu Aug 13 13:44:04 2009 -0400 @@ -334,28 +334,37 @@ """ #these metadata values are not accessable by users, always overwrite + try: + maf_reader = bx.align.maf.Reader( open( dataset.file_name ) ) + except: + return #not a maf file species = [] species_chromosomes = {} indexes = bx.interval_index_file.Indexes() - try: - maf_reader = bx.align.maf.Reader( open( dataset.file_name ) ) - while True: - pos = maf_reader.file.tell() - block = maf_reader.next() - if block is None: break - for c in block.components: - spec = c.src - chrom = None - if "." in spec: - spec, chrom = spec.split( ".", 1 ) - if spec not in species: - species.append(spec) - species_chromosomes[spec] = [] - if chrom and chrom not in species_chromosomes[spec]: - species_chromosomes[spec].append( chrom ) - indexes.add( c.src, c.forward_strand_start, c.forward_strand_end, pos, max=c.src_size ) - except: #bad MAF file - pass + while True: + pos = maf_reader.file.tell() + block = maf_reader.next() + if block is None: break + for c in block.components: + spec = c.src + chrom = None + if "." in spec: + spec, chrom = spec.split( ".", 1 ) + if spec not in species: + species.append(spec) + species_chromosomes[spec] = [] + if chrom and chrom not in species_chromosomes[spec]: + species_chromosomes[spec].append( chrom ) + forward_strand_start = c.forward_strand_start + forward_strand_end = c.forward_strand_end + try: + forward_strand_start = int( forward_strand_start ) + forward_strand_end = int( forward_strand_end ) + except ValueError: + continue #start and end are not integers, can't add component to index, goto next component + if forward_strand_end > forward_strand_start: + #require positive length; i.e. certain lines have start = end = 0 and cannot be indexed + indexes.add( c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size ) dataset.metadata.species = species #only overwrite the contents if our newly determined chromosomes don't match stored chrom_file = dataset.metadata.species_chromosomes diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Aug 13 13:44:04 2009 -0400 @@ -274,7 +274,7 @@ elif idata.state == idata.states.ERROR: job_wrapper.fail( "input data %d is in error state" % ( idata.hid ) ) return JOB_INPUT_ERROR - elif idata.state != idata.states.OK: + elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ): # need to requeue return JOB_WAIT return JOB_READY @@ -543,7 +543,7 @@ # Certain tools require tasks to be completed after job execution # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ). if self.tool.tool_type is not None: - self.tool.exec_after_process( self.queue.app, inp_data, out_data, param_dict ) + self.tool.exec_after_process( self.queue.app, inp_data, out_data, param_dict, job = job ) # Call 'exec_after_process' hook self.tool.call_hook( 'exec_after_process', self.queue.app, inp_data=inp_data, out_data=out_data, param_dict=param_dict, diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/jobs/runners/local.py Thu Aug 13 13:44:04 2009 -0400 @@ -104,7 +104,7 @@ #run the metadata setting script here #this is terminatable when output dataset/job is deleted #so that long running set_meta()s can be cancelled without having to reboot the server - if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and self.app.config.set_metadata_externally: + if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and self.app.config.set_metadata_externally and job_wrapper.output_paths: external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) external_metadata_proc = subprocess.Popen( args = external_metadata_script, diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/__init__.py Thu Aug 13 13:44:04 2009 -0400 @@ -310,30 +310,6 @@ raise "Invalid LibraryDatasetDatasetAssociation specified: %s" % library_item.__class__.__name__ self.role = role -class LibraryItemInfoPermissions( object ): - def __init__( self, action, library_item, role ): - # LIBRARY_ADD -> Not Applicable - # LIBRARY_MODIFY -> Can modify LibraryItemInfoElement.contents - # LIBRARY_MANAGE -> Can change permissions on LibraryItemInfo - self.action = action - if isinstance( library_item, LibraryItemInfo ): - self.library_item_info = library_item - else: - raise "Invalid LibraryItemInfo specified: %s" % library_item.__class__.__name__ - self.role = role - -class LibraryItemInfoTemplatePermissions( object ): - def __init__( self, action, library_item, role ): - # LIBRARY_ADD -> Not Applicable - # LIBRARY_MODIFY -> Can add or delete LibraryItemInfoTemplateElements - # LIBRARY_MANAGE -> Can change permissions on LibraryItemInfoTemplate - self.action = action - if isinstance( library_item, LibraryItemInfoTemplate ): - self.library_item_info_template = library_item - else: - raise "Invalid LibraryItemInfoTemplate specified: %s" % library_item.__class__.__name__ - self.role = role - class DefaultUserPermissions( object ): def __init__( self, user, action, role ): self.user = user @@ -354,7 +330,8 @@ OK = 'ok', EMPTY = 'empty', ERROR = 'error', - DISCARDED = 'discarded' ) + DISCARDED = 'discarded', + SETTING_METADATA = 'setting_metadata' ) permitted_actions = get_permitted_actions( filter='DATASET' ) file_path = "/tmp/" engine = None @@ -701,12 +678,10 @@ self.name = name or "Unnamed library" self.description = description self.root_folder = root_folder - def get_library_item_info_templates( self, template_list=[], restrict=False ): - # We only want the next available template in the inheritable hierarchy, so we'll only extend - # template_list if it is empty - if not template_list and self.library_info_template_associations: - template_list.extend( [ lita.library_item_info_template for lita in self.library_info_template_associations if lita.library_item_info_template not in template_list ] ) - return template_list + def get_info_association( self, restrict=False ): + if self.info_association: + return self.info_association[0] + return None class LibraryFolder( object ): def __init__( self, name=None, description=None, item_count=0, order_id=None ): @@ -725,18 +700,19 @@ folder.parent_id = self.id folder.order_id = self.item_count self.item_count += 1 - def get_library_item_info_templates( self, template_list=[], restrict=False ): - # If restrict is True, we'll return only those templates directly associated with this Folder - # We only want the next available template in the inheritable hierarchy, so we'll only extend - # template_list if it is empty - if not template_list and self.library_folder_info_template_associations: - template_list.extend( [ lfita.library_item_info_template for lfita in self.library_folder_info_template_associations if lfita.library_item_info_template not in template_list ] ) - if not template_list and restrict not in [ 'True', True ] and self.parent: - self.parent.get_library_item_info_templates( template_list ) - elif not template_list and restrict not in [ 'True', True, 'folder' ] and self.library_root: - for library_root in self.library_root: - library_root.get_library_item_info_templates( template_list ) - return template_list + def get_info_association( self, restrict=False ): + # If restrict is True, we will return this folder's info_association whether it + # exists or not. If restrict is False, we'll return the next available info_association + # in the inheritable hierarchy + if self.info_association: + return self.info_association[0] + if restrict: + return None + if self.parent: + return self.parent.get_info_association() + if self.library_root: + return self.library_root[0].get_info_association() + return None @property def active_components( self ): return list( self.active_folders ) + list( self.active_datasets ) @@ -796,15 +772,6 @@ if not purged and self.purged: raise Exception( "Cannot unpurge once purged" ) purged = property( get_purged, set_purged ) - def get_library_item_info_templates( self, template_list=[], restrict=False ): - # If restrict is True, we'll return only those templates directly associated with this LibraryDataset - # We only want the next available template in the inheritable hierarchy, so we'll only extend - # template_list if it is empty - if not template_list and self.library_dataset_info_template_associations: - template_list.extend( [ ldita.library_item_info_template for ldita in self.library_dataset_info_template_associations if ldita.library_item_info_template not in template_list ] ) - if not template_list and restrict not in [ 'True', True ]: - self.folder.get_library_item_info_templates( template_list, restrict ) - return template_list class LibraryDatasetDatasetAssociation( DatasetInstance ): def __init__( self, @@ -867,105 +834,34 @@ return ldda def clear_associated_files( self, metadata_safe = False, purge = False ): return - def get_library_item_info_templates( self, template_list=[], restrict=False ): - # If restrict is True, we'll return only those templates directly associated with this LibraryDatasetDatasetAssociation - # We only want the next available template in the inheritable hierarchy, so we'll only extend - # template_list if it is empty - if not template_list and self.library_dataset_dataset_info_template_associations: - template_list.extend( [ lddita.library_item_info_template for lddita in self.library_dataset_dataset_info_template_associations if lddita.library_item_info_template not in template_list ] ) - if not template_list: - self.library_dataset.get_library_item_info_templates( template_list, restrict ) - return template_list - -class LibraryInfoTemplateAssociation( object ): - pass - -class LibraryFolderInfoTemplateAssociation( object ): - pass - -class LibraryDatasetInfoTemplateAssociation( object ): - pass - -class LibraryDatasetDatasetInfoTemplateAssociation( object ): - pass - -class LibraryItemInfoTemplate( object ): - def add_element( self, element = None, name = None, description = None ): - if element: - raise "undefined" - else: - new_elem = LibraryItemInfoTemplateElement() - new_elem.name = name - new_elem.description = description - new_elem.order_id = self.item_count - self.item_count += 1 - self.flush() - new_elem.library_item_info_template_id = self.id - new_elem.flush() - return new_elem - -class LibraryItemInfoTemplateElement( object ): - pass + def get_info_association( self, restrict=False ): + # If restrict is True, we will return this ldda's info_association whether it + # exists or not. If restrict is False, we'll return the next available info_association + # in the inheritable hierarchy + if self.info_association: + return self.info_association[0] + if restrict: + return None + return self.library_dataset.folder.get_info_association() class LibraryInfoAssociation( object ): - def __init__( self, user=None ): - self.user = user - def set_library_item( self, library_item ): - if isinstance( library_item, Library ): - self.library = library_item - else: - raise "Invalid Library specified: %s" % library_item.__class__.__name__ + def __init__( self, library, form_definition, info ): + self.library = library + self.template = form_definition + self.info = info class LibraryFolderInfoAssociation( object ): - def __init__( self, user=None ): - self.user = user - def set_library_item( self, library_item ): - if isinstance( library_item, LibraryFolder ): - self.folder = library_item - else: - raise "Invalid Library specified: %s" % library_item.__class__.__name__ - -class LibraryDatasetInfoAssociation( object ): - def __init__( self, user=None ): - self.user = user - def set_library_item( self, library_item ): - if isinstance( library_item, LibraryDataset ): - self.library_dataset = library_item - else: - raise "Invalid Library specified: %s" % library_item.__class__.__name__ + def __init__( self, folder, form_definition, info ): + self.folder = folder + self.template = form_definition + self.info = info class LibraryDatasetDatasetInfoAssociation( object ): - def __init__( self, user=None ): - self.user = user - def set_library_item( self, library_item ): - if isinstance( library_item, LibraryDatasetDatasetAssociation ): - self.library_dataset_dataset_association = library_item - else: - raise "Invalid Library specified: %s" % library_item.__class__.__name__ + def __init__( self, library_dataset_dataset_association, form_definition, info ): + self.library_dataset_dataset_association = library_dataset_dataset_association + self.template = form_definition + self.info = info -class LibraryItemInfo( object ): - def __init__( self, user=None ): - self.user = user - def get_element_by_template_element( self, template_element, create_element=False ): - for element in self.elements: - if element.library_item_info_template_element == template_element: - return element - if create_element: - # Template elements may have been added to the template after the - # library item initially inherited it, so we'll add the additional - # element to the library item - element = LibraryItemInfoElement() - element.library_item_info_template_element = template_element - element.library_item_info = self - element.flush() - self.elements.append( element ) - return element - else: - return None - -class LibraryItemInfoElement( object ): - pass - class ValidationError( object ): def __init__( self, message=None, err_type=None, attributes=None ): self.message = message @@ -1102,8 +998,7 @@ raise # Return filename inside hashed directory return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) ) - - + class FormDefinition( object ): def __init__(self, name=None, desc=None, fields=[], current_form=None): self.name = name diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/mapping.py Thu Aug 13 13:44:04 2009 -0400 @@ -216,22 +216,6 @@ Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) -LibraryItemInfoPermissions.table = Table( "library_item_info_permissions", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "action", TEXT ), - Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), nullable=True, index=True ), - Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) - -LibraryItemInfoTemplatePermissions.table = Table( "library_item_info_template_permissions", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "action", TEXT ), - Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), nullable=True, index=True ), - Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) - DefaultUserPermissions.table = Table( "default_user_permissions", metadata, Column( "id", Integer, primary_key=True ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), @@ -299,105 +283,23 @@ Column( "purged", Boolean, index=True, default=False ), Column( "genome_build", TrimmedString( 40 ) ) ) -LibraryItemInfoTemplateElement.table = Table( "library_item_info_template_element", metadata, +LibraryInfoAssociation.table = Table( 'library_info_association', metadata, Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "optional", Boolean, index=True, default=True ), - Column( "deleted", Boolean, index=True, default=False ), - Column( "name", TEXT ), - Column( "description", TEXT ), - Column( "type", TEXT, default='string' ), - Column( "order_id", Integer ), - Column( "options", JSONType() ), - Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), index=True ) ) - -LibraryItemInfoTemplate.table = Table( "library_item_info_template", metadata, + Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) + +LibraryFolderInfoAssociation.table = Table( 'library_folder_info_association', metadata, Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "optional", Boolean, index=True, default=True ), - Column( "deleted", Boolean, index=True, default=False ), - Column( "name", TEXT ), - Column( "description", TEXT ), - Column( "item_count", Integer, default=0 ) ) + Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) -LibraryInfoTemplateAssociation.table = Table( "library_info_template_association", metadata, +LibraryDatasetDatasetInfoAssociation.table = Table( 'library_dataset_dataset_info_association', metadata, Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ), - Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), index=True ) ) - -LibraryFolderInfoTemplateAssociation.table = Table( "library_folder_info_template_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), - Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), index=True ) ) - -LibraryDatasetInfoTemplateAssociation.table = Table( "library_dataset_info_template_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ), - Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), index=True ) ) - -LibraryDatasetDatasetInfoTemplateAssociation.table = Table( "library_dataset_dataset_info_template_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), - Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), index=True ) ) - -LibraryItemInfoElement.table = Table( "library_item_info_element", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "contents", JSONType() ), - Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), - Column( "library_item_info_template_element_id", Integer, ForeignKey( "library_item_info_template_element.id" ), index=True ) ) - -LibraryItemInfo.table = Table( "library_item_info", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "deleted", Boolean, index=True, default=False ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ), - Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), nullable=True, index=True ) - ) - -LibraryInfoAssociation.table = Table( "library_info_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ), - Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) - -LibraryFolderInfoAssociation.table = Table( "library_folder_info_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), - Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) - -LibraryDatasetInfoAssociation.table = Table( "library_dataset_info_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ), - Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) - -LibraryDatasetDatasetInfoAssociation.table = Table( "library_dataset_dataset_info_association", metadata, - Column( "id", Integer, primary_key=True ), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), - Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), - Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) Job.table = Table( "job", metadata, Column( "id", Integer, primary_key=True ), @@ -545,7 +447,6 @@ Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) - FormDefinitionCurrent.table = Table('form_definition_current', metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), @@ -553,20 +454,17 @@ Column( "latest_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), Column( "deleted", Boolean, index=True, default=False )) -# new table to store all the forms which is created by the admin FormDefinition.table = Table('form_definition', metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), nullable=False ), Column( "desc", TEXT ), - Column( "form_definition_current_id", + Column( "form_definition_current_id", Integer, - ForeignKey( "form_definition_current.id", - name='for_def_form_def_current_id_fk', - use_alter=True), + ForeignKey( "form_definition_current.id", name='for_def_form_def_current_id_fk', use_alter=True ), index=True ), - Column( "fields", JSONType())) + Column( "fields", JSONType() ) ) RequestType.table = Table('request_type', metadata, Column( "id", Integer, primary_key=True), @@ -598,15 +496,8 @@ Column( "state", TrimmedString( 255 ), index=True ), Column( "deleted", Boolean, index=True, default=False ) ) -RequestState_table = Table('request_state', metadata, - Column( "id", Integer, primary_key=True), - Column( "create_time", DateTime, default=now ), - Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "name", TrimmedString( 255 ), nullable=False ), - Column( "desc", TEXT )) - Sample.table = Table('sample', metadata, - Column( "id", Integer, primary_key=True), + Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), nullable=False ), @@ -616,10 +507,8 @@ Column( "bar_code", TrimmedString( 255 ), index=True ), Column( "deleted", Boolean, index=True, default=False ) ) -# new table to store all the possible sample states and the sample type it -# belongs to SampleState.table = Table('sample_state', metadata, - Column( "id", Integer, primary_key=True), + Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "name", TrimmedString( 255 ), nullable=False ), @@ -627,14 +516,12 @@ Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) ) SampleEvent.table = Table('sample_event', metadata, - Column( "id", Integer, primary_key=True), + Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), Column( "comment", TEXT ) ) - - # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -652,7 +539,8 @@ assign_mapper( context, FormValues, FormValues.table, properties=dict( form_definition=relation( FormDefinition, primaryjoin=( FormValues.table.c.form_definition_id == FormDefinition.table.c.id ) ) - ) ) + ) +) assign_mapper( context, Request, Request.table, properties=dict( values=relation( FormValues, @@ -863,25 +751,20 @@ ) ) -assign_mapper( context, LibraryItemInfoPermissions, LibraryItemInfoPermissions.table, +assign_mapper( context, Library, Library.table, properties=dict( - library_item_info = relation( LibraryItemInfo, backref="actions" ), - role=relation( Role, backref="library_item_info_actions" ) - ) + root_folder=relation( LibraryFolder, backref=backref( "library_root" ) ) + ) ) -assign_mapper( context, LibraryItemInfoTemplatePermissions, LibraryItemInfoTemplatePermissions.table, - properties=dict( - library_item_info_template = relation( LibraryItemInfoTemplate, backref="actions" ), - role=relation( Role, backref="library_item_info_template_actions" ) - ) -) - -assign_mapper( context, Library, Library.table, - properties=dict( - root_folder=relation( LibraryFolder, - backref=backref( "library_root" ) ) - ) ) +assign_mapper( context, LibraryInfoAssociation, LibraryInfoAssociation.table, + properties=dict( library=relation( Library, + primaryjoin=( LibraryInfoAssociation.table.c.library_id == Library.table.c.id ), backref="info_association" ), + template=relation( FormDefinition, + primaryjoin=( LibraryInfoAssociation.table.c.form_definition_id == FormDefinition.table.c.id ) ), + info=relation( FormValues, + primaryjoin=( LibraryInfoAssociation.table.c.form_values_id == FormValues.table.c.id ) ) + ) ) assign_mapper( context, LibraryFolder, LibraryFolder.table, properties=dict( @@ -900,6 +783,15 @@ lazy=False, viewonly=True ) ) ) + +assign_mapper( context, LibraryFolderInfoAssociation, LibraryFolderInfoAssociation.table, + properties=dict( folder=relation( LibraryFolder, + primaryjoin=( LibraryFolderInfoAssociation.table.c.library_folder_id == LibraryFolder.table.c.id ), backref="info_association" ), + template=relation( FormDefinition, + primaryjoin=( LibraryFolderInfoAssociation.table.c.form_definition_id == FormDefinition.table.c.id ) ), + info=relation( FormValues, + primaryjoin=( LibraryFolderInfoAssociation.table.c.form_values_id == FormValues.table.c.id ) ) + ) ) assign_mapper( context, LibraryDataset, LibraryDataset.table, properties=dict( @@ -931,65 +823,14 @@ primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ) ) ) -assign_mapper( context, LibraryItemInfoTemplateElement, LibraryItemInfoTemplateElement.table, - properties=dict( library_item_info_template=relation( LibraryItemInfoTemplate, backref="elements" ), - ) ) - -assign_mapper( context, LibraryItemInfoTemplate, LibraryItemInfoTemplate.table ) - -assign_mapper( context, LibraryInfoTemplateAssociation, LibraryInfoTemplateAssociation.table, - properties=dict( library=relation( Library, backref="library_info_template_associations" ), - library_item_info_template = relation( LibraryItemInfoTemplate, backref="library_info_template_associations" ), - ) ) - -assign_mapper( context, LibraryFolderInfoTemplateAssociation, LibraryFolderInfoTemplateAssociation.table, - properties=dict( folder=relation( LibraryFolder, backref="library_folder_info_template_associations" ), - library_item_info_template = relation( LibraryItemInfoTemplate, backref="library_folder_info_template_associations" ), - ) ) - -assign_mapper( context, LibraryDatasetInfoTemplateAssociation, LibraryDatasetInfoTemplateAssociation.table, - properties=dict( library_dataset=relation( LibraryDataset, backref="library_dataset_info_template_associations" ), - library_item_info_template = relation( LibraryItemInfoTemplate, backref="library_dataset_info_template_associations" ), - ) ) - -assign_mapper( context, LibraryDatasetDatasetInfoTemplateAssociation, LibraryDatasetDatasetInfoTemplateAssociation.table, - properties=dict( library_dataset_dataset_association = relation( LibraryDatasetDatasetAssociation, backref="library_dataset_dataset_info_template_associations" ), - library_item_info_template = relation( LibraryItemInfoTemplate, backref="library_dataset_dataset_info_template_associations" ), - ) ) - -assign_mapper( context, LibraryItemInfoElement, LibraryItemInfoElement.table, - properties=dict( library_item_info=relation( LibraryItemInfo, backref="elements" ), - library_item_info_template_element=relation( LibraryItemInfoTemplateElement ) - ) ) - -assign_mapper( context, LibraryItemInfo, LibraryItemInfo.table, - properties=dict( library_item_info_template=relation( LibraryItemInfoTemplate, backref="library_item_infos" ), - user=relation( User.mapper ) - ) ) - -assign_mapper( context, LibraryInfoAssociation, LibraryInfoAssociation.table, - properties=dict( library=relation( Library, backref="library_info_associations" ), - library_item_info = relation( LibraryItemInfo, backref="library_info_associations" ), - user=relation( User.mapper ) - ) ) - -assign_mapper( context, LibraryFolderInfoAssociation, LibraryFolderInfoAssociation.table, - properties=dict( folder=relation( LibraryFolder, backref="library_folder_info_associations" ), - library_item_info = relation( LibraryItemInfo, backref="library_folder_info_associations" ), - user=relation( User.mapper ) - ) ) - -assign_mapper( context, LibraryDatasetInfoAssociation, LibraryDatasetInfoAssociation.table, - properties=dict( library_dataset=relation( LibraryDataset, backref="library_dataset_info_associations" ), - library_item_info = relation( LibraryItemInfo, backref="library_dataset_info_associations" ), - user=relation( User.mapper ) - ) ) - assign_mapper( context, LibraryDatasetDatasetInfoAssociation, LibraryDatasetDatasetInfoAssociation.table, - properties=dict( library_dataset_dataset_association = relation( LibraryDatasetDatasetAssociation, backref="library_dataset_dataset_info_associations" ), - library_item_info = relation( LibraryItemInfo, backref="library_dataset_dataset_info_associations" ), - user=relation( User.mapper ) - ) ) + properties=dict( library_dataset_dataset_association=relation( LibraryDatasetDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetInfoAssociation.table.c.library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), backref="info_association" ), + template=relation( FormDefinition, + primaryjoin=( LibraryDatasetDatasetInfoAssociation.table.c.form_definition_id == FormDefinition.table.c.id ) ), + info=relation( FormValues, + primaryjoin=( LibraryDatasetDatasetInfoAssociation.table.c.form_values_id == FormValues.table.c.id ) ) + ) ) assign_mapper( context, JobToInputDatasetAssociation, JobToInputDatasetAssociation.table, properties=dict( job=relation( Job ), dataset=relation( HistoryDatasetAssociation, lazy=False ) ) ) diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py --- a/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,3 +1,7 @@ +""" +This migration script changes certain values in the history_dataset_association.extension +column, specifically 'qual' is chaged to be 'qual454'. +""" from sqlalchemy import * from sqlalchemy.orm import * from migrate import * @@ -13,9 +17,17 @@ metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) + +def display_migration_details(): + print "========================================" + print "This migration script changes certain values in the history_dataset_association.extension" + print "column, specifically 'qual' is chaged to be 'qual454'." + print "========================================" + HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) - + def upgrade(): + display_migration_details() # Load existing tables metadata.reflect() # Add 2 indexes to the galaxy_user table @@ -42,6 +54,5 @@ except Exception, e: log.debug( "Dropping index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) ) - def downgrade(): pass diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0007_sharing_histories.py --- a/lib/galaxy/model/migrate/versions/0007_sharing_histories.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0007_sharing_histories.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,3 +1,8 @@ +""" +This migration script creates the new history_user_share_association table, and adds +a new boolean type column to the history table. This provides support for sharing +histories in the same way that workflows are shared. +""" from sqlalchemy import * from sqlalchemy.orm import * from migrate import * @@ -14,6 +19,13 @@ metadata = MetaData( migrate_engine ) +def display_migration_details(): + print "========================================" + print "This migration script creates the new history_user_share_association table, and adds" + print "a new boolean type column to the history table. This provides support for sharing" + print "histories in the same way that workflows are shared." + print "========================================" + HistoryUserShareAssociation_table = Table( "history_user_share_association", metadata, Column( "id", Integer, primary_key=True ), Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), @@ -21,6 +33,7 @@ ) def upgrade(): + display_migration_details() # Load existing tables metadata.reflect() # Create the history_user_share_association table diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0008_galaxy_forms.py --- a/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0008_galaxy_forms.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,3 +1,14 @@ +""" +This migration script adds the following new tables for supporting Galaxy forms: +1) form_definition_current +2) form_definition +3) form_values +4) request_type +5) request +6) sample +7) sample_state +8) sample_event +""" from sqlalchemy import * from sqlalchemy.orm import * from sqlalchemy.exceptions import * @@ -22,15 +33,26 @@ metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +def display_migration_details(): + print "========================================" + print "This migration script adds the following new tables for supporting Galaxy forms:" + print "1) form_definition_current" + print "2) form_definition" + print "3) form_values" + print "4) request_type" + print "5) request" + print "6) sample" + print "7) sample_state" + print "8) sample_event" + print "========================================" FormDefinitionCurrent_table = Table('form_definition_current', metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), - Column( "latest_form_id", Integer, - #ForeignKey( "form_definition.id", use_alter=True, name='form_definition_current_latest_form_id_fk'), - index=True ), + Column( "latest_form_id", Integer, index=True ), Column( "deleted", Boolean, index=True, default=False )) + FormDefinition_table = Table('form_definition', metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), @@ -55,7 +77,7 @@ Column( "desc", TEXT ), Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ), Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ) ) -# request table + Request_table = Table('request', metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), @@ -94,13 +116,10 @@ Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ), Column( "comment", TEXT ) ) - - - def upgrade(): + display_migration_details() # Load existing tables metadata.reflect() - # Add all of the new tables above # metadata.create_all() try: @@ -145,8 +164,6 @@ SampleEvent_table.create() except Exception, e: log.debug( "Creating sample_event table failed: %s" % str( e ) ) - - def downgrade(): # Load existing tables @@ -183,7 +200,3 @@ SampleEvent_table.drop() except Exception, e: log.debug( "Dropping sample_event table failed: %s" % str( e ) ) - - - - diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0009_request_table.py --- a/lib/galaxy/model/migrate/versions/0009_request_table.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0009_request_table.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,3 +1,8 @@ +""" +This migration script adds a new column to 2 tables: +1) a new boolean type column named 'submitted' to the 'request' table +2) a new string type column named 'bar_code' to the 'sample' table +""" from sqlalchemy import * from sqlalchemy.orm import * from migrate import * @@ -15,11 +20,17 @@ metadata = MetaData( migrate_engine ) +def display_migration_details(): + print "========================================" + print "This migration script adds a new column to 2 tables:" + print "1) a new boolean type column named 'submitted' to the 'request' table" + print "2) a new string type column named 'bar_code' to the 'sample' table" + print "========================================" def upgrade(): + display_migration_details() # Load existing tables metadata.reflect() - # Add 1 column to the request table try: Request_table = Table( "request", metadata, autoload=True ) @@ -33,7 +44,6 @@ assert col is Request_table.c.submitted except Exception, e: log.debug( "Adding column 'submitted' to request table failed: %s" % ( str( e ) ) ) - # Add 1 column to the sample table try: Sample_table = Table( "sample", metadata, autoload=True ) @@ -49,4 +59,4 @@ log.debug( "Adding column 'bar_code' to sample table failed: %s" % ( str( e ) ) ) def downgrade(): - pass \ No newline at end of file + pass diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py --- a/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,3 +1,13 @@ +""" +This migration script adds the history_dataset_association_display_at_authorization table, +which allows 'private' datasets to be displayed at external sites without making them public. +If using mysql, this script will display the following error, which is corrected in the next +migration script: + +history_dataset_association_display_at_authorization table failed: (OperationalError) +(1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' +is too long +""" from sqlalchemy import * from sqlalchemy.orm import * from sqlalchemy.exceptions import * @@ -22,6 +32,17 @@ metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +def display_migration_details(): + print "========================================" + print "This migration script adds the history_dataset_association_display_at_authorization table, which" + print "allows 'private' datasets to be displayed at external sites without making them public." + print "" + print "If using mysql, this script will display the following error, which is corrected in the next migration" + print "script: history_dataset_association_display_at_authorization table failed: (OperationalError)" + print "(1059, 'Identifier name 'ix_history_dataset_association_display_at_authorization_update_time'" + print "is too long." + print "========================================" + HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -31,13 +52,14 @@ Column( "site", TrimmedString( 255 ) ) ) def upgrade(): + display_migration_details() # Load existing tables metadata.reflect() try: HistoryDatasetAssociationDisplayAtAuthorization_table.create() except Exception, e: log.debug( "Creating history_dataset_association_display_at_authorization table failed: %s" % str( e ) ) - + def downgrade(): # Load existing tables metadata.reflect() diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py --- a/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,3 +1,8 @@ +""" +This script fixes a problem introduced in 0010_hda_display_at_atuhz_table.py. MySQL has a +name length limit and thus the index "ix_hdadaa_history_dataset_association_id" has to be +manually created. +""" from sqlalchemy import * from sqlalchemy.orm import * from sqlalchemy.exceptions import * @@ -22,6 +27,13 @@ metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +def display_migration_details(): + print "========================================" + print "This script fixes a problem introduced in the previous migration script ( 9->10 ). MySQL" + print "has a name length limit and thus the index 'ix_hdadaa_history_dataset_association_id' has" + print "to be manually created." + print "========================================" + HistoryDatasetAssociationDisplayAtAuthorization_table = Table( "history_dataset_association_display_at_authorization", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -31,6 +43,7 @@ Column( "site", TrimmedString( 255 ) ) ) def upgrade(): + display_migration_details() if migrate_engine.name == 'mysql': # Load existing tables metadata.reflect() @@ -39,7 +52,7 @@ i.create() except Exception, e: log.debug( "Adding index 'ix_hdadaa_history_dataset_association_id' to table 'history_dataset_association_display_at_authorization' table failed: %s" % str( e ) ) - + def downgrade(): if migrate_engine.name == 'mysql': # Load existing tables diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0012_user_address.py --- a/lib/galaxy/model/migrate/versions/0012_user_address.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/model/migrate/versions/0012_user_address.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,13 +1,20 @@ +""" +This script adds a new user_address table that is currently only used with sample requests, where +a user can select from a list of his addresses to associate with the request. This script also +drops the request.submitted column which was boolean and replaces it with a request.state column +which is a string, allowing for more flexibility with request states. +""" from sqlalchemy import * from sqlalchemy.orm import * from sqlalchemy.exceptions import * from migrate import * from migrate.changeset import * - import datetime now = datetime.datetime.utcnow +import sys, logging +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * -import sys, logging log = logging.getLogger( __name__ ) log.setLevel(logging.DEBUG) handler = logging.StreamHandler( sys.stdout ) @@ -16,12 +23,16 @@ handler.setFormatter( formatter ) log.addHandler( handler ) -# Need our custom types, but don't import anything else from model -from galaxy.model.custom_types import * - metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +def display_migration_details(): + print "========================================" + print "This script adds a new user_address table that is currently only used with sample requests, where" + print "a user can select from a list of his addresses to associate with the request. This script also" + print "drops the request.submitted column which was boolean and replaces it with a request.state column" + print "which is a string, allowing for more flexibility with request states." + print "========================================" UserAddress_table = Table( "user_address", metadata, Column( "id", Integer, primary_key=True), @@ -40,27 +51,15 @@ Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) -#RequestState_table = Table('request_state', metadata, -# Column( "id", Integer, primary_key=True), -# Column( "create_time", DateTime, default=now ), -# Column( "update_time", DateTime, default=now, onupdate=now ), -# Column( "name", TrimmedString( 255 ), nullable=False ), -# Column( "desc", TEXT )) - def upgrade(): + display_migration_details() # Load existing tables metadata.reflect() - # Add all of the new tables above try: UserAddress_table.create() except Exception, e: log.debug( "Creating user_address table failed: %s" % str( e ) ) -# try: -# RequestState_table.create() -# except Exception, e: -# log.debug( "Creating request_state table failed: %s" % str( e ) ) - # Add 1 column to the request_type table try: RequestType_table = Table( "request_type", metadata, autoload=True ) @@ -74,7 +73,6 @@ assert col is RequestType_table.c.deleted except Exception, e: log.debug( "Adding column 'deleted' to request_type table failed: %s" % ( str( e ) ) ) - # Delete the submitted column try: Request_table = Table( "request", metadata, autoload=True ) @@ -92,27 +90,6 @@ assert col is Request_table.c.state except Exception, e: log.debug( "Adding column 'state' to request table failed: %s" % ( str( e ) ) ) -# -# # new column which points to the current state in the request_state table -# try: -# col = Column( "request_state_id", Integer, index=True ) -# col.create( Request_table ) -# assert col is Request_table.c.request_state_id -# except Exception, e: -# log.debug( "Adding column 'request_state_id' to request table failed: %s" % ( str( e ) ) ) -# # Add 1 foreign key constraint to the form_definition_current table -# if RequestState_table and Request_table: -# try: -# cons = ForeignKeyConstraint( [Request_table.c.request_state_id], -# [RequestState_table.c.id], -# name='request_request_state_id_fk' ) -# # Create the constraint -# cons.create() -# except Exception, e: -# log.debug( "Adding foreign key constraint 'request_request_state_id_fk' to table 'request' failed: %s" % ( str( e ) ) ) - def downgrade(): pass - - diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Thu Aug 13 13:44:04 2009 -0400 @@ -0,0 +1,255 @@ +""" +This migration script eliminates all of the tables that were used for the 1st version of the +library templates where template fields and contents were each stored as a separate table row +in various library item tables. All of these tables are dropped in this script, eliminating all +existing template data. A total of 14 existing tables are dropped. + +We're now basing library templates on forms, so field contents are +stored as a jsonified list in the form_values table. This script introduces the following 3 +new association tables: +1) library_info_association +2) library_folder_info_association +3) library_dataset_dataset_info_association + +If using mysql, this script will throw an (OperationalError) exception due to a long index name on +the library_dataset_dataset_info_association table, which is OK because the script creates an index +with a shortened name. +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +from migrate.changeset import * +import sys, logging + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) + +def display_migration_details(): + print "========================================" + print "This migration script eliminates all of the tables that were used for the 1st version of the" + print "library templates where template fields and contents were each stored as a separate table row" + print "in various library item tables. All of these tables are dropped in this script, eliminating all" + print "existing template data. A total of 14 existing tables are dropped." + print "" + print "We're now basing library templates on Galaxy forms, so field contents are stored as a jsonified" + print "list in the form_values table. This script introduces the following 3 new association tables:" + print "1) library_info_association" + print "2) library_folder_info_association" + print "3) library_dataset_dataset_info_association" + print "" + print "If using mysql, this script will throw an (OperationalError) exception due to a long index name" + print "on the library_dataset_dataset_info_association table, which is OK because the script creates" + print "an index with a shortened name." + print "========================================" + +if migrate_engine.name == 'postgres': + # http://blog.pythonisito.com/2008/01/cascading-drop-table-with-sqlalchemy.ht… + from sqlalchemy.databases import postgres + class PGCascadeSchemaDropper(postgres.PGSchemaDropper): + def visit_table(self, table): + for column in table.columns: + if column.default is not None: + self.traverse_single(column.default) + self.append("\nDROP TABLE " + + self.preparer.format_table(table) + + " CASCADE") + self.execute() + postgres.dialect.schemadropper = PGCascadeSchemaDropper + +LibraryInfoAssociation_table = Table( 'library_info_association', metadata, + Column( "id", Integer, primary_key=True), + Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) + +LibraryFolderInfoAssociation_table = Table( 'library_folder_info_association', metadata, + Column( "id", Integer, primary_key=True), + Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) + +LibraryDatasetDatasetInfoAssociation_table = Table( 'library_dataset_dataset_info_association', metadata, + Column( "id", Integer, primary_key=True), + Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ), + Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), + Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ) ) + +def upgrade(): + display_migration_details() + # Load existing tables + metadata.reflect() + # Drop all of the original library_item_info tables + # NOTE: all existing library item into template data is eliminated here via table drops + try: + LibraryItemInfoPermissions_table = Table( "library_item_info_permissions", metadata, autoload=True ) + except NoSuchTableError: + LibraryItemInfoPermissions_table = None + log.debug( "Failed loading table library_item_info_permissions" ) + try: + LibraryItemInfoPermissions_table.drop() + except Exception, e: + log.debug( "Dropping library_item_info_permissions table failed: %s" % str( e ) ) + + try: + LibraryItemInfoTemplatePermissions_table = Table( "library_item_info_template_permissions", metadata, autoload=True ) + except NoSuchTableError: + LibraryItemInfoTemplatePermissions_table = None + log.debug( "Failed loading table library_item_info_template_permissions" ) + try: + LibraryItemInfoTemplatePermissions_table.drop() + except Exception, e: + log.debug( "Dropping library_item_info_template_permissions table failed: %s" % str( e ) ) + + try: + LibraryItemInfoElement_table = Table( "library_item_info_element", metadata, autoload=True ) + except NoSuchTableError: + LibraryItemInfoElement_table = None + log.debug( "Failed loading table library_item_info_element" ) + try: + LibraryItemInfoElement_table.drop() + except Exception, e: + log.debug( "Dropping library_item_info_element table failed: %s" % str( e ) ) + + try: + LibraryItemInfoTemplateElement_table = Table( "library_item_info_template_element", metadata, autoload=True ) + except NoSuchTableError: + LibraryItemInfoTemplateElement_table = None + log.debug( "Failed loading table library_item_info_template_element" ) + try: + LibraryItemInfoTemplateElement_table.drop() + except Exception, e: + log.debug( "Dropping library_item_info_template_element table failed: %s" % str( e ) ) + + try: + LibraryInfoTemplateAssociation_table = Table( "library_info_template_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryInfoTemplateAssociation_table = None + log.debug( "Failed loading table library_info_template_association" ) + try: + LibraryInfoTemplateAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_info_template_association table failed: %s" % str( e ) ) + + try: + LibraryFolderInfoTemplateAssociation_table = Table( "library_folder_info_template_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryFolderInfoTemplateAssociation_table = None + log.debug( "Failed loading table library_folder_info_template_association" ) + try: + LibraryFolderInfoTemplateAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_folder_info_template_association table failed: %s" % str( e ) ) + + try: + LibraryDatasetInfoTemplateAssociation_table = Table( "library_dataset_info_template_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryDatasetInfoTemplateAssociation_table = None + log.debug( "Failed loading table library_dataset_info_template_association" ) + try: + LibraryDatasetInfoTemplateAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_dataset_info_template_association table failed: %s" % str( e ) ) + + try: + LibraryDatasetDatasetInfoTemplateAssociation_table = Table( "library_dataset_dataset_info_template_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryDatasetDatasetInfoTemplateAssociation_table = None + log.debug( "Failed loading table library_dataset_dataset_info_template_association" ) + try: + LibraryDatasetDatasetInfoTemplateAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_dataset_dataset_info_template_association table failed: %s" % str( e ) ) + + try: + LibraryInfoAssociation_table = Table( "library_info_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryInfoAssociation_table = None + log.debug( "Failed loading table library_info_association" ) + try: + LibraryInfoAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_info_association table failed: %s" % str( e ) ) + + try: + LibraryFolderInfoAssociation_table = Table( "library_folder_info_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryFolderInfoAssociation_table = None + log.debug( "Failed loading table library_folder_info_association" ) + try: + LibraryFolderInfoAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_folder_info_association table failed: %s" % str( e ) ) + + try: + LibraryDatasetInfoAssociation_table = Table( "library_dataset_info_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryDatasetInfoAssociation_table = None + log.debug( "Failed loading table library_dataset_info_association" ) + try: + LibraryDatasetInfoAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_dataset_info_association table failed: %s" % str( e ) ) + + try: + LibraryDatasetDatasetInfoAssociation_table = Table( "library_dataset_dataset_info_association", metadata, autoload=True ) + except NoSuchTableError: + LibraryDatasetDatasetInfoAssociation_table = None + log.debug( "Failed loading table library_dataset_dataset_info_association" ) + try: + LibraryDatasetDatasetInfoAssociation_table.drop() + except Exception, e: + log.debug( "Dropping library_dataset_dataset_info_association table failed: %s" % str( e ) ) + + try: + LibraryItemInfo_table = Table( "library_item_info", metadata, autoload=True ) + except NoSuchTableError: + LibraryItemInfo_table = None + log.debug( "Failed loading table library_item_info" ) + try: + LibraryItemInfo_table.drop() + except Exception, e: + log.debug( "Dropping library_item_info table failed: %s" % str( e ) ) + + try: + LibraryItemInfoTemplate_table = Table( "library_item_info_template", metadata, autoload=True ) + except NoSuchTableError: + LibraryItemInfoTemplate_table = None + log.debug( "Failed loading table library_item_info_template" ) + try: + LibraryItemInfoTemplate_table.drop() + except Exception, e: + log.debug( "Dropping library_item_info_template table failed: %s" % str( e ) ) + + # Create all new tables above + try: + LibraryInfoAssociation_table.create() + except Exception, e: + log.debug( "Creating library_info_association table failed: %s" % str( e ) ) + try: + LibraryFolderInfoAssociation_table.create() + except Exception, e: + log.debug( "Creating library_folder_info_association table failed: %s" % str( e ) ) + try: + LibraryDatasetDatasetInfoAssociation_table.create() + except Exception, e: + log.debug( "Creating library_dataset_dataset_info_association table failed: %s" % str( e ) ) + # Fix index on LibraryDatasetDatasetInfoAssociation_table for mysql + if migrate_engine.name == 'mysql': + # Load existing tables + metadata.reflect() + i = Index( "ix_lddaia_ldda_id", LibraryDatasetDatasetInfoAssociation_table.c.library_dataset_dataset_association_id ) + try: + i.create() + except Exception, e: + log.debug( "Adding index 'ix_lddaia_ldda_id' to table 'library_dataset_dataset_info_association' table failed: %s" % str( e ) ) + +def downgrade(): + log.debug( "Downgrade is not possible." ) diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/security/__init__.py Thu Aug 13 13:44:04 2009 -0400 @@ -75,12 +75,10 @@ self.permitted_actions = permitted_actions # List of "library_item" objects and their associated permissions and info template objects self.library_item_assocs = ( - ( self.model.Library, self.model.LibraryPermissions, self.model.LibraryInfoAssociation ), - ( self.model.LibraryFolder, self.model.LibraryFolderPermissions, self.model.LibraryFolderInfoAssociation ), - ( self.model.LibraryDataset, self.model.LibraryDatasetPermissions, self.model.LibraryDatasetInfoAssociation ), - ( self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions, self.model.LibraryDatasetDatasetInfoAssociation ), - ( self.model.LibraryItemInfo, self.model.LibraryItemInfoPermissions, None ), - ( self.model.LibraryItemInfoTemplate, self.model.LibraryItemInfoTemplatePermissions, None ) ) + ( self.model.Library, self.model.LibraryPermissions ), + ( self.model.LibraryFolder, self.model.LibraryFolderPermissions ), + ( self.model.LibraryDataset, self.model.LibraryDatasetPermissions ), + ( self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions ) ) def allow_action( self, user, action, **kwd ): if 'dataset' in kwd: return self.allow_dataset_action( user, action, kwd[ 'dataset' ] ) @@ -117,7 +115,7 @@ user_role_ids = [ r.id for r in user.all_roles() ] # Check to see if user has access to any of the roles allowed_role_assocs = [] - for item_class, permission_class, info_association_class in self.library_item_assocs: + for item_class, permission_class in self.library_item_assocs: if isinstance( library_item, item_class ): if permission_class == self.model.LibraryPermissions: allowed_role_assocs = permission_class.filter_by( action=action.action, library_id=library_item.id ).all() @@ -127,10 +125,6 @@ allowed_role_assocs = permission_class.filter_by( action=action.action, library_dataset_id=library_item.id ).all() elif permission_class == self.model.LibraryDatasetDatasetAssociationPermissions: allowed_role_assocs = permission_class.filter_by( action=action.action, library_dataset_dataset_association_id=library_item.id ).all() - elif permission_class == self.model.LibraryItemInfoPermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, library_item_info_id=library_item.id ).all() - elif permission_class == self.model.LibraryItemInfoTemplatePermissions: - allowed_role_assocs = permission_class.filter_by( action=action.action, library_item_info_template_id=library_item.id ).all() for allowed_role_assoc in allowed_role_assocs: if allowed_role_assoc.role_id in user_role_ids: return True @@ -366,7 +360,7 @@ role_assoc.delete() role_assoc.flush() # Add the new permissions on library_item - for item_class, permission_class, info_association_class in self.library_item_assocs: + for item_class, permission_class in self.library_item_assocs: if isinstance( library_item, item_class ): for action, roles in permissions.items(): if isinstance( action, Action ): @@ -396,12 +390,12 @@ permissions[role_assoc.action] = [ role_assoc.role ] self.set_all_library_permissions( target_library_item, permissions ) if user: - # The user passed will be the current Galaxy user. Make sure user's private role is included item_class = None - for item_class, permission_class, info_association_class in self.library_item_assocs: + for item_class, permission_class in self.library_item_assocs: if isinstance( target_library_item, item_class ): break if item_class: + # Make sure user's private role is included private_role = self.model.security_agent.get_private_user_role( user ) for name, action in self.permitted_actions.items(): if not permission_class.filter_by( role_id = private_role.id, action = action.action ).first(): diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Aug 13 13:44:04 2009 -0400 @@ -128,7 +128,7 @@ tree = util.parse_xml( config_file ) root = tree.getroot() # Allow specifying a different tool subclass to instantiate - if root.find( "type" ): + if root.find( "type" ) is not None: type_elem = root.find( "type" ) module = type_elem.get( 'module', 'galaxy.tools' ) cls = type_elem.get( 'class' ) @@ -1468,7 +1468,7 @@ out_data[ name ] = data return out_data - def exec_after_process( self, app, inp_data, out_data, param_dict ): + def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): if self.tool_type == 'data_source': name, data = out_data.items()[0] data.set_size() @@ -1572,6 +1572,18 @@ dataset.history.add( new_data ) new_data.flush() return primary_datasets + +class SetMetadataTool( Tool ): + def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): + for name, dataset in inp_data.iteritems(): + external_metadata = galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper( job ) + if external_metadata.external_metadata_set_successfully( dataset ): + dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset ).filename_out ) + # If setting external metadata has failed, how can we inform the user? + # For now, we'll leave the default metadata and set the state back to its original. + dataset.datatype.after_edit( dataset ) + dataset.state = param_dict.get( '__ORIGINAL_DATASET_STATE__' ) + dataset.flush() # ---- Utility classes to be factored out ----------------------------------- diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/tools/actions/metadata.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/tools/actions/metadata.py Thu Aug 13 13:44:04 2009 -0400 @@ -0,0 +1,48 @@ +from . import ToolAction +from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper + +import logging +log = logging.getLogger( __name__ ) + +class SetMetadataToolAction( ToolAction ): + """Tool action used for setting external metadata on an existing dataset""" + + def execute( self, tool, trans, incoming = {}, set_output_hid = False ): + for name, value in incoming.iteritems(): + if isinstance( value, trans.app.model.HistoryDatasetAssociation ): + dataset = value + dataset_name = name + break + else: + raise Exception( 'The dataset to set metadata on could not be determined.' ) + + # Create the job object + job = trans.app.model.Job() + job.session_id = trans.get_galaxy_session().id + job.history_id = trans.history.id + job.tool_id = tool.id + try: + # For backward compatibility, some tools may not have versions yet. + job.tool_version = tool.version + except: + job.tool_version = "1.0.0" + job.flush() #ensure job.id is available + + #add parameters to job_parameter table + incoming[ '__ORIGINAL_DATASET_STATE__' ] = dataset.state #store original dataset state, so we can restore it. A seperate table might be better (no chance of 'loosing' the original state)? + external_metadata_wrapper = JobExternalOutputMetadataWrapper( job ) + cmd_line = external_metadata_wrapper.setup_external_metadata( dataset, exec_dir = None, tmp_dir = trans.app.config.new_file_path, dataset_files_path = trans.app.model.Dataset.file_path, output_fnames = None, config_root = None, datatypes_config = None, kwds = { 'overwrite' : True } ) + incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line + for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): + job.add_parameter( name, value ) + #add the dataset to job_to_input_dataset table + job.add_input_dataset( dataset_name, dataset ) + #Need a special state here to show that metadata is being set and also allow the job to run + # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state + dataset.state = dataset.states.SETTING_METADATA + trans.app.model.flush() + + # Queue the job for execution + trans.app.job_queue.put( job.id, tool ) + trans.log_event( "Added set external metadata job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) + return [] diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,4 +1,5 @@ import os, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile +from . import ToolAction from galaxy import datatypes, jobs from galaxy.datatypes import sniff from galaxy import model, util @@ -8,7 +9,7 @@ import logging log = logging.getLogger( __name__ ) -class UploadToolAction( object ): +class UploadToolAction( ToolAction ): # Action for uploading files def __init__( self ): self.empty = False diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Thu Aug 13 13:44:04 2009 -0400 @@ -1,9 +1,9 @@ -import shutil, StringIO, operator, urllib, gzip, tempfile, sets, string +import shutil, StringIO, operator, urllib, gzip, tempfile, sets, string, sys from datetime import datetime, timedelta from galaxy import util, datatypes from galaxy.web.base.controller import * from galaxy.model.orm import * -import sys +from galaxy.web.controllers.forms import get_all_forms, get_form_widgets import logging log = logging.getLogger( __name__ ) @@ -710,6 +710,7 @@ library=trans.app.model.Library.get( id ), deleted=deleted, created_ldda_ids=created_ldda_ids, + forms=get_all_forms( trans, filter=dict(deleted=False) ), msg=msg, messagetype=messagetype, show_deleted=show_deleted ) @@ -751,6 +752,22 @@ messagetype='done' ) ) return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype ) elif action == 'information': + # See if we have any associated templates + info_association = library.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents + info = info_association.info + if info: + field_contents = {} + for index, value in enumerate( info.content ): + key = 'field_%i' % index + field_contents[ key ] = value + widgets = get_form_widgets( trans, template, field_contents ) + else: + widgets = get_form_widgets( trans, template ) + else: + widgets = [] if params.get( 'rename_library_button', False ): old_name = library.name new_name = util.restore_text( params.name ) @@ -759,8 +776,7 @@ msg = 'Enter a valid name' return trans.fill_template( '/admin/library/library_info.mako', library=library, - restrict=params.get( 'restrict', False ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype='error' ) else: @@ -780,12 +796,10 @@ messagetype='done' ) ) return trans.fill_template( '/admin/library/library_info.mako', library=library, - restrict=params.get( 'restrict', False ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) elif action == 'delete': - # TODO: need to revamp the way we delete libraries, folders and contained LibraryDatasets. def delete_folder( library_folder ): library_folder.refresh() for folder in library_folder.folders: @@ -939,6 +953,22 @@ msg=msg, messagetype=messagetype ) elif action == 'information': + # See if we have any associated templates + info_association = folder.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents + info = info_association.info + if info: + field_contents = {} + for index, value in enumerate( info.content ): + key = 'field_%i' % index + field_contents[ key ] = value + widgets = get_form_widgets( trans, template, field_contents ) + else: + widgets = get_form_widgets( trans, template ) + else: + widgets = [] if params.get( 'rename_folder_button', False ): old_name = folder.name new_name = util.restore_text( params.name ) @@ -948,8 +978,7 @@ return trans.fill_template( '/admin/library/folder_info.mako', folder=folder, library_id=library_id, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype='error' ) else: @@ -967,12 +996,10 @@ return trans.fill_template( '/admin/library/folder_info.mako', folder=folder, library_id=library_id, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) elif action == 'delete': - # TODO: need to revamp the way we delete folders and contained LibraryDatasets def delete_folder( folder ): folder.refresh() for subfolder in folder.active_folders: @@ -1045,8 +1072,6 @@ return trans.fill_template( '/admin/library/library_dataset_info.mako', library_dataset=library_dataset, library_id=library_id, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), msg=msg, messagetype=messagetype ) elif action == 'permissions': @@ -1101,7 +1126,7 @@ created_ldda_ids = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans, controller='admin', library_id=library_id, - folder_id=folder_id, + folder_id=folder_id, replace_dataset=replace_dataset, **kwd ) if created_ldda_ids: @@ -1126,6 +1151,13 @@ msg=util.sanitize_text( msg ), messagetype=messagetype ) ) elif not id or replace_dataset: + # See if we have any associated templates + info_association = folder.get_info_association() + if info_association: + template = info_association.template + widgets = get_form_widgets( trans, template ) + else: + widgets = [] upload_option = params.get( 'upload_option', 'upload_file' ) # No dataset(s) specified, so display the upload form. Send list of data formats to the form # so the "extension" select list can be populated dynamically @@ -1150,6 +1182,7 @@ last_used_build=last_used_build, roles=roles, history=history, + widgets=widgets, msg=msg, messagetype=messagetype, replace_dataset=replace_dataset ) @@ -1175,6 +1208,22 @@ id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) + # See if we have any associated templates + info_association = ldda.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents + info = info_association.info + if info: + field_contents = {} + for index, value in enumerate( info.content ): + key = 'field_%i' % index + field_contents[ key ] = value + widgets = get_form_widgets( trans, template, field_contents ) + else: + widgets = get_form_widgets( trans, template ) + else: + widgets = [] if action == 'permissions': if params.get( 'update_roles_button', False ): permissions = {} @@ -1242,6 +1291,7 @@ library_id=library_id, deleted=deleted, show_deleted=show_deleted, + widgets=widgets, msg=msg, messagetype=messagetype ) elif action == 'edit_info': @@ -1255,8 +1305,7 @@ ldda=ldda, library_id=library_id, datatypes=ldatatypes, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) else: @@ -1293,8 +1342,7 @@ ldda=ldda, library_id=library_id, datatypes=ldatatypes, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) elif params.get( 'detect', False ): @@ -1312,8 +1360,7 @@ ldda=ldda, library_id=library_id, datatypes=ldatatypes, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) elif params.get( 'delete', False ): @@ -1324,8 +1371,7 @@ ldda=ldda, library_id=library_id, datatypes=ldatatypes, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) ldda.datatype.before_edit( ldda ) @@ -1340,8 +1386,7 @@ ldda=ldda, library_id=library_id, datatypes=ldatatypes, - restrict=params.get( 'restrict', True ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) elif ids: @@ -1553,26 +1598,17 @@ last_used_build=last_used_build, roles=roles, history=history, + widgets=widgets, msg=msg, messagetype=messagetype ) @web.expose @web.require_admin - def info_template( self, trans, library_id, id=None, num_fields=0, folder_id=None, ldda_id=None, library_dataset_id=None, **kwd ): + def info_template( self, trans, library_id, id=None, folder_id=None, ldda_id=None, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - if not num_fields: - num_fields = 0 - else: - num_fields = int( num_fields ) - if params.get( 'new_template', False ): - action = 'new_template' - elif params.get( 'permissions', False ): - action = 'permissions' - else: - action = 'edit_template' if id: - library_item = trans.app.model.LibraryItemInfoTemplate.get( int( id ) ) + library_item = trans.app.model.FormDefinition.get( int( id ) ) library_item_desc = 'information template' response_action = 'info_template' response_id = id @@ -1586,174 +1622,51 @@ library_item_desc = 'library dataset' response_action = 'library_dataset_dataset_association' response_id = ldda_id - elif library_dataset_id: - library_item = trans.app.model.LibraryDataset.get( int( library_dataset_id ) ) - library_item_desc = 'dataset' - response_action = 'library_dataset_dataset_association' - response_id = library_item.library_dataset_dataset_association.id else: library_item = trans.app.model.Library.get( int( library_id ) ) library_item_desc = 'library' response_action = 'browse_library' response_id = library_id - if action == 'new_template': - if params.get( 'create_info_template_button', False ): - return trans.fill_template( '/admin/library/new_info_template.mako', - library_item_name=library_item.name, - library_item_desc=library_item_desc, - num_fields=num_fields, - library_id=library_id, - folder_id=folder_id, - ldda_id=ldda_id, - library_dataset_id=library_dataset_id, - msg=msg, - messagetype=messagetype ) - elif params.get( 'new_info_template_button', False ): - # Make sure at least 1 template field is filled in - # TODO: Eventually we'll enhance templates to allow for required and optional fields. - proceed = False - for i in range( int( params.get( 'set_num_fields', 0 ) ) ): - elem_name = params.get( 'new_element_name_%i' % i, None ) - elem_description = params.get( 'new_element_description_%i' % i, None ) - if elem_name or elem_description: - proceed = True - break - if not proceed: - msg = "At least 1 of the fields must be completed." - return trans.fill_template( '/admin/library/new_info_template.mako', - library_item_name=library_item.name, - library_item_desc=library_item_desc, - num_fields=num_fields, - library_id=library_id, - folder_id=folder_id, - ldda_id=ldda_id, - library_dataset_id=library_dataset_id, - msg=msg, - messagetype=messagetype ) - # Create template - liit = trans.app.model.LibraryItemInfoTemplate() - liit.name = util.restore_text( params.get( 'name', '' ) ) - liit.description = util.restore_text( params.get( 'description', '' ) ) - liit.flush() - # Inherit the template's permissions from the library_item - trans.app.security_agent.copy_library_permissions( library_item, liit ) - # Create template association + forms = get_all_forms( trans, filter=dict(deleted=False) ) + if not forms: + msg = "There are no forms on which to base the template, so create a form and " + msg += "try again to add the information template to the %s." % library_item_desc + trans.response.send_redirect( web.url_for( controller='forms', + action='new', + new=True, + msg=msg, + messagetype='done' ) ) + if params.get( 'add', False ): + if params.get( 'add_info_template_button', False ): + form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) ) + #fields = list( copy.deepcopy( form.fields ) ) + form_values = trans.app.model.FormValues( form, [] ) + form_values.flush() if folder_id: - liit_assoc = trans.app.model.LibraryFolderInfoTemplateAssociation() - liit_assoc.folder = trans.app.model.LibraryFolder.get( folder_id ) + assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values ) elif ldda_id: - liit_assoc = trans.app.model.LibraryDatasetDatasetInfoTemplateAssociation() - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_id ) - liit_assoc.library_dataset_dataset_association = ldda - # This response_action method requires a folder_id - folder_id = ldda.library_dataset.folder.id - elif library_dataset_id: - liit_assoc = trans.app.model.LibraryDatasetInfoTemplateAssociation() - library_dataset = trans.app.model.LibraryDataset.get( library_dataset_id ) - liit_assoc.library_dataset = library_dataset - # This response_action method requires a folder_id - folder_id = library_dataset.folder.id + assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values ) else: - # We'll always be sent a library_id - liit_assoc = trans.app.model.LibraryInfoTemplateAssociation() - liit_assoc.library = trans.app.model.Library.get( library_id ) - liit_assoc.library_item_info_template = liit - liit_assoc.flush() - # Create and add elements - for i in range( int( params.get( 'set_num_fields', 0 ) ) ): - elem_name = params.get( 'new_element_name_%i' % i, None ) - elem_description = params.get( 'new_element_description_%i' % i, None ) - if elem_description and not elem_name: - # If we have a description but no name, the description will be both - # ( a name cannot be empty, but a description can ) - elem_name = elem_description - if elem_name: - # Skip any elements that have a missing name - liit.add_element( name=elem_name, description=elem_description ) - msg = "The new information template has been created." - return trans.response.send_redirect( web.url_for( controller='admin', - action=response_action, - id=response_id, - library_id=library_id, - folder_id=folder_id, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/create_info_template.mako', - library_item=library_item, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - elif action == 'edit_template': - define_or_save = 'define' - edit_info_template_button = params.get( 'edit_info_template_button', False ) - if edit_info_template_button: - if edit_info_template_button == 'Define fields': - define_or_save = 'save' - else: - define_or_save = 'define' - # Save changes to existing attributes, only set name if nonempty/nonNone is passed, but always set description - name = params.get( 'name', None ) - if name: - library_item.name = name - library_item.description = params.get( 'description', '' ) - library_item.flush() - # Save changes to exisiting elements - for elem_id in util.listify( params.get( 'element_ids', [] ) ): - liit_element = trans.app.model.LibraryItemInfoTemplateElement.get( elem_id ) - name = params.get( 'element_name_%s' % elem_id, None ) - if name: - liit_element.name = name - liit_element.description = params.get( 'element_description_%s' % elem_id, None ) - liit_element.flush() - # Add new elements - for i in range( int( params.get( 'set_num_fields', 0 ) ) ): - elem_name = params.get( 'new_element_name_%i' % i, None ) - elem_description = params.get( 'new_element_description_%i' % i, None ) - # Skip any elements that have a missing name and description - if not elem_name: - # If we have a description but no name, the description will be both - # ( a name cannot be empty, but a description can ) - elem_name = elem_description - if elem_name: - library_item.add_element( name=elem_name, description=elem_description ) - library_item.refresh() - msg = "Information template '%s' has been updated" % library_item.name - return trans.fill_template( "/admin/library/edit_info_template.mako", - liit=library_item, - num_fields=num_fields, - library_id=library_id, - library_dataset_id=library_dataset_id, - ldda_id=ldda_id, - folder_id=folder_id, + assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values ) + assoc.flush() + msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) + trans.response.send_redirect( web.url_for( controller='admin', + action=response_action, + id=response_id, + msg=msg, + message_type='done' ) ) + return trans.fill_template( '/admin/library/select_info_template.mako', library_item_name=library_item.name, library_item_desc=library_item_desc, - define_or_save=define_or_save, - msg=msg, - messagetype=messagetype ) - elif action == 'permissions': - if params.get( 'update_roles_button', False ): - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( library_item, permissions ) - library_item.refresh() - msg = "Permissions updated for information template '%s'" % library_item.name - return trans.response.send_redirect( web.url_for( controller='admin', - action='info_template', - library_id=library_id, - id=id, - permissions=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/info_template_permissions.mako', - liit=library_item, library_id=library_id, + folder_id=folder_id, + ldda_id=ldda_id, + forms=forms, msg=msg, messagetype=messagetype ) @web.expose @web.require_admin - def library_item_info( self, trans, library_id, id=None, library_item_id=None, library_item_type=None, **kwd ): + def edit_template_info( self, trans, library_id, num_widgets, library_item_id=None, library_item_type=None, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -1768,8 +1681,6 @@ library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id ) # This response_action method requires a folder_id folder_id = library_item.library_dataset.folder.id - elif library_item_type == 'library_item_info_elememt': - library_item = trans.app.model.LibraryItemInfoElement.get( library_item_id ) else: msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) ) return trans.response.send_redirect( web.url_for( controller='admin', @@ -1777,107 +1688,47 @@ id=library_id, msg=util.sanitize_text( msg ), messagetype='error' ) ) - if params.get( 'new_info', False ): - if library_item: - if params.get( 'create_new_info_button', False ): - library_item_info_template_id = params.get( 'library_item_info_template_id', None ) - library_item_info_template = trans.app.model.LibraryItemInfoTemplate.get( int( library_item_info_template_id ) ) - # Make sure at least 1 template field is filled in - # TODO: Eventually we'll enhance templates to allow for required and optional fields. - proceed = False - for template_element in library_item_info_template.elements: - if params.get( "info_element_%s_%s" % ( library_item_info_template.id, template_element.id ), None ): - proceed = True - break - if not proceed: - msg = "At least 1 of the fields must be completed." - return trans.response.send_redirect( web.url_for( controller='admin', - action=library_item_type, - id=library_item.id, - library_id=library_id, - folder_id=folder_id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - user = trans.get_user() - library_item_info = trans.app.model.LibraryItemInfo( user=user ) - library_item_info.library_item_info_template = library_item_info_template - library_item_info.flush() - trans.app.security_agent.copy_library_permissions( library_item_info_template, library_item_info ) - for template_element in library_item_info_template.elements: - info_element_value = params.get( "info_element_%s_%s" % ( library_item_info_template.id, template_element.id ), None ) - info_element = trans.app.model.LibraryItemInfoElement() - info_element.contents = info_element_value - info_element.library_item_info_template_element = template_element - info_element.library_item_info = library_item_info - info_element.flush() - info_association_class = None - for item_class, permission_class, info_association_class in trans.app.security_agent.library_item_assocs: - if isinstance( library_item, item_class ): - break - if info_association_class: - library_item_info_association = info_association_class( user=user ) - library_item_info_association.set_library_item( library_item ) - library_item_info_association.library_item_info = library_item_info - library_item_info_association.flush() - else: - raise 'Invalid class (%s) specified for library_item (%s)' % ( library_item.__class__, library_item.__class__.__name__ ) - msg = 'The information has been saved' - return trans.response.send_redirect( web.url_for( controller='admin', - action=library_item_type, - id=library_item.id, - library_id=library_id, - folder_id=folder_id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( "/admin/library/new_info.mako", - library_id=library_id, - library_item=library_item, - library_item_type=library_item_type, - msg=msg, - messagetype=messagetype ) - elif params.get( 'edit_info', False ): - if params.get( 'edit_info_button', False ): - ids = util.listify( id ) - for id in ids: - library_item_info_element = trans.app.model.LibraryItemInfoElement.get( int( id ) ) - new_contents = util.restore_text( params.get( ( 'info_element_%s' % id ), '' ) ) - library_item_info_element.contents = new_contents - library_item_info_element.flush() - msg = 'The information has been updated.' - return trans.response.send_redirect( web.url_for( controller='admin', - action=library_item_type, - id=library_item.id, - library_id=library_id, - folder_id=folder_id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - elif params.get( 'permissions', False ): - if params.get( 'update_roles_button', False ): - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( library_item.library_item_info, permissions ) - library_item.library_item_info.refresh() - library_item.refresh() - msg = "Permissions updated for field '%s'" % library_item.library_item_info_template_element.name - return trans.response.send_redirect( web.url_for( controller='admin', - action='library_item_info', - library_id=library_id, - id=id, - library_item_id=library_item_id, - library_item_type=library_item_type, - permissions=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/info_permissions.mako', - library_item_info_element=library_item, - library_id=library_id, - msg=msg, - messagetype=messagetype ) + # Save updated template field contents + field_contents = [] + for index in range( int( num_widgets ) ): + field_contents.append( util.restore_text( params.get( 'field_%i' % ( index ), '' ) ) ) + if field_contents: + # Since information templates are inherited, the template fields can be displayed on the information + # page for a folder or library dataset when it has no info_association object. If the user has added + # field contents on an inherited template via a parent's info_association, we'll need to create a new + # form_values and info_association for the current object. + info_association = library_item.get_info_association( restrict=True ) + if info_association: + template = info_association.template + info = info_association.info + form_values = trans.app.model.FormValues.get( info.id ) + # Update existing content only if it has changed + if form_values.content != field_contents: + form_values.content = field_contents + form_values.flush() + else: + # Inherit the next available info_association so we can get the template + info_association = library_item.get_info_association() + template = info_association.template + # Create a new FormValues object + form_values = trans.app.model.FormValues( template, field_contents ) + form_values.flush() + # Create a new info_association between the current library item and form_values + if library_item_type == 'folder': + info_association = trans.app.model.LibraryFolderInfoAssociation( library_item, template, form_values ) + info_association.flush() + elif library_item_type == 'library_dataset_dataset_association': + info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, template, form_values ) + info_association.flush() + msg = 'The information has been updated.' + return trans.response.send_redirect( web.url_for( controller='admin', + action=library_item_type, + id=library_item.id, + library_id=library_id, + folder_id=folder_id, + edit_info=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) @web.expose @web.require_admin def download_dataset_from_folder(self, trans, id, library_id=None, **kwd): @@ -2101,19 +1952,6 @@ else: last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 ) return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, messagetype = messagetype ) - - def _get_all_forms(self, trans, all_versions=False): - ''' - This method returns all the latest forms from the - form_definition_current table if all_versions is set to True. Otherwise - this method return all the versions of all the forms from form_definition - table - ''' - if all_versions: - return trans.app.model.FormDefinition.query().all() - else: - fdc_list = trans.app.model.FormDefinitionCurrent.query().all() - return [fdc.latest_form for fdc in fdc_list] @web.expose @web.require_admin def manage_request_types( self, trans, **kwd ): @@ -2121,7 +1959,7 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_filter = util.restore_text( params.get( 'show_filter', 'Active' ) ) - forms = self._get_all_forms(trans, all_versions=True) + forms = get_all_forms(trans, all_versions=True) request_types_list = trans.app.model.RequestType.query().all() if show_filter == 'All': request_types = request_types_list @@ -2141,37 +1979,38 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - if params.get('create', False) == 'True': + if params.get( 'create', False ): return trans.fill_template( '/admin/requests/create_request_type.mako', - forms=self._get_all_forms(trans, all_versions=False), + forms=get_all_forms( trans, + filter=dict(deleted=False) ), msg=msg, messagetype=messagetype) - elif params.get('add_states', False) == 'True': + elif params.get( 'define_states_button', False ): return trans.fill_template( '/admin/requests/add_states.mako', - sample_type_name=util.restore_text( params.name ), + request_type_name=util.restore_text( params.name ), desc=util.restore_text( params.description ), num_states=int(util.restore_text( params.num_states )), request_form_id=int(util.restore_text( params.request_form_id )), sample_form_id=int(util.restore_text( params.sample_form_id )), msg=msg, messagetype=messagetype) - elif params.get('save_new', False) == 'True': + elif params.get( 'save_request_type', False ): st, msg = self._save_request_type(trans, **kwd) if not st: return trans.fill_template( '/admin/requests/create_request_type.mako', - forms=self._get_all_forms(trans, all_versions=False), + forms=get_all_forms( trans ), msg=msg, messagetype='error') return trans.response.send_redirect( web.url_for( controller='admin', action='manage_request_types', msg='Request type <b>%s</b> has been created' % st.name, messagetype='done') ) - elif params.get('edit', False) == 'True': + elif params.get('view', False): rt = trans.app.model.RequestType.get(int(util.restore_text( params.id ))) ss_list = trans.app.model.SampleState.filter(trans.app.model.SampleState.table.c.request_type_id == rt.id).all() return trans.fill_template( '/admin/requests/view_request_type.mako', request_type=rt, - forms=self._get_all_forms(trans, all_versions=False), + forms=get_all_forms( trans ), states_list=ss_list, deleted=False, show_deleted=False, @@ -2200,9 +2039,6 @@ for ss in ss_list: ss.delete() ss.flush() - # unsubmitted state - #ss = trans.app.model.SampleState('Unsubmitted', 'Sample not yet submitted', rt) - ##ss.flush() for i in range( num_states ): name = util.restore_text( params.get( 'new_element_name_%i' % i, None )) desc = util.restore_text( params.get( 'new_element_description_%i' % i, None )) @@ -2236,5 +2072,5 @@ rt.flush() return trans.response.send_redirect( web.url_for( controller='admin', action='manage_request_types', - msg='Request type <b>%s</b> has been deleted' % rt.name, + msg='Request type <b>%s</b> has been undeleted' % rt.name, messagetype='done') ) diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Thu Aug 13 13:44:04 2009 -0400 @@ -10,7 +10,6 @@ import copy log = logging.getLogger( __name__ ) - class Forms( BaseController ): @web.expose @@ -44,45 +43,30 @@ show_filter=show_filter, msg=msg, messagetype=messagetype ) - def _get_all_forms(self, trans, all_versions=False): - ''' - This method returns all the latest forms from the - form_definition_current table if all_versions is set to True. Otherwise - this method return all the versions of all the forms from form_definition - table - ''' - if all_versions: - return trans.app.model.FormDefinition.query().all() - else: - fdc_list = trans.app.model.FormDefinitionCurrent.query().all() - return [fdc.latest_form for fdc in fdc_list] @web.expose @web.require_admin def new( self, trans, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if params.get('new', False) and not params.get('create_form', False): - self.current_form = {} - self.current_form['name'] = 'New Form' - self.current_form['desc'] = '' - self.current_form['fields'] = [] - inputs = [ ( 'Name', TextField('name', 40,self.current_form['name'] ) ), - ( 'Description', TextField('description', 40, self.current_form['desc']) ), - ( 'Import from csv file (Optional)', TextField('csv_file', 40, '') ) ] - return trans.fill_template( '/admin/forms/create_form.mako', - inputs=inputs, - msg=msg, - messagetype=messagetype ) - elif params.get('create_form', False) == 'True': - if 'submitted' in params.new: - self.num_add_fields = 0 - fd, msg = self.__save_form(trans, fdc_id=None, **kwd) - self.__get_saved_form(fd) - return trans.response.send_redirect( web.url_for( controller='forms', - action='edit', - form_id=fd.id, - show_form=True) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get( 'create_form_button', False ): + fd, msg = self.__save_form( trans, fdc_id=None, **kwd ) + self.__get_saved_form( fd ) + return trans.response.send_redirect( web.url_for( controller='forms', + action='edit', + form_id=fd.id, + show_form=True ) ) + self.current_form = {} + self.current_form[ 'name' ] = 'New Form' + self.current_form[ 'desc' ] = '' + self.current_form[ 'fields' ] = [] + inputs = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ), + ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ), + ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ] + return trans.fill_template( '/admin/forms/create_form.mako', + inputs=inputs, + msg=msg, + messagetype=messagetype ) @web.expose @web.require_admin def delete( self, trans, **kwd ): @@ -111,73 +95,75 @@ @web.require_admin def edit( self, trans, **kwd ): ''' - This callback method is for handling all the editing functions like: - remaning fields, adding/deleting fields, changing fields attributes + This callback method is for handling all the editing functions like + renaming fields, adding/deleting fields, changing fields attributes. ''' params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - fd = trans.app.model.FormDefinition.get(int(util.restore_text( params.form_id ))) - # SHOW THE FORM FOR EDITING. - if params.get('show_form', False) == 'True': - self.__get_saved_form(fd) - # the following two dicts store the unsaved select box options + form_id = params.get( 'form_id', None ) + if not form_id: + msg = 'Invalid form id %s' % str( form_id ) + trans.response.send_redirect( web.url_for( controller='forms', + action='manage', + msg=msg, + messagetype='error' ) ) + fd = trans.app.model.FormDefinition.get( int( params.form_id ) ) + # Show the form for editing + if params.get( 'show_form', False ): + self.__get_saved_form( fd ) + # The following two dicts store the unsaved select box options self.del_options = {} self.add_options = {} - return self.__show(trans=trans, form=fd, msg=msg, - messagetype=messagetype, **kwd) - # DELETE FIELD - elif params.get('remove_button', False): - self.__update_current_form(**kwd) - index = int(params.get('remove_button', None).split(' ')[2])-1 - self.__remove_field(index) - return self.__show(trans=trans, form=fd, msg=msg, - messagetype=messagetype, **kwd) - # SAVE CHANGES - elif params.get('save_changes_button', False) == 'Save': - self.__update_current_form(**kwd) - fd_new, msg = self.__save_form(trans, fd.form_definition_current.id, **kwd) + if fd.fields: + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + else: + # If the form is empty, we'll simulate a click on the add_field_button so the + # form will be displayed with the field choice, saving a mouse click. + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, empty_form=True, **kwd ) + # Delete a field + elif params.get( 'remove_button', False ): + self.__update_current_form( trans, **kwd ) + index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1 + self.__remove_field( index ) + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + # Save changes + elif params.get( 'save_changes_button', False ): + self.__update_current_form( trans, **kwd ) + fd_new, msg = self.__save_form( trans, fd.form_definition_current.id, **kwd ) if not fd_new: - return self.__show(trans=trans, form=fd, msg=msg, - messagetype='error', **kwd) + return self.__show( trans=trans, form=fd, msg=msg, messagetype='error', **kwd ) else: fd = fd_new msg = "The form '%s' has been updated with the changes." % fd.name - return self.__show(trans=trans, form=fd, msg=msg, - messagetype=messagetype, **kwd) - #ADD A FIELD - elif params.get('add_field_button', False) == 'Add field': - self.__update_current_form(**kwd) + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + #Add a field + elif params.get( 'add_field_button', False ): + self.__update_current_form( trans, **kwd ) self.__add_field() # show the form again with one empty field - return self.__show(trans=trans, form=fd, msg=msg, - messagetype=messagetype, **kwd) - # SHOW FORM READ ONLY - elif params.get('read_only', False): + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + # Show form read-only + elif params.get( 'read_only', False ): return trans.fill_template( '/admin/forms/show_form_read_only.mako', form=fd, msg=msg, messagetype=messagetype ) - # REFRESH PAGE, SelectField is selected/deselected as the type of a field - elif params.get('refresh', False) == 'true': - self.__update_current_form(**kwd) - return self.__show(trans=trans, form=fd, msg=msg, - messagetype=messagetype, **kwd) - # REMOVE SelectField OPTION - elif params.get('select_box_options', False) == 'remove': - #self.__update_current_form(**kwd) - index = int(params.get( 'field_index', None )) - option = int(params.get( 'option_index', None )) - del self.current_form['fields'][index]['selectlist'][option] - return self.__show(trans=trans, form=fd, msg=msg, - messagetype=messagetype, **kwd) - # ADD SelectField OPTION - elif params.get('select_box_options', False) == 'add': - #self.__update_current_form(**kwd) - index = int(params.get( 'field_index', None )) - self.current_form['fields'][index]['selectlist'].append('') - return self.__show(trans=trans, form=fd, msg=msg, - messagetype=messagetype, **kwd) + # Refresh page, SelectField is selected/deselected as the type of a field + elif params.get( 'refresh', False ): + self.__update_current_form( trans, **kwd ) + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + # Remove SelectField option + elif params.get( 'select_box_options', False ) == 'remove': + index = int( kwd[ 'field_index' ] ) + option = int( kwd[ 'option_index' ] ) + del self.current_form[ 'fields' ][ index ][ 'selectlist' ][ option ] + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) + # Add SelectField option + elif params.get( 'select_box_options', False ) == 'add': + index = int( kwd[ 'field_index' ] ) + self.current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' ) + return self.__show( trans=trans, form=fd, msg=msg, messagetype=messagetype, **kwd ) def __remove_field(self, index): del self.current_form['fields'][index] def __add_field(self): @@ -193,6 +179,10 @@ self.current_form['fields'].append(empty_field) def __get_field(self, index, **kwd): params = util.Params( kwd ) + #TODO: RC this needs to be handled so that it does not throw an exception. + # To reproduce, create a new form, click the "add field" button, click the + # browser back arrow, then click the "add field" button again. + # You should never attempt to "restore_text()" on a None object... name = util.restore_text( params.get( 'field_name_%i' % index, None ) ) helptext = util.restore_text( params.get( 'field_helptext_%i' % index, None ) ) required = params.get( 'field_required_%i' % index, False ) @@ -245,29 +235,28 @@ if not util.restore_text(params.get( 'field_name_%i' % i, None )): return None, "All the field label(s) must be completed." return True, '' - def __get_form(self, **kwd): + def __get_form(self, trans, **kwd): params = util.Params( kwd ) name = util.restore_text( params.name ) desc = util.restore_text( params.description ) or "" - if params.get( 'csv_file', None ): - csv_file = util.restore_text( params.get( 'csv_file', '' ) ) - if csv_file: - fields = self.__import_fields(csv_file) - else: + csv_file = params.get( 'file_data', '' ) + if csv_file == '': # set form fields fields = [] for i in range( len(self.current_form['fields']) ): fields.append(self.__get_field(i, **kwd)) fields = fields + else: + fields = self.__import_fields(trans, csv_file) return name, desc, fields - def __update_current_form(self, **kwd): - name, desc, fields = self.__get_form(**kwd) + def __update_current_form(self, trans, **kwd): + name, desc, fields = self.__get_form(trans, **kwd) self.current_form = {} self.current_form['name'] = name self.current_form['desc'] = desc self.current_form['fields'] = fields - def __import_fields(self, csv_file): + def __import_fields(self, trans, csv_file): ''' "company","name of the company", "True", "required", "TextField",, "due date","turnaround time", "True", "optional", "SelectField","24 hours, 1 week, 1 month" @@ -275,7 +264,7 @@ import csv fields = [] try: - reader = csv.reader(open(csv_file)) + reader = csv.reader(csv_file.file) for row in reader: options = row[5].split(',') fields.append({'label': row[0], @@ -301,7 +290,7 @@ if not flag: return None, msg fd = trans.app.model.FormDefinition() - fd.name, fd.desc, fd.fields = self.__get_form(**kwd) + fd.name, fd.desc, fd.fields = self.__get_form(trans, **kwd) if fdc_id: # save changes to the existing form # change the pointer in the form_definition_current table to point # to this new record @@ -314,9 +303,6 @@ trans.sa_session.save_or_update( fdc ) trans.sa_session.flush() msg = "The new form named '%s' has been created. " % (fd.name) - request_types = trans.app.model.RequestType.query().all() - if not request_types: - msg = msg + "Now you can create requests to associate with this form." return fd, msg class FieldUI(object): @@ -381,18 +367,31 @@ def label(self): return str(self.index)+'.'+self.label - def __show(self, trans, form, msg=None, messagetype='done', **kwd): + def __show( self, trans, form, msg='', messagetype='done', empty_form=False, **kwd ): ''' - This method displays the form and any of the changes made to it + This method displays the form and any of the changes made to it, + The empty_form param allows for this method to simulate clicking + the "add_field_button" on the edit_form.mako page so that the page + is displayed with the first field to be added, saving a mouse click. ''' + if empty_form: + # Send params that will simulate a button click on the add_field_button + # button on edit_form.mako. + param_dict = { 'form_id' : str( form.id ), + 'num_fields' : '0', + 'refresh' : 'true', + 'name' : form.name, + 'description' : form.desc, + 'add_field_button' : 'Add field' } + self.edit( trans, **param_dict ) params = util.Params( kwd ) # name & description - form_details = [ ( 'Name', TextField('name', 40, self.current_form['name']) ), - ( 'Description', TextField('description', 40, self.current_form['desc']) ) ] + form_details = [ ( 'Name', TextField( 'name', 40, self.current_form[ 'name' ] ) ), + ( 'Description', TextField( 'description', 40, self.current_form[ 'desc' ] ) ) ] # fields field_details = [] - for index, field in enumerate(self.current_form['fields']): - field_ui = self.FieldUI(index, field) + for index, field in enumerate( self.current_form[ 'fields' ] ): + field_ui = self.FieldUI( index, field ) field_details.append( field_ui.get() ) return trans.fill_template( '/admin/forms/edit_form.mako', form_details=form_details, @@ -401,3 +400,61 @@ field_types=BaseField.form_field_types(), msg=msg, messagetype=messagetype ) + +# Common methods for all components that use forms +def get_all_forms( trans, all_versions=False, filter=None ): + ''' + Return all the latest forms from the form_definition_current table + if all_versions is set to True. Otherwise return all the versions + of all the forms from the form_definition table. + + TODO: when we add the concept of a form_definition_type ( e.g., + 'request_header', 'request_sample', 'library_template' ), filter + the query if received filter is not None. + ''' + if all_versions: + return trans.app.model.FormDefinition.query().all() + if filter: + fdc_list = trans.app.model.FormDefinitionCurrent.query().filter_by(**filter) + else: + fdc_list = trans.app.model.FormDefinitionCurrent.query().all() + return [ fdc.latest_form for fdc in fdc_list ] +def get_form_widgets( trans, form, contents={} ): + ''' + Return the list of widgets that comprise a form definition, + including field contents if any. + ''' + widgets = [] + for index, field in enumerate( form.fields ): + field_name = 'field_%i' % index + if field_name in contents: + value = contents[ field_name ] + elif field[ 'type' ] == 'CheckboxField': + # Since we do not have contents, set checkbox value to False + value = False + else: + # Set other field types to empty string + value = '' + field_widget = eval( field[ 'type' ] )( field_name ) + if field[ 'type' ] == 'TextField': + field_widget.set_size( 40 ) + field_widget.value = value + elif field[ 'type' ] == 'TextArea': + field_widget.set_size( 3, 40 ) + field_widget.value = value + elif field[ 'type' ] == 'SelectField': + for option in field[ 'selectlist' ]: + if option == value: + field_widget.add_option( option, option, selected=True ) + else: + field_widget.add_option( option, option ) + elif field[ 'type' ] == 'CheckboxField': + field_widget.checked = value + if field[ 'required' ] == 'required': + req = 'Required' + else: + req = 'Optional' + widgets.append( dict( label=field[ 'label' ], + widget=field_widget, + helptext='%s (%s)' % ( field[ 'helptext' ], req ) ) ) + return widgets diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Aug 13 13:44:04 2009 -0400 @@ -12,7 +12,6 @@ # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" - class HistoryListGrid( grids.Grid ): # Custom column types @@ -70,8 +69,43 @@ def apply_default_filter( self, trans, query ): return query.filter_by( user=trans.user, purged=False ) +class SharedHistoryListGrid( grids.Grid ): + # Custom column types + class DatasetsByStateColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + rval = [] + for state in ( 'ok', 'running', 'queued', 'error' ): + total = sum( 1 for d in history.active_datasets if d.state == state ) + if total: + rval.append( '<div class="count-box state-color-%s">%s</div>' % ( state, total ) ) + else: + rval.append( '' ) + return rval + class SharedByColumn( grids.GridColumn ): + def get_value( self, trans, grid, history ): + return history.user.email + # Grid definition + title = "Histories shared with you by others" + model_class = model.History + default_sort_key = "-update_time" + columns = [ + grids.GridColumn( "Name", key="name" ), + DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), + SharedByColumn( "Shared by", key="user_id" ) + ] + operations = [ + grids.GridOperation( "Clone" ), + grids.GridOperation( "Unshare" ) + ] + standard_filters = [] + def build_initial_query( self, session ): + return session.query( self.model_class ).join( 'users_shared_with' ) + def apply_default_filter( self, trans, query ): + return query.filter( model.HistoryUserShareAssociation.user == trans.user ) + class HistoryController( BaseController ): - @web.expose def index( self, trans ): return "" @@ -80,7 +114,8 @@ """XML history list for functional tests""" return trans.fill_template( "/history/list_as_xml.mako" ) - list_grid = HistoryListGrid() + stored_list_grid = HistoryListGrid() + shared_list_grid = SharedHistoryListGrid() @web.expose @web.require_login( "work with multiple histories" ) @@ -91,7 +126,6 @@ if 'operation' in kwargs: history_ids = util.listify( kwargs.get( 'id', [] ) ) histories = [] - shared_by_others = [] operation = kwargs['operation'].lower() if operation == "share": return self.share( trans, **kwargs ) @@ -127,7 +161,7 @@ status, message = self._list_undelete( trans, histories ) trans.sa_session.flush() # Render the list view - return self.list_grid( trans, status=status, message=message, template='/history/grid.mako', **kwargs ) + return self.stored_list_grid( trans, status=status, message=message, template='/history/stored_grid.mako', **kwargs ) def _list_delete( self, trans, histories ): """Delete histories""" n_deleted = 0 @@ -195,18 +229,38 @@ # No message return None, None @web.expose - def list_shared( self, trans, **kwd ): + def list_shared( self, trans, **kwargs ): """List histories shared with current user by others""" - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - shared_by_others = trans.sa_session \ - .query( model.HistoryUserShareAssociation ) \ - .filter_by( user=trans.user ) \ - .join( 'history' ) \ - .filter( model.History.deleted == False ) \ - .order_by( desc( model.History.update_time ) ) \ - .all() - return trans.fill_template( "/history/list_shared.mako", shared_by_others=shared_by_others, msg=msg, messagetype='done' ) + msg = util.restore_text( kwargs.get( 'msg', '' ) ) + status = message = None + if 'operation' in kwargs: + id = kwargs.get( 'id', None ) + operation = kwargs['operation'].lower() + if operation == "clone": + if not id: + message = "Select a history to clone" + return self.shared_list_grid( trans, status='error', message=message, template='/history/shared_grid.mako', **kwargs ) + # When cloning shared histories, only copy active datasets + new_kwargs = { 'clone_choice' : 'active' } + return self.clone( trans, id, **new_kwargs ) + elif operation == 'unshare': + if not id: + message = "Select a history to unshare" + return self.shared_list_grid( trans, status='error', message=message, template='/history/shared_grid.mako', **kwargs ) + ids = util.listify( id ) + histories = [] + for history_id in ids: + history = get_history( trans, history_id, check_ownership=False ) + histories.append( history ) + for history in histories: + # Current user is the user with which the histories were shared + association = trans.app.model.HistoryUserShareAssociation.filter_by( user=trans.user, history=history ).one() + association.delete() + association.flush() + message = "Unshared %d shared histories" % len( ids ) + status = 'done' + # Render the list view + return self.shared_list_grid( trans, status=status, message=message, template='/history/shared_grid.mako', **kwargs ) @web.expose def delete_current( self, trans ): """Delete just the active history -- this does not require a logged in user.""" @@ -323,6 +377,9 @@ can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \ self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err, unique=True ) send_to_err += err_msg + if cannot_change and not no_change_needed and not can_change: + send_to_err = "The histories you are sharing do not contain any datasets that can be accessed by the users with which you are sharing." + return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) if can_change or cannot_change: return trans.fill_template( "/history/share.mako", histories=histories, @@ -350,8 +407,6 @@ email=email, err_msg=err_msg, share_button=True ) ) - if action == "no_share": - trans.response.send_redirect( url_for( controller='root', action='history_options' ) ) user = trans.get_user() histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email ) send_to_err = '' @@ -629,29 +684,38 @@ @web.expose @web.require_login( "clone shared Galaxy history" ) def clone( self, trans, id, **kwd ): - history = get_history( trans, id, check_ownership=False ) + """Clone a list of histories""" params = util.Params( kwd ) + ids = util.listify( id ) + histories = [] + for history_id in ids: + history = get_history( trans, history_id, check_ownership=False ) + histories.append( history ) clone_choice = params.get( 'clone_choice', None ) if not clone_choice: return trans.fill_template( "/history/clone.mako", history=history ) user = trans.get_user() - if history.user == user: - owner = True + for history in histories: + if history.user == user: + owner = True + else: + if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \ + .filter_by( user=user, history=history ).count() == 0: + return trans.show_error_message( "The history you are attempting to clone is not owned by you or shared with you. " ) + owner = False + name = "Clone of '%s'" % history.name + if not owner: + name += " shared by '%s'" % history.user.email + if clone_choice == 'activatable': + new_history = history.copy( name=name, target_user=user, activatable=True ) + elif clone_choice == 'active': + name += " (active items only)" + new_history = history.copy( name=name, target_user=user ) + if len( histories ) == 1: + msg = 'Clone with name "%s" is now included in your previously stored histories.' % new_history.name else: - if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \ - .filter_by( user=user, history=history ).count() == 0: - return trans.show_error_message( "The history you are attempting to clone is not owned by you or shared with you. " ) - owner = False - name = "Clone of '%s'" % history.name - if not owner: - name += " shared by '%s'" % history.user.email - if clone_choice == 'activatable': - new_history = history.copy( name=name, target_user=user, activatable=True ) - elif clone_choice == 'active': - name += " (active items only)" - new_history = history.copy( name=name, target_user=user ) - # Render the list view - return trans.show_ok_message( 'Clone with name "%s" is now included in your list of stored histories.' % new_history.name ) + msg = '%d cloned histories are now included in your previously stored histories.' % len( histories ) + return trans.show_ok_message( msg ) ## ---- Utility methods ------------------------------------------------------- diff -r f1f2d1de5f3e -r 5b6146705e80 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Thu Aug 13 13:43:25 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Thu Aug 13 13:44:04 2009 -0400 @@ -2,6 +2,7 @@ from galaxy.model.orm import * from galaxy.datatypes import sniff from galaxy import util +from galaxy.web.controllers.forms import get_all_forms, get_form_widgets from galaxy.util.streamball import StreamBall import logging, tempfile, zipfile, tarfile, os, sys @@ -130,6 +131,21 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) if action == 'information': + # See if we have any associated templates + if library.info_association: + template = library.info_association[0].template + # See if we have any field contents + info = library.info_association[0].info + if info: + field_contents = {} + for index, value in enumerate( info.content ): + key = 'field_%i' % index + field_contents[ key ] = value + widgets = get_form_widgets( trans, template, field_contents ) + else: + widgets = get_form_widgets( trans, template ) + else: + widgets = [] if params.get( 'rename_library_button', False ): old_name = library.name new_name = util.restore_text( params.name ) @@ -138,8 +154,7 @@ msg = 'Enter a valid name' return trans.fill_template( '/library/library_info.mako', library=library, - restrict=params.get( 'restrict', False ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype='error' ) else: @@ -159,8 +174,7 @@ messagetype='done' ) ) return trans.fill_template( '/library/library_info.mako', library=library, - restrict=params.get( 'restrict', False ), - render_templates=params.get( 'render_templates', False ), + widgets=widgets, msg=msg, messagetype=messagetype ) elif action == 'permissions': @@ -377,8 +391,6 @@ return trans.fill_template( '/library/library_dataset_info.mako', library_dataset=library_dataset, library_id=library_id, - restrict=params.get( 'restrict', True ),

1 0

[hg] galaxy 2572: Allows storing of multiple preferences in one ...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a6be5c3955e9 changeset: 2572:a6be5c3955e9 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 10 12:09:50 2009 -0400 description: Allows storing of multiple preferences in one cookie using JSON. Use this to store workflow overview settings 3 file(s) affected in this change: static/scripts/json2.js static/scripts/json_cookie.js templates/workflow/editor.mako diffs (641 lines): diff -r 3c64aa0a0f85 -r a6be5c3955e9 static/scripts/json2.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/json2.js Mon Aug 10 12:09:50 2009 -0400 @@ -0,0 +1,476 @@ +/* + http://www.JSON.org/json2.js + 2009-06-29 + + Public Domain. + + NO WARRANTY EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK. + + See http://www.JSON.org/js.html + + This file creates a global JSON object containing two methods: stringify + and parse. + + JSON.stringify(value, replacer, space) + value any JavaScript value, usually an object or array. + + replacer an optional parameter that determines how object + values are stringified for objects. It can be a + function or an array of strings. + + space an optional parameter that specifies the indentation + of nested structures. If it is omitted, the text will + be packed without extra whitespace. If it is a number, + it will specify the number of spaces to indent at each + level. If it is a string (such as '\t' or ' '), + it contains the characters used to indent at each level. + + This method produces a JSON text from a JavaScript value. + + When an object value is found, if the object contains a toJSON + method, its toJSON method will be called and the result will be + stringified. A toJSON method does not serialize: it returns the + value represented by the name/value pair that should be serialized, + or undefined if nothing should be serialized. The toJSON method + will be passed the key associated with the value, and this will be + bound to the object holding the key. + + For example, this would serialize Dates as ISO strings. + + Date.prototype.toJSON = function (key) { + function f(n) { + // Format integers to have at least two digits. + return n < 10 ? '0' + n : n; + } + + return this.getUTCFullYear() + '-' + + f(this.getUTCMonth() + 1) + '-' + + f(this.getUTCDate()) + 'T' + + f(this.getUTCHours()) + ':' + + f(this.getUTCMinutes()) + ':' + + f(this.getUTCSeconds()) + 'Z'; + }; + + You can provide an optional replacer method. It will be passed the + key and value of each member, with this bound to the containing + object. The value that is returned from your method will be + serialized. If your method returns undefined, then the member will + be excluded from the serialization. + + If the replacer parameter is an array of strings, then it will be + used to select the members to be serialized. It filters the results + such that only members with keys listed in the replacer array are + stringified. + + Values that do not have JSON representations, such as undefined or + functions, will not be serialized. Such values in objects will be + dropped; in arrays they will be replaced with null. You can use + a replacer function to replace those with JSON values. + JSON.stringify(undefined) returns undefined. + + The optional space parameter produces a stringification of the + value that is filled with line breaks and indentation to make it + easier to read. + + If the space parameter is a non-empty string, then that string will + be used for indentation. If the space parameter is a number, then + the indentation will be that many spaces. + + Example: + + text = JSON.stringify(['e', {pluribus: 'unum'}]); + // text is '["e",{"pluribus":"unum"}]' + + + text = JSON.stringify(['e', {pluribus: 'unum'}], null, '\t'); + // text is '[\n\t"e",\n\t{\n\t\t"pluribus": "unum"\n\t}\n]' + + text = JSON.stringify([new Date()], function (key, value) { + return this[key] instanceof Date ? + 'Date(' + this[key] + ')' : value; + }); + // text is '["Date(---current time---)"]' + + + JSON.parse(text, reviver) + This method parses a JSON text to produce an object or array. + It can throw a SyntaxError exception. + + The optional reviver parameter is a function that can filter and + transform the results. It receives each of the keys and values, + and its return value is used instead of the original value. + If it returns what it received, then the structure is not modified. + If it returns undefined then the member is deleted. + + Example: + + // Parse the text. Values that look like ISO date strings will + // be converted to Date objects. + + myData = JSON.parse(text, function (key, value) { + var a; + if (typeof value === 'string') { + a = +/^(\d{4})-(\d{2})-(\d{2})T(\d{2}):(\d{2}):(\d{2}(?:\.\d*)?)Z$/.exec(value); + if (a) { + return new Date(Date.UTC(+a[1], +a[2] - 1, +a[3], +a[4], + +a[5], +a[6])); + } + } + return value; + }); + + myData = JSON.parse('["Date(09/09/2001)"]', function (key, value) { + var d; + if (typeof value === 'string' && + value.slice(0, 5) === 'Date(' && + value.slice(-1) === ')') { + d = new Date(value.slice(5, -1)); + if (d) { + return d; + } + } + return value; + }); + + + This is a reference implementation. You are free to copy, modify, or + redistribute. + + This code should be minified before deployment. + See http://javascript.crockford.com/jsmin.html + + USE YOUR OWN COPY. IT IS EXTREMELY UNWISE TO LOAD CODE FROM SERVERS YOU DO + NOT CONTROL. +*/ + +/*jslint evil: true */ + +/*members "", "\b", "\t", "\n", "\f", "\r", "\"", JSON, "\\", apply, + call, charCodeAt, getUTCDate, getUTCFullYear, getUTCHours, + getUTCMinutes, getUTCMonth, getUTCSeconds, hasOwnProperty, join, + lastIndex, length, parse, prototype, push, replace, slice, stringify, + test, toJSON, toString, valueOf +*/ + +// Create a JSON object only if one does not already exist. We create the +// methods in a closure to avoid creating global variables. + +var JSON = JSON || {}; + +(function () { + + function f(n) { + // Format integers to have at least two digits. + return n < 10 ? '0' + n : n; + } + + if (typeof Date.prototype.toJSON !== 'function') { + + Date.prototype.toJSON = function (key) { + + return isFinite(this.valueOf()) ? + this.getUTCFullYear() + '-' + + f(this.getUTCMonth() + 1) + '-' + + f(this.getUTCDate()) + 'T' + + f(this.getUTCHours()) + ':' + + f(this.getUTCMinutes()) + ':' + + f(this.getUTCSeconds()) + 'Z' : null; + }; + + String.prototype.toJSON = + Number.prototype.toJSON = + Boolean.prototype.toJSON = function (key) { + return this.valueOf(); + }; + } + + var cx = /[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g, + escapable = /[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g, + gap, + indent, + meta = { // table of character substitutions + '\b': '\\b', + '\t': '\\t', + '\n': '\\n', + '\f': '\\f', + '\r': '\\r', + '"' : '\\"', + '\\': '\\\\' + }, + rep; + + + function quote(string) { + +// If the string contains no control characters, no quote characters, and no +// backslash characters, then we can safely slap some quotes around it. +// Otherwise we must also replace the offending characters with safe escape +// sequences. + + escapable.lastIndex = 0; + return escapable.test(string) ? + '"' + string.replace(escapable, function (a) { + var c = meta[a]; + return typeof c === 'string' ? c : + '\\u' + ('0000' + a.charCodeAt(0).toString(16)).slice(-4); + }) + '"' : + '"' + string + '"'; + } + + + function str(key, holder) { + +// Produce a string from holder[key]. + + var i, // The loop counter. + k, // The member key. + v, // The member value. + length, + mind = gap, + partial, + value = holder[key]; + +// If the value has a toJSON method, call it to obtain a replacement value. + + if (value && typeof value === 'object' && + typeof value.toJSON === 'function') { + value = value.toJSON(key); + } + +// If we were called with a replacer function, then call the replacer to +// obtain a replacement value. + + if (typeof rep === 'function') { + value = rep.call(holder, key, value); + } + +// What happens next depends on the value's type. + + switch (typeof value) { + case 'string': + return quote(value); + + case 'number': + +// JSON numbers must be finite. Encode non-finite numbers as null. + + return isFinite(value) ? String(value) : 'null'; + + case 'boolean': + case 'null': + +// If the value is a boolean or null, convert it to a string. Note: +// typeof null does not produce 'null'. The case is included here in +// the remote chance that this gets fixed someday. + + return String(value); + +// If the type is 'object', we might be dealing with an object or an array or +// null. + + case 'object': + +// Due to a specification blunder in ECMAScript, typeof null is 'object', +// so watch out for that case. + + if (!value) { + return 'null'; + } + +// Make an array to hold the partial results of stringifying this object value. + + gap += indent; + partial = []; + +// Is the value an array? + + if (Object.prototype.toString.apply(value) === '[object Array]') { + +// The value is an array. Stringify every element. Use null as a placeholder +// for non-JSON values. + + length = value.length; + for (i = 0; i < length; i += 1) { + partial[i] = str(i, value) || 'null'; + } + +// Join all of the elements together, separated with commas, and wrap them in +// brackets. + + v = partial.length === 0 ? '[]' : + gap ? '[\n' + gap + + partial.join(',\n' + gap) + '\n' + + mind + ']' : + '[' + partial.join(',') + ']'; + gap = mind; + return v; + } + +// If the replacer is an array, use it to select the members to be stringified. + + if (rep && typeof rep === 'object') { + length = rep.length; + for (i = 0; i < length; i += 1) { + k = rep[i]; + if (typeof k === 'string') { + v = str(k, value); + if (v) { + partial.push(quote(k) + (gap ? ': ' : ':') + v); + } + } + } + } else { + +// Otherwise, iterate through all of the keys in the object. + + for (k in value) { + if (Object.hasOwnProperty.call(value, k)) { + v = str(k, value); + if (v) { + partial.push(quote(k) + (gap ? ': ' : ':') + v); + } + } + } + } + +// Join all of the member texts together, separated with commas, +// and wrap them in braces. + + v = partial.length === 0 ? '{}' : + gap ? '{\n' + gap + partial.join(',\n' + gap) + '\n' + + mind + '}' : '{' + partial.join(',') + '}'; + gap = mind; + return v; + } + } + +// If the JSON object does not yet have a stringify method, give it one. + + if (typeof JSON.stringify !== 'function') { + JSON.stringify = function (value, replacer, space) { + +// The stringify method takes a value and an optional replacer, and an optional +// space parameter, and returns a JSON text. The replacer can be a function +// that can replace values, or an array of strings that will select the keys. +// A default replacer method can be provided. Use of the space parameter can +// produce text that is more easily readable. + + var i; + gap = ''; + indent = ''; + +// If the space parameter is a number, make an indent string containing that +// many spaces. + + if (typeof space === 'number') { + for (i = 0; i < space; i += 1) { + indent += ' '; + } + +// If the space parameter is a string, it will be used as the indent string. + + } else if (typeof space === 'string') { + indent = space; + } + +// If there is a replacer, it must be a function or an array. +// Otherwise, throw an error. + + rep = replacer; + if (replacer && typeof replacer !== 'function' && + (typeof replacer !== 'object' || + typeof replacer.length !== 'number')) { + throw new Error('JSON.stringify'); + } + +// Make a fake root object containing our value under the key of ''. +// Return the result of stringifying the value. + + return str('', {'': value}); + }; + } + + +// If the JSON object does not yet have a parse method, give it one. + + if (typeof JSON.parse !== 'function') { + JSON.parse = function (text, reviver) { + +// The parse method takes a text and an optional reviver function, and returns +// a JavaScript value if the text is a valid JSON text. + + var j; + + function walk(holder, key) { + +// The walk method is used to recursively walk the resulting structure so +// that modifications can be made. + + var k, v, value = holder[key]; + if (value && typeof value === 'object') { + for (k in value) { + if (Object.hasOwnProperty.call(value, k)) { + v = walk(value, k); + if (v !== undefined) { + value[k] = v; + } else { + delete value[k]; + } + } + } + } + return reviver.call(holder, key, value); + } + + +// Parsing happens in four stages. In the first stage, we replace certain +// Unicode characters with escape sequences. JavaScript handles many characters +// incorrectly, either silently deleting them, or treating them as line endings. + + cx.lastIndex = 0; + if (cx.test(text)) { + text = text.replace(cx, function (a) { + return '\\u' + + ('0000' + a.charCodeAt(0).toString(16)).slice(-4); + }); + } + +// In the second stage, we run the text against regular expressions that look +// for non-JSON patterns. We are especially concerned with '()' and 'new' +// because they can cause invocation, and '=' because it can cause mutation. +// But just to be safe, we want to reject all unexpected forms. + +// We split the second stage into 4 regexp operations in order to work around +// crippling inefficiencies in IE's and Safari's regexp engines. First we +// replace the JSON backslash pairs with '@' (a non-JSON character). Second, we +// replace all simple value tokens with ']' characters. Third, we delete all +// open brackets that follow a colon or comma or that begin the text. Finally, +// we look to see that the remaining characters are only whitespace or ']' or +// ',' or ':' or '{' or '}'. If that is so, then the text is safe for eval. + + if (/^[\],:{}\s]*$/. +test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g, '@'). +replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g, ']'). +replace(/(?:^|:|,)(?:\s*\[)+/g, ''))) { + +// In the third stage we use the eval function to compile the text into a +// JavaScript structure. The '{' operator is subject to a syntactic ambiguity +// in JavaScript: it can begin a block or an object literal. We wrap the text +// in parens to eliminate the ambiguity. + + j = eval('(' + text + ')'); + +// In the optional fourth stage, we recursively walk the new structure, passing +// each name/value pair to a reviver function for possible transformation. + + return typeof reviver === 'function' ? + walk({'': j}, '') : j; + } + +// If the text is not JSON parseable, then a SyntaxError is thrown. + + throw new SyntaxError('JSON.parse'); + }; + } +}()); diff -r 3c64aa0a0f85 -r a6be5c3955e9 static/scripts/json_cookie.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/json_cookie.js Mon Aug 10 12:09:50 2009 -0400 @@ -0,0 +1,61 @@ +/* + JSONCookie: Uses JSON to allow the settings of multiple preferences in one cookie. + Kanwei Li, 2009 + + cookie = new JSONCookie("cookie_name"); // Pass in the name of the cookie + + // Gets the value of a preference, returns optional second argument if pref not found + cookie.get("pref", "val_if_not_found"); + + cookie.set("pref", "val"); // Sets a value for the preference and saves cookie + cookie.unset("pref"); // Unsets the preference and saves cookie + cookie.clear() // Deletes the cookie + +*/ + +function JSONCookie(name) { + this.cookie_name = name; + +} + +JSONCookie.prototype = { + json_data : function() { + cookie = $.cookie(this.cookie_name); + return cookie ? JSON.parse(cookie) : null; + }, + + save : function(data) { + $.cookie(this.cookie_name, JSON.stringify(data)); + }, + + get : function(attr, else_val) { + data = this.json_data(); + if (data && data[attr]) { return data[attr]; + } else if (else_val) { return else_val; + } else { return null; + } + }, + + set : function(attr, val) { + data = this.json_data(); + if (data) { + data[attr] = val; + } else { + data = { attr : val } + } + this.save(data); + }, + + unset : function(attr) { + data = this.json_data(); + if (data) { + delete data[attr]; + } + this.save(data); + }, + + clear : function() { + this.save(null); + } + +}; \ No newline at end of file diff -r 3c64aa0a0f85 -r a6be5c3955e9 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Thu Aug 06 16:11:40 2009 -0400 +++ b/templates/workflow/editor.mako Mon Aug 10 12:09:50 2009 -0400 @@ -31,6 +31,9 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.hover.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.form.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.json.js')}"> </script> + <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.cookie.js')}"> </script> + <script type='text/javascript' src="${h.url_for('/static/scripts/json2.js')}"> </script> + <script type='text/javascript' src="${h.url_for('/static/scripts/json_cookie.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.base.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.workflow_editor.canvas.js')}"> </script> @@ -56,6 +59,10 @@ } // Canvas overview management canvas_manager = new CanvasManager( $("#canvas-viewport"), $("#overview") ); + + // Preferences cookie stored as JSON so that only one cookie is needed for multiple settings + var prefs_cookie = new JSONCookie("galaxy.workflow"); + // Initialize workflow state reset(); // Load the datatype info @@ -121,17 +128,42 @@ canvas_manager.draw_overview(); }); - /* Lets the viewport be toggled visible and invisible, adjusting the arrows accordingly */ + // Stores the size of the overview in a cookie when it's resized + $("#overview-border").bind( "dragend", function( e ) { + var op = $(this).offsetParent(); + var opo = op.offset(); + var new_size = Math.max( op.width() - ( e.offsetX - opo.left ), + op.height() - ( e.offsetY - opo.top ) ); + prefs_cookie.set("overview-size", new_size); + }); + + // On load, set the size to the pref stored in cookie if it exists + overview_size = prefs_cookie.get("overview-size"); + if (overview_size) { + $("#overview-border").css( { + width: overview_size, + height: overview_size + }); + } + + function show_overview() { + prefs_cookie.unset("overview-off"); + $("#overview-border").css("right", "0px"); + $("#close-viewport").css("background-position", "0px 0px"); + } + + function hide_overview() { + prefs_cookie.set("overview-off", true); + $("#overview-border").css("right", "20000px"); + $("#close-viewport").css("background-position", "12px 0px"); + } + + // Show viewport on load unless pref says it's off + prefs_cookie.get("overview-off") == true ? hide_overview() : show_overview() + + // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly $("#close-viewport").click( function() { - if ( $("#overview-border").css("right") == "0px" ) { - $("#overview-border").css("right", "20000px"); - $("#close-viewport").css("background-position", "12px 0px"); - - } else { - $("#overview-border").css("right", "0px"); - $("#close-viewport").css("background-position", "0px 0px"); - } - + $("#overview-border").css("right") == "0px" ? hide_overview() : show_overview(); }); // Unload handler @@ -642,7 +674,7 @@ <div id="canvas-viewport" style="width: 100%; height: 100%; position: absolute; overflow: hidden; background: #EEEEEE; background: white url(${h.url_for('/static/images/light_gray_grid.gif')}) repeat;"> <div id="canvas-container" style="position: absolute; width: 100%; height: 100%;"></div> </div> - <div id="overview-border" style="position: absolute; width: 150px; height: 150px; right: 0px; bottom: 0px; border-top: solid gray 1px; border-left: solid grey 1px; padding: 7px 0 0 7px; background: #EEEEEE no-repeat url(${h.url_for('/static/images/resizable.png')}); z-index: 20000; overflow: hidden; max-width: 300px; max-height: 300px; min-width: 50px; min-height: 50px"> + <div id="overview-border" style="position: absolute; width: 150px; height: 150px; right: 20000px; bottom: 0px; border-top: solid gray 1px; border-left: solid grey 1px; padding: 7px 0 0 7px; background: #EEEEEE no-repeat url(${h.url_for('/static/images/resizable.png')}); z-index: 20000; overflow: hidden; max-width: 300px; max-height: 300px; min-width: 50px; min-height: 50px"> <div style="position: relative; overflow: hidden; width: 100%; height: 100%; border-top: solid gray 1px; border-left: solid grey 1px;"> <div id="overview" style="position: absolute;"> <canvas width="0" height="0" style="background: white; width: 100%; height: 100%;" id="overview-canvas"></canvas> @@ -650,7 +682,7 @@ </div> </div> </div> - <div id="close-viewport" style="border-left: 1px solid #999; border-top: 1px solid #999; background: #ddd url(${h.url_for('/static/images/overview_arrows.png')}); position: absolute; right: 0px; bottom: 0px; width: 12px; height: 12px; z-index: 25000;"></div> + <div id="close-viewport" style="border-left: 1px solid #999; border-top: 1px solid #999; background: #ddd url(${h.url_for('/static/images/overview_arrows.png')}) 12px 0px; position: absolute; right: 0px; bottom: 0px; width: 12px; height: 12px; z-index: 25000;"></div> </div> </%def>

1 0

[hg] galaxy 2576: Slight tweak to resizing workflow overview
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f1f2d1de5f3e changeset: 2576:f1f2d1de5f3e user: Kanwei Li <kanwei(a)gmail.com> date: Thu Aug 13 13:43:25 2009 -0400 description: Slight tweak to resizing workflow overview 2 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js static/scripts/packed/galaxy.workflow_editor.canvas.js diffs (24 lines): diff -r 55c0eb35fad7 -r f1f2d1de5f3e static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Aug 13 13:16:58 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Aug 13 13:43:25 2009 -0400 @@ -805,9 +805,9 @@ self.draw_overview(); }); - /* Disable dragging for child elements of the panel so that resizing can - only be done with the border panels */ - $("#overview-border>*").bind("drag", function(e) { }); + /* Disable dragging for child element of the panel so that resizing can + only be done by dragging the borders */ + $("#overview-border div").bind("drag", function(e) { }); }, update_viewport_overlay: function() { diff -r 55c0eb35fad7 -r f1f2d1de5f3e static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 13 13:16:58 2009 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 13 13:43:25 2009 -0400 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.ha ndle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_ form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[sucessors[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$( this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prot otype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this; var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({wi dth:f,height:f});b.draw_overview()})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewp ort_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatype=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var b in this.datatypes){if(a.datatype=="input"){return true}if(issubtype(a.datatype,this.datatypes[b])){return true}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a) {this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f; this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropstart",function(g){g.dragProxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g){g.dragProxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g){(new Connector(g.dragTarget.terminal,g.dropTarget.terminal)).redraw()}).bind("hov er",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j){var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var k=new Connector();k.dragging=true;k.connect(this.terminal,i.terminal);$.dropManage({filter:function(h){return this.terminal.can_accept(f)}}).addClass("input-terminal-active");ret urn i}).bind("drag",function(i){var h=function(){var k=$(i.dragProxy).offsetParent().offset(),j=i.offsetX-k.left,l=i.offsetY-k.top;$(i.dragProxy).css({left:j,top:l});i.dragProxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h){h.dragProxy.terminal.connectors[0].destroy();$(h.dragProxy).remove();$.dropManage().removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b .appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(g){var d=this.element;if(g.type){this.type=g.type}this.name=g.name;this.form_html=g.form_html;this.tool_state=g.tool_state;this.tool_errors=g.tool_errors;if(this.tool_errors){d.addClass("tool-node-error")}else{d.removeClass("tool-node-error")}var c=this;var a=d.find(".toolFormBody");a.find("div").remove();var h=$("<div class='inputs'></div>").appendTo(a);$.each(g.data_inputs,function(j,b){var f=$("<div class='terminal input-terminal'></div>");c.enable_input_terminal(f,b.name,b.extensions);h.append($("<div class='form-row dataRow input-data-row' name='"+b.name+"'>"+b.label+"</div>").prepend(f))});if((g.data_inputs.length>0)&&(g.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(g.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");c.enable_output_terminal(j,b.name,b.extension);var f=b.name;if(b.extension!="input"){f=f+" ("+b.extensio n+")"}a.append($("<div class='form-row dataRow'>"+f+"</div>").append(j))});workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var g=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=g.find("div.input-data-row");$.each(f.data_inputs,function(k,h){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,h.name,h.extensions);g.find("div[name="+h.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){j[0].terminal.connectors[0]=i;i.handle2=j[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+h.name+"'>"+h.label+"</div>").prepend(j))});g.replaceWith(b);g.find("div.input-data-row > .terminal").each(function(){this.terminal.destr oy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},to_simple:function(){var a={};$.each(this.nodes,function(b,d){var f={};$.each(d.input_terminals,function(g,h){f[h.name]=null;$.each(h.connectors,function(j,k){f[h.name]={id:k.ha ndle1.node.id,output_name:k.handle1.name}})});var c={id:d.id,type:d.type,tool_id:d.tool_id,tool_state:d.tool_state,tool_errors:d.tool_errors,input_connections:f,position:$(d.element).position()};a[d.id]=c});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.clear_active_node();parent.show_ form_for_tool(a.form_html,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){parent.show_form_for_tool(a.form_html,a)}},layout:function(){var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[sucessors[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$( this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img src='../images/delete_icon.png' />").click(function(b){g.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o){var f=$(this).offsetParent().offset(),b=o.offsetX-f.left,p=o.offsetY-f.top;$(this).css({left:b,top:p});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prot otype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this; var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(g){var h=$(this).offset();var f=b.cc.position();c=f.top-h.top;d=f.left-h.left}).bind("drag",function(f){a(f.offsetX+d,f.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k){var j=b.cc.width(),g=b.cc.height(),f=b.oc.width(),h=b.oc.height(),i=$(this).offsetParent().offset(),m=k.offsetX-i.left,l=k.offsetY-i.top;a(-(m/f*j),-(l/h*g))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g){var i=$(this).offsetParent();var h=i.offset();var f=Math.max(i.width()-(g.offsetX-h.left),i.height()-(g.offsetY-h.top));$(this).css({wi dth:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(f){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;$.each(workflow.nodes,function(t,q){var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;i.fillRe ct(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file

1 0

[hg] galaxy 2575: Implemented local storage for preferences, obs...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/55c0eb35fad7 changeset: 2575:55c0eb35fad7 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Aug 13 13:16:58 2009 -0400 description: Implemented local storage for preferences, obsoleting cookies that were used for this purpose 7 file(s) affected in this change: static/jStore.Flash.html static/jStore.swf static/scripts/jquery.jstore-all.js static/scripts/packed/jquery.jstore-all.js static/scripts/packed/json2.js templates/root/history.mako templates/workflow/editor.mako diffs (1380 lines): diff -r 7df41ad788de -r 55c0eb35fad7 static/jStore.Flash.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/jStore.Flash.html Thu Aug 13 13:16:58 2009 -0400 @@ -0,0 +1,19 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"> + <head> + <title>Flash External Object</title> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <script type="text/javascript"> + /** + * This function captures the flash_ready event. We need to relay this + * back to the parent so it knows flash is ready. + */ + function flash_ready(){ + parent.flash_ready(); + } + </script> + </head> + <body> + <object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#versi…" width="1" height="1" id="jStoreFlash"><param name="allowScriptAccess" value="always" /><param name="movie" value="jStore.swf" /><param name="quality" value="high" /><param name="bgcolor" value="#ffcc00" /><embed src="jStore.swf" quality="high" bgcolor="#ffcc00" width="1" height="1" name="jStoreFlash" align="middle" allowScriptAccess="always" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" /></object> + </body> +</html> \ No newline at end of file diff -r 7df41ad788de -r 55c0eb35fad7 static/jStore.swf Binary file static/jStore.swf has changed diff -r 7df41ad788de -r 55c0eb35fad7 static/scripts/jquery.jstore-all.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/jquery.jstore-all.js Thu Aug 13 13:16:58 2009 -0400 @@ -0,0 +1,748 @@ +/*! + * jStore - Persistent Client-Side Storage + * + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * + * Dual licensed under: + * MIT: http://www.opensource.org/licenses/mit-license.php + * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html + *//** + * Javascript Class Framework + * + * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) + * Inspired by base2 and Prototype + */ +(function(){ + var initializing = false, fnTest = /xyz/.test(function(){xyz;}) ? /\b_super\b/ : /.*/; + + // The base Class implementation (does nothing) + this.Class = function(){}; + + // Create a new Class that inherits from this class + Class.extend = function(prop) { + var _super = this.prototype; + + // Instantiate a base class (but only create the instance, + // don't run the init constructor) + initializing = true; + var prototype = new this(); + initializing = false; + + // Copy the properties over onto the new prototype + for (var name in prop) { + // Check if we're overwriting an existing function + prototype[name] = typeof prop[name] == "function" && + typeof _super[name] == "function" && fnTest.test(prop[name]) ? + (function(name, fn){ + return function() { + var tmp = this._super; + + // Add a new ._super() method that is the same method + // but on the super-class + this._super = _super[name]; + + // The method only need to be bound temporarily, so we + // remove it when we're done executing + var ret = fn.apply(this, arguments); + this._super = tmp; + + return ret; + }; + })(name, prop[name]) : + prop[name]; + } + + // The dummy class constructor + function Class() { + // All construction is actually done in the init method + if ( !initializing && this.init ) + this.init.apply(this, arguments); + } + + // Populate our constructed prototype object + Class.prototype = prototype; + + // Enforce the constructor to be what we expect + Class.constructor = Class; + + // And make this class extendable + Class.extend = arguments.callee; + + return Class; + }; +})(); +/*! + * jStore Delegate Framework + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + this.jStoreDelegate = Class.extend({ + init: function(parent){ + // The Object this delgate operates for + this.parent = parent; + // Container for callbacks to dispatch. + // eventType => [ callback, callback, ... ] + this.callbacks = {}; + }, + bind: function(event, callback){ + if ( !$.isFunction(callback) ) return this; + if ( !this.callbacks[ event ] ) this.callbacks[ event ] = []; + + this.callbacks[ event ].push(callback); + + return this; + }, + trigger: function(){ + var parent = this.parent, + args = [].slice.call(arguments), + event = args.shift(), + handlers = this.callbacks[ event ]; + + if ( !handlers ) return false; + + $.each(handlers, function(){ this.apply(parent, args) }); + return this; + } + }); + +})(jQuery);/** + * jStore-jQuery Interface + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Setup the jStore namespace in jQuery for options storage + $.jStore = {}; + + // Seed the options in + $.extend($.jStore, { + EngineOrder: [], + // Engines should put their availability tests within jStore.Availability + Availability: {}, + // Defined engines should enter themselves into the jStore.Engines + Engines: {}, + // Instanciated engines should exist within jStore.Instances + Instances: {}, + // The current engine to use for storage + CurrentEngine: null, + // Provide global settings for overwriting + defaults: { + project: null, + engine: null, + autoload: true, + flash: 'jStore.Flash.html' + }, + // Boolean for ready state handling + isReady: false, + // Boolean for flash ready state handling + isFlashReady: false, + // An event delegate + delegate: new jStoreDelegate($.jStore) + .bind('jStore-ready', function(engine){ + $.jStore.isReady = true; + if ($.jStore.defaults.autoload) engine.connect(); + }) + .bind('flash-ready', function(){ + $.jStore.isFlashReady = true; + }) + }); + + // Enable ready callback for jStore + $.jStore.ready = function(callback){ + if ($.jStore.isReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); + else $.jStore.delegate.bind('jStore-ready', callback); + } + + // Enable failure callback registration for jStore + $.jStore.fail = function(callback){ + $.jStore.delegate.bind('jStore-failure', callback); + } + + // Enable ready callback for Flash + $.jStore.flashReady = function(callback){ + if ($.jStore.isFlashReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); + else $.jStore.delegate.bind('flash-ready', callback); + } + + // Enable and test an engine + $.jStore.use = function(engine, project, identifier){ + project = project || $.jStore.defaults.project || location.hostname.replace(/\./g, '-') || 'unknown'; + + var e = $.jStore.Engines[engine.toLowerCase()] || null, + name = (identifier ? identifier + '.' : '') + project + '.' + engine; + + if ( !e ) throw 'JSTORE_ENGINE_UNDEFINED'; + + // Instanciate the engine + e = new e(project, name); + + // Prevent against naming conflicts + if ($.jStore.Instances[name]) throw 'JSTORE_JRI_CONFLICT'; + + // Test the engine + if (e.isAvailable()){ + $.jStore.Instances[name] = e; // The Easy Way + if (!$.jStore.CurrentEngine){ + $.jStore.CurrentEngine = e; + } + $.jStore.delegate.trigger('jStore-ready', e); + } else { + if (!e.autoload) // Not available + throw 'JSTORE_ENGINE_UNAVILABLE'; + else { // The hard way + e.included(function(){ + if (this.isAvailable()) { // Worked out + $.jStore.Instances[name] = this; + // If there is no current engine, use this one + if (!$.jStore.CurrentEngine){ + $.jStore.CurrentEngine = this; + } + $.jStore.delegate.trigger('jStore-ready', this); + } + else $.jStore.delegate.trigger('jStore-failure', this); + }).include(); + } + } + } + + // Set the current storage engine + $.jStore.setCurrentEngine = function(name){ + if (!$.jStore.Instances.length ) // If no instances exist, attempt to load one + return $.jStore.FindEngine(); + + if (!name && $.jStore.Instances.length >= 1) { // If no name is specified, use the first engine + $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[0]); + return $.jStore.CurrentEngine = $.jStore.Instances[0]; + } + + if (name && $.jStore.Instances[name]) { // If a name is specified and exists, use it + $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[name]); + return $.jStore.CurrentEngine = $.jStore.Instances[name]; + } + + throw 'JSTORE_JRI_NO_MATCH'; + } + + // Test all possible engines for straightforward useability + $.jStore.FindEngine = function(){ + $.each($.jStore.EngineOrder, function(k){ + if ($.jStore.Availability[this]()){ // Find the first, easiest option and use it. + $.jStore.use(this, $.jStore.defaults.project, 'default'); + return false; + } + }) + } + + // Provide a simple interface for storing/getting values + $.jStore.store = function(key, value){ + if (!$.jStore.CurrentEngine) return false; + + if ( !value ) // Executing a get command + return $.jStore.CurrentEngine.get(key); + // Executing a set command + return $.jStore.CurrentEngine.set(key, value); + } + // Provide a simple interface for storing/getting values + $.jStore.remove = function(key){ + if (!$.jStore.CurrentEngine) return false; + + return $.jStore.CurrentEngine.rem(key); + } + + // Provide a chainable interface for storing values/getting a value at the end of a chain + $.fn.store = function(key, value){ + if (!$.jStore.CurrentEngine) return this; + + var result = $.jStore.store(key, value); + + return !value ? result : this; + } + + // Provide a chainable interface for removing values + $.fn.removeStore = function(key){ + $.jStore.remove(key); + + return this; + } + + // Provide a way for users to call for auto-loading + $.jStore.load = function(){ + if ($.jStore.defaults.engine) + return $.jStore.use($.jStore.defaults.engine, $.jStore.defaults.project, 'default'); + + // Attempt to find a valid engine, and catch any exceptions if we can't + try { + $.jStore.FindEngine(); + } catch (e) {} + } + +})(jQuery); +/** + * jStore Engine Core + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + this.StorageEngine = Class.extend({ + init: function(project, name){ + // Configure the project name + this.project = project; + // The JRI name given by the manager + this.jri = name; + // Cache the data so we can work synchronously + this.data = {}; + // The maximum limit of the storage engine + this.limit = -1; + // Third party script includes + this.includes = []; + // Create an event delegate for users to subscribe to event triggers + this.delegate = new jStoreDelegate(this) + .bind('engine-ready', function(){ + this.isReady = true; + }) + .bind('engine-included', function(){ + this.hasIncluded = true; + }); + // If enabled, the manager will check availability, then run include(), then check again + this.autoload = false; // This should be changed by the engines, if they have required includes + // When set, we're ready to transact data + this.isReady = false; + // When the includer is finished, it will set this to true + this.hasIncluded = false; + }, + // Performs all necessary script includes + include: function(){ + var self = this, + total = this.includes.length, + count = 0; + + $.each(this.includes, function(){ + $.ajax({type: 'get', url: this, dataType: 'script', cache: true, + success: function(){ + count++; + if (count == total) self.delegate.trigger('engine-included'); + } + }) + }); + }, + // This should be overloaded with an actual functionality presence check + isAvailable: function(){ + return false; + }, + /** Event Subscription Shortcuts **/ + ready: function(callback){ + if (this.isReady) callback.apply(this); + else this.delegate.bind('engine-ready', callback); + return this; + }, + included: function(callback){ + if (this.hasIncluded) callback.apply(this); + else this.delegate.bind('engine-included', callback); + return this; + }, + /** Cache Data Access **/ + get: function(key){ + return this.data[key] || null; + }, + set: function(key, value){ + this.data[key] = value; + return value; + }, + rem: function(key){ + var beforeDelete = this.data[key]; + this.data[key] = null; + return beforeDelete; + } + }); + +})(jQuery); +/*! + * jStore DOM Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var sessionAvailability = $.jStore.Availability.session = function(){ + return !!window.sessionStorage; + }, + localAvailability = $.jStore.Availability.local = function(){ + return !!(window.localStorage || window.globalStorage); + }; + + this.jStoreDom = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'DOM'; + + // Set the Database limit + this.limit = 5 * 1024 * 1024; + }, + connect: function(){ + // Fire our delegate to indicate we're ready for data transactions + this.delegate.trigger('engine-ready'); + }, + get: function(key){ + var out = this.db.getItem(key); + // Gecko's getItem returns {value: 'the value'}, WebKit returns 'the value' + return out && out.value ? out.value : out + }, + set: function(key, value){ + this.db.setItem(key,value); + return value; + }, + rem: function(key){ + var out = this.get(key); + this.db.removeItem(key); + return out + } + }) + + this.jStoreLocal = jStoreDom.extend({ + connect: function(){ + // Gecko uses a non-standard globalStorage[ www.example.com ] DOM access object for persistant storage. + this.db = !window.globalStorage ? window.localStorage : window.globalStorage[location.hostname]; + this._super(); + }, + isAvailable: localAvailability + }) + + this.jStoreSession = jStoreDom.extend({ + connect: function(){ + this.db = sessionStorage; + this._super(); + }, + isAvailable: sessionAvailability + }) + + $.jStore.Engines.local = jStoreLocal; + $.jStore.Engines.session = jStoreSession; + + // Store the ordering preference + $.jStore.EngineOrder[ 1 ] = 'local'; + +})(jQuery); +/*! + * jStore Flash Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.flash = function(){ + return !!($.jStore.hasFlash('8.0.0')); + } + + this.jStoreFlash = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'Flash'; + + // Bind our flashReady function to the jStore Delegate + var self = this; + $.jStore.flashReady(function(){ self.flashReady() }); + }, + connect: function(){ + var name = 'jstore-flash-embed-' + this.project; + + // To make Flash Storage work on IE, we have to load up an iFrame + // which contains an HTML page that embeds the object using an + // object tag wrapping an embed tag. Of course, this is unnecessary for + // all browsers except for IE, which, to my knowledge, is the only browser + // in existance where you need to complicate your code to fix bugs. Goddamnit. :( + $(document.body) + .append('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" ' + + 'id="jStoreFlashFrame" src="' +$.jStore.defaults.flash + '"></iframe>'); + }, + flashReady: function(e){ + var iFrame = $('#jStoreFlashFrame')[0]; + + // IE + if (iFrame.Document && $.isFunction(iFrame.Document['jStoreFlash'].f_get_cookie)) this.db = iFrame.Document['jStoreFlash']; + // Safari && Firefox + else if (iFrame.contentWindow && iFrame.contentWindow.document){ + var doc = iFrame.contentWindow.document; + // Safari + if ($.isFunction($('object', $(doc))[0].f_get_cookie)) this.db = $('object', $(doc))[0]; + // Firefox + else if ($.isFunction($('embed', $(doc))[0].f_get_cookie)) this.db = $('embed', $(doc))[0]; + } + + // We're ready to process data + if (this.db) this.delegate.trigger('engine-ready'); + }, + isAvailable: avilability, + get: function(key){ + var out = this.db.f_get_cookie(key); + return out == 'null' ? null : out; + }, + set: function(key, value){ + this.db.f_set_cookie(key, value); + return value; + }, + rem: function(key){ + var beforeDelete = this.get(key); + this.db.f_delete_cookie(key); + return beforeDelete; + } + }) + + $.jStore.Engines.flash = jStoreFlash; + + // Store the ordering preference + $.jStore.EngineOrder[ 2 ] = 'flash'; + + /** + * Flash Detection functions copied from the jQuery Flash Plugin + * Copyright (c) 2006 Luke Lutman (http://jquery.lukelutman.com/plugins/flash) + * Dual licensed under the MIT and GPL licenses. + * http://www.opensource.org/licenses/mit-license.php + * http://www.opensource.org/licenses/gpl-license.php + */ + $.jStore.hasFlash = function(version){ + var pv = $.jStore.flashVersion().match(/\d+/g), + rv = version.match(/\d+/g); + + for(var i = 0; i < 3; i++) { + pv[i] = parseInt(pv[i] || 0); + rv[i] = parseInt(rv[i] || 0); + // player is less than required + if(pv[i] < rv[i]) return false; + // player is greater than required + if(pv[i] > rv[i]) return true; + } + // major version, minor version and revision match exactly + return true; + } + + $.jStore.flashVersion = function(){ + // ie + try { + try { + // avoid fp6 minor version lookup issues + // see: http://blog.deconcept.com/2006/01/11/getvariable-setvariable-crash-internet… + var axo = new ActiveXObject('ShockwaveFlash.ShockwaveFlash.6'); + try { axo.AllowScriptAccess = 'always'; } + catch(e) { return '6,0,0'; } + } catch(e) {} + return new ActiveXObject('ShockwaveFlash.ShockwaveFlash').GetVariable('$version').replace(/\D+/g, ',').match(/^,?(.+),?$/)[1]; + // other browsers + } catch(e) { + try { + if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){ + return (navigator.plugins["Shockwave Flash 2.0"] || navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g, ",").match(/^,?(.+),?$/)[1]; + } + } catch(e) {} + } + return '0,0,0'; + } + +})(jQuery); + +// Callback fired when ExternalInterface is established +function flash_ready(){ + $.jStore.delegate.trigger('flash-ready'); +} +/*! + * jStore Google Gears Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.gears = function(){ + return !!(window.google && window.google.gears) + } + + this.jStoreGears = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'Google Gears'; + + // Add required third-party scripts + this.includes.push('http://code.google.com/apis/gears/gears_init.js'); + + // Allow Autoloading on fail + this.autoload = true; + }, + connect: function(){ + // Create our database connection + var db = this.db = google.gears.factory.create('beta.database'); + db.open( 'jstore-' + this.project ); + db.execute( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); + + // Cache the data from the table + this.updateCache(); + }, + updateCache: function(){ + // Read the database into our cache object + var result = this.db.execute( 'SELECT k,v FROM jstore' ); + while (result.isValidRow()){ + this.data[result.field(0)] = result.field(1); + result.next(); + } result.close(); + + // Fire our delegate to indicate we're ready for data transactions + this.delegate.trigger('engine-ready'); + }, + isAvailable: avilability, + set: function(key, value){ + // Update the database + var db = this.db; + db.execute( 'BEGIN' ); + db.execute( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value] ); + db.execute( 'COMMIT' ); + return this._super(key, value); + }, + rem: function(key){ + // Update the database + var db = this.db; + db.execute( 'BEGIN' ); + db.execute( 'DELETE FROM jstore WHERE k = ?', [key] ); + db.execute( 'COMMIT' ); + return this._super(key); + } + }) + + $.jStore.Engines.gears = jStoreGears; + + // Store the ordering preference + $.jStore.EngineOrder[ 3 ] = 'gears'; + +})(jQuery); +/*! + * jStore HTML5 Specification Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.html5 = function(){ + return !!window.openDatabase + } + + this.jStoreHtml5 = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'HTML5'; + + // Set the Database limit + this.limit = 1024 * 200; + }, + connect: function(){ + // Create our database connection + var db = this.db = openDatabase('jstore-' + this.project, '1.0', this.project, this.limit); + if (!db) throw 'JSTORE_ENGINE_HTML5_NODB'; + db.transaction(function(db){ + db.executeSql( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); + }); + + // Cache the data from the table + this.updateCache(); + }, + updateCache: function(){ + var self = this; + // Read the database into our cache object + this.db.transaction(function(db){ + db.executeSql( 'SELECT k,v FROM jstore', [], function(db, result){ + var rows = result.rows, i = 0, row; + for (; i < rows.length; ++i){ + row = rows.item(i); + self.data[row.k] = row.v; + } + + // Fire our delegate to indicate we're ready for data transactions + self.delegate.trigger('engine-ready'); + }); + }); + }, + isAvailable: avilability, + set: function(key, value){ + // Update the database + this.db.transaction(function(db){ + db.executeSql( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value]); + }); + return this._super(key, value); + }, + rem: function(key){ + // Update the database + this.db.transaction(function(db){ + db.executeSql( 'DELETE FROM jstore WHERE k = ?', [key] ) + }) + return this._super(key); + } + }) + + $.jStore.Engines.html5 = jStoreHtml5; + + // Store the ordering preference + $.jStore.EngineOrder[ 0 ] = 'html5'; + +})(jQuery); +/*!* + * jStore IE Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function($){ + + // Set up a static test function for this instance + var avilability = $.jStore.Availability.ie = function(){ + return !!window.ActiveXObject; + } + + this.jStoreIE = StorageEngine.extend({ + init: function(project, name){ + // Call the parental init object + this._super(project, name); + + // The type of storage engine + this.type = 'IE'; + + // Allow Autoloading on fail + this.limit = 64 * 1024; + }, + connect: function(){ + // Create a hidden div to store attributes in + this.db = $('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-' + this.project + '"></div>') + .appendTo(document.body).get(0); + // Fire our delegate to indicate we're ready for data transactions + this.delegate.trigger('engine-ready'); + }, + isAvailable: avilability, + get: function(key){ + this.db.load(this.project); + return this.db.getAttribute(key); + }, + set: function(key, value){ + this.db.setAttribute(key, value); + this.db.save(this.project); + return value; + }, + rem: function(key){ + var beforeDelete = this.get(key); + this.db.removeAttribute(key); + this.db.save(this.project); + return beforeDelete; + } + }) + + $.jStore.Engines.ie = jStoreIE; + + // Store the ordering preference + $.jStore.EngineOrder[ 4 ] = 'ie'; + +})(jQuery); \ No newline at end of file diff -r 7df41ad788de -r 55c0eb35fad7 static/scripts/packed/jquery.jstore-all.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/jquery.jstore-all.js Thu Aug 13 13:16:58 2009 -0400 @@ -0,0 +1,41 @@ +/* + * jStore - Persistent Client-Side Storage + * + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * + * Dual licensed under: + * MIT: http://www.opensource.org/licenses/mit-license.php + * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html + */ +(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=typeof g[d]=="function"&&typeof f[d]=="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}})(d,g[d]):g[d]}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}})(); +/* + * jStore Delegate Framework + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(a){this.jStoreDelegate=Class.extend({init:function(b){this.parent=b;this.callbacks={}},bind:function(b,c){if(!a.isFunction(c)){return this}if(!this.callbacks[b]){this.callbacks[b]=[]}this.callbacks[b].push(c);return this},trigger:function(){var d=this.parent,c=[].slice.call(arguments),e=c.shift(),b=this.callbacks[e];if(!b){return false}a.each(b,function(){this.apply(d,c)});return this}})})(jQuery);(function(a){a.jStore={};a.extend(a.jStore,{EngineOrder:[],Availability:{},Engines:{},Instances:{},CurrentEngine:null,defaults:{project:null,engine:null,autoload:true,flash:"jStore.Flash.html"},isReady:false,isFlashReady:false,delegate:new jStoreDelegate(a.jStore).bind("jStore-ready",function(b){a.jStore.isReady=true;if(a.jStore.defaults.autoload){b.connect()}}).bind("flash-ready",function(){a.jStore.isFlashReady=true})});a.jStore.ready=function(b){if(a.jStore.isReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("jStore-ready",b)}};a.jStore.fail =function(b){a.jStore.delegate.bind("jStore-failure",b)};a.jStore.flashReady=function(b){if(a.jStore.isFlashReady){b.apply(a.jStore,[a.jStore.CurrentEngine])}else{a.jStore.delegate.bind("flash-ready",b)}};a.jStore.use=function(d,g,c){g=g||a.jStore.defaults.project||location.hostname.replace(/\./g,"-")||"unknown";var f=a.jStore.Engines[d.toLowerCase()]||null,b=(c?c+".":"")+g+"."+d;if(!f){throw"JSTORE_ENGINE_UNDEFINED"}f=new f(g,b);if(a.jStore.Instances[b]){throw"JSTORE_JRI_CONFLICT"}if(f.isAvailable()){a.jStore.Instances[b]=f;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=f}a.jStore.delegate.trigger("jStore-ready",f)}else{if(!f.autoload){throw"JSTORE_ENGINE_UNAVILABLE"}else{f.included(function(){if(this.isAvailable()){a.jStore.Instances[b]=this;if(!a.jStore.CurrentEngine){a.jStore.CurrentEngine=this}a.jStore.delegate.trigger("jStore-ready",this)}else{a.jStore.delegate.trigger("jStore-failure",this)}}).include()}}};a.jStore.setCurrentEngine=function(b){if(!a.jStore.Instanc es.length){return a.jStore.FindEngine()}if(!b&&a.jStore.Instances.length>=1){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[0]);return a.jStore.CurrentEngine=a.jStore.Instances[0]}if(b&&a.jStore.Instances[b]){a.jStore.delegate.trigger("jStore-ready",a.jStore.Instances[b]);return a.jStore.CurrentEngine=a.jStore.Instances[b]}throw"JSTORE_JRI_NO_MATCH"};a.jStore.FindEngine=function(){a.each(a.jStore.EngineOrder,function(b){if(a.jStore.Availability[this]()){a.jStore.use(this,a.jStore.defaults.project,"default");return false}})};a.jStore.store=function(b,c){if(!a.jStore.CurrentEngine){return false}if(!c){return a.jStore.CurrentEngine.get(b)}return a.jStore.CurrentEngine.set(b,c)};a.jStore.remove=function(b){if(!a.jStore.CurrentEngine){return false}return a.jStore.CurrentEngine.rem(b)};a.fn.store=function(c,d){if(!a.jStore.CurrentEngine){return this}var b=a.jStore.store(c,d);return !d?b:this};a.fn.removeStore=function(b){a.jStore.remove(b);return this};a.jStore.load=f unction(){if(a.jStore.defaults.engine){return a.jStore.use(a.jStore.defaults.engine,a.jStore.defaults.project,"default")}try{a.jStore.FindEngine()}catch(b){}}})(jQuery);(function(a){this.StorageEngine=Class.extend({init:function(c,b){this.project=c;this.jri=b;this.data={};this.limit=-1;this.includes=[];this.delegate=new jStoreDelegate(this).bind("engine-ready",function(){this.isReady=true}).bind("engine-included",function(){this.hasIncluded=true});this.autoload=false;this.isReady=false;this.hasIncluded=false},include:function(){var b=this,d=this.includes.length,c=0;a.each(this.includes,function(){a.ajax({type:"get",url:this,dataType:"script",cache:true,success:function(){c++;if(c==d){b.delegate.trigger("engine-included")}}})})},isAvailable:function(){return false},ready:function(b){if(this.isReady){b.apply(this)}else{this.delegate.bind("engine-ready",b)}return this},included:function(b){if(this.hasIncluded){b.apply(this)}else{this.delegate.bind("engine-included",b)}return th is},get:function(b){return this.data[b]||null},set:function(b,c){this.data[b]=c;return c},rem:function(b){var c=this.data[b];this.data[b]=null;return c}})})(jQuery); +/* + * jStore DOM Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(c){var b=c.jStore.Availability.session=function(){return !!window.sessionStorage},a=c.jStore.Availability.local=function(){return !!(window.localStorage||window.globalStorage)};this.jStoreDom=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="DOM";this.limit=5*1024*1024},connect:function(){this.delegate.trigger("engine-ready")},get:function(e){var d=this.db.getItem(e);return d&&d.value?d.value:d},set:function(d,e){this.db.setItem(d,e);return e},rem:function(e){var d=this.get(e);this.db.removeItem(e);return d}});this.jStoreLocal=jStoreDom.extend({connect:function(){this.db=!window.globalStorage?window.localStorage:window.globalStorage[location.hostname];this._super()},isAvailable:a});this.jStoreSession=jStoreDom.extend({connect:function(){this.db=sessionStorage;this._super()},isAvailable:b});c.jStore.Engines.local=jStoreLocal;c.jStore.Engines.session=jStoreSession;c.jStore.EngineOrder[1]="local"})(jQuery); +/* + * jStore Flash Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) + */ +(function(b){var a=b.jStore.Availability.flash=function(){return !!(b.jStore.hasFlash("8.0.0"))};this.jStoreFlash=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="Flash";var c=this;b.jStore.flashReady(function(){c.flashReady()})},connect:function(){var c="jstore-flash-embed-"+this.project;b(document.body).append('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" id="jStoreFlashFrame" src="'+b.jStore.defaults.flash+'"></iframe>')},flashReady:function(f){var c=b("#jStoreFlashFrame")[0];if(c.Document&&b.isFunction(c.Document.jStoreFlash.f_get_cookie)){this.db=c.Document.jStoreFlash}else{if(c.contentWindow&&c.contentWindow.document){var d=c.contentWindow.document;if(b.isFunction(b("object",b(d))[0].f_get_cookie)){this.db=b("object",b(d))[0]}else{if(b.isFunction(b("embed",b(d))[0].f_get_cookie)){this.db=b("embed",b(d))[0]}}}}if(this.db){this.delegate.trigger("engine-ready")}},isAvailable:a,get:function(d){var c=this.db.f_g et_cookie(d);return c=="null"?null:c},set:function(c,d){this.db.f_set_cookie(c,d);return d},rem:function(c){var d=this.get(c);this.db.f_delete_cookie(c);return d}});b.jStore.Engines.flash=jStoreFlash;b.jStore.EngineOrder[2]="flash";b.jStore.hasFlash=function(c){var e=b.jStore.flashVersion().match(/\d+/g),f=c.match(/\d+/g);for(var d=0;d<3;d++){e[d]=parseInt(e[d]||0);f[d]=parseInt(f[d]||0);if(e[d]<f[d]){return false}if(e[d]>f[d]){return true}}return true};b.jStore.flashVersion=function(){try{try{var c=new ActiveXObject("ShockwaveFlash.ShockwaveFlash.6");try{c.AllowScriptAccess="always"}catch(d){return"6,0,0"}}catch(d){}return new ActiveXObject("ShockwaveFlash.ShockwaveFlash").GetVariable("$version").replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}catch(d){try{if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){return(navigator.plugins["Shockwave Flash 2.0"]||navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g,",").match(/^,?(.+),?$/)[1]}}catch(d){}}r eturn"0,0,0"}})(jQuery);function flash_ready(){$.jStore.delegate.trigger("flash-ready")} +/* + * jStore Google Gears Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(b){var a=b.jStore.Availability.gears=function(){return !!(window.google&&window.google.gears)};this.jStoreGears=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="Google Gears";this.includes.push("http://code.google.com/apis/gears/gears_init.js");this.autoload=true},connect:function(){var c=this.db=google.gears.factory.create("beta.database");c.open("jstore-"+this.project);c.execute("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)");this.updateCache()},updateCache:function(){var c=this.db.execute("SELECT k,v FROM jstore");while(c.isValidRow()){this.data[c.field(0)]=c.field(1);c.next()}c.close();this.delegate.trigger("engine-ready")},isAvailable:a,set:function(d,e){var c=this.db;c.execute("BEGIN");c.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[d,e]);c.execute("COMMIT");return this._super(d,e)},rem:function(d){var c=this.db;c.execute("BEGIN");c.execute("DELETE FROM jstore WHERE k = ?",[d]);c.ex ecute("COMMIT");return this._super(d)}});b.jStore.Engines.gears=jStoreGears;b.jStore.EngineOrder[3]="gears"})(jQuery); +/* + * jStore HTML5 Specification Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(b){var a=b.jStore.Availability.html5=function(){return !!window.openDatabase};this.jStoreHtml5=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="HTML5";this.limit=1024*200},connect:function(){var c=this.db=openDatabase("jstore-"+this.project,"1.0",this.project,this.limit);if(!c){throw"JSTORE_ENGINE_HTML5_NODB"}c.transaction(function(d){d.executeSql("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)")});this.updateCache()},updateCache:function(){var c=this;this.db.transaction(function(d){d.executeSql("SELECT k,v FROM jstore",[],function(f,e){var h=e.rows,g=0,j;for(;g<h.length;++g){j=h.item(g);c.data[j.k]=j.v}c.delegate.trigger("engine-ready")})})},isAvailable:a,set:function(c,d){this.db.transaction(function(e){e.executeSql("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[c,d])});return this._super(c,d)},rem:function(c){this.db.transaction(function(d){d.executeSql("DELETE FROM jstore WHERE k = ?",[c])});ret urn this._super(c)}});b.jStore.Engines.html5=jStoreHtml5;b.jStore.EngineOrder[0]="html5"})(jQuery); +/** + * jStore IE Storage Engine + * Copyright (c) 2009 Eric Garside (http://eric.garside.name) + */ +(function(b){var a=b.jStore.Availability.ie=function(){return !!window.ActiveXObject};this.jStoreIE=StorageEngine.extend({init:function(d,c){this._super(d,c);this.type="IE";this.limit=64*1024},connect:function(){this.db=b('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+this.project+'"></div>').appendTo(document.body).get(0);this.delegate.trigger("engine-ready")},isAvailable:a,get:function(c){this.db.load(this.project);return this.db.getAttribute(c)},set:function(c,d){this.db.setAttribute(c,d);this.db.save(this.project);return d},rem:function(c){var d=this.get(c);this.db.removeAttribute(c);this.db.save(this.project);return d}});b.jStore.Engines.ie=jStoreIE;b.jStore.EngineOrder[4]="ie"})(jQuery); \ No newline at end of file diff -r 7df41ad788de -r 55c0eb35fad7 static/scripts/packed/json2.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/json2.js Thu Aug 13 13:16:58 2009 -0400 @@ -0,0 +1,1 @@ +var JSON=JSON||{};(function(){function f(n){return n<10?"0"+n:n}if(typeof Date.prototype.toJSON!=="function"){Date.prototype.toJSON=function(key){return isFinite(this.valueOf())?this.getUTCFullYear()+"-"+f(this.getUTCMonth()+1)+"-"+f(this.getUTCDate())+"T"+f(this.getUTCHours())+":"+f(this.getUTCMinutes())+":"+f(this.getUTCSeconds())+"Z":null};String.prototype.toJSON=Number.prototype.toJSON=Boolean.prototype.toJSON=function(key){return this.valueOf()}}var cx=/[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,escapable=/[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,gap,indent,meta={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},rep;function quote(string){escapable.lastIndex=0;return escapable.test(string)?'"'+string.replace(escapable,function(a){var c=meta[a];return typeof c==="string"?c:"\\u"+("0000"+a.charCodeAt(0) .toString(16)).slice(-4)})+'"':'"'+string+'"'}function str(key,holder){var i,k,v,length,mind=gap,partial,value=holder[key];if(value&&typeof value==="object"&&typeof value.toJSON==="function"){value=value.toJSON(key)}if(typeof rep==="function"){value=rep.call(holder,key,value)}switch(typeof value){case"string":return quote(value);case"number":return isFinite(value)?String(value):"null";case"boolean":case"null":return String(value);case"object":if(!value){return"null"}gap+=indent;partial=[];if(Object.prototype.toString.apply(value)==="[object Array]"){length=value.length;for(i=0;i<length;i+=1){partial[i]=str(i,value)||"null"}v=partial.length===0?"[]":gap?"[\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"]":"["+partial.join(",")+"]";gap=mind;return v}if(rep&&typeof rep==="object"){length=rep.length;for(i=0;i<length;i+=1){k=rep[i];if(typeof k==="string"){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}else{for(k in value){if(Object.hasOwnProperty.call(value,k)){v=str( k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}v=partial.length===0?"{}":gap?"{\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"}":"{"+partial.join(",")+"}";gap=mind;return v}}if(typeof JSON.stringify!=="function"){JSON.stringify=function(value,replacer,space){var i;gap="";indent="";if(typeof space==="number"){for(i=0;i<space;i+=1){indent+=" "}}else{if(typeof space==="string"){indent=space}}rep=replacer;if(replacer&&typeof replacer!=="function"&&(typeof replacer!=="object"||typeof replacer.length!=="number")){throw new Error("JSON.stringify")}return str("",{"":value})}}if(typeof JSON.parse!=="function"){JSON.parse=function(text,reviver){var j;function walk(holder,key){var k,v,value=holder[key];if(value&&typeof value==="object"){for(k in value){if(Object.hasOwnProperty.call(value,k)){v=walk(value,k);if(v!==undefined){value[k]=v}else{delete value[k]}}}}return reviver.call(holder,key,value)}cx.lastIndex=0;if(cx.test(text)){text=text.replace(cx,function(a){return"\\u"+("000 0"+a.charCodeAt(0).toString(16)).slice(-4)})}if(/^[\],:{}\s]*$/.test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))){j=eval("("+text+")");return typeof reviver==="function"?walk({"":j},""):j}throw new SyntaxError("JSON.parse")}}}()); \ No newline at end of file diff -r 7df41ad788de -r 55c0eb35fad7 templates/root/history.mako --- a/templates/root/history.mako Tue Aug 11 15:46:23 2009 -0400 +++ b/templates/root/history.mako Thu Aug 13 13:16:58 2009 -0400 @@ -15,219 +15,242 @@ <meta http-equiv="Pragma" content="no-cache"> ${h.css( "base", "history" )} -${h.js( "jquery", "jquery.cookie", "cookie_set" )} - +${h.js( "jquery", "json2", "jquery.jstore-all" )} + <script type="text/javascript"> - $( document ).ready( function() { - initShowHide(); - setupHistoryItem( $("div.historyItemWrapper") ); - // Collapse all - $("#top-links").append( "| " ).append( $("<a href='#'>${_('collapse all')}</a>").click( function() { - $( "div.historyItemBody:visible" ).each( function() { - if ( $.browser.mozilla ) - { - $(this).find( "pre.peek" ).css( "overflow", "hidden" ); +$(function() { + // Load jStore for local storage + $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) + $.jStore.load(); // Auto-select best storage + + $.jStore.ready(function(engine) { + engine.ready(function() { + // Init stuff that requires the local storage to be running + initShowHide(); + setupHistoryItem( $("div.historyItemWrapper") ); + }); + }); + + // Generate 'collapse all' link + $("#top-links").append( "| " ).append( $("<a href='#'>${_('collapse all')}</a>").click( function() { + $( "div.historyItemBody:visible" ).each( function() { + if ( $.browser.mozilla ) { + $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + } + $(this).slideUp( "fast" ); + }); + $.jStore.remove("history_expand_state"); + })); + + $("#history-rename").click( function() { + var old_name = $("#history-name").text() + var t = $("<input type='text' value='" + old_name + "'></input>" ); + t.blur( function() { + $(this).remove(); + $("#history-name").show(); + }); + t.keyup( function( e ) { + if ( e.keyCode == 27 ) { + // Escape key + $(this).trigger( "blur" ); + } else if ( e.keyCode == 13 ) { + // Enter key + new_value = this.value; + $(this).trigger( "blur" ); + $.ajax({ + url: "${h.url_for( controller='history', action='rename_async', id=history.id )}", + data: { "_": true, new_name: new_value }, + error: function() { alert( "Rename failed" ) }, + success: function() { + $("#history-name").text( new_value ); + } + }); + } + }); + $("#history-name").hide(); + $("#history-name-area").append( t ); + t.focus(); + return false; + }); + // Updater + updater({ + %for i, data in enumerate( reversed( datasets ) ): + %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: + %if i > 0: + , + %endif + "${data.id}": "${data.state}" + %endif + %endfor + }); +}); +// Functionized so AJAX'd datasets can call them +// Get shown/hidden state from cookie +function initShowHide() { + + // Load saved state and show as neccesary + try { + var stored = $.jStore.store("history_expand_state"); + if (stored) { + var st = JSON.parse(stored); + for (var id in st) { + $("#" + id + " div.historyItemBody" ).show(); + } + } + } catch(err) { + // Something was wrong with values in storage, so clear storage + $.jStore.remove("history_expand_state"); + } + + // If Mozilla, hide scrollbars in hidden items since they cause animation bugs + if ( $.browser.mozilla ) { + $( "div.historyItemBody" ).each( function() { + if ( ! $(this).is( ":visible" ) ) $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + }) + } +} +// Add show/hide link and delete link to a history item +function setupHistoryItem( query ) { + query.each( function() { + var id = this.id; + var body = $(this).children( "div.historyItemBody" ); + var peek = body.find( "pre.peek" ) + $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { + if ( body.is(":visible") ) { + // Hiding stuff here + if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } + body.slideUp( "fast" ); + + // Save setting + var stored = $.jStore.store("history_expand_state") + var prefs = stored ? JSON.parse(stored) : null + if (prefs) { + delete prefs[id]; + $.jStore.store("history_expand_state", JSON.stringify(prefs)); } - $(this).slideUp( "fast" ); - }) - var state = new CookieSet( "galaxy.history.expand_state" ); - state.removeAll().save(); - return false; - })); - $("#history-rename").click( function() { - var old_name = $("#history-name").text() - var t = $("<input type='text' value='" + old_name + "'></input>" ); - t.blur( function() { - $(this).remove(); - $("#history-name").show(); - }); - t.keyup( function( e ) { - if ( e.keyCode == 27 ) { - // Escape key - $(this).trigger( "blur" ); - } else if ( e.keyCode == 13 ) { - // Enter key - new_value = this.value; - $(this).trigger( "blur" ); - $.ajax({ - url: "${h.url_for( controller='history', action='rename_async', id=history.id )}", - data: { "_": true, new_name: new_value }, - error: function() { alert( "Rename failed" ) }, - success: function() { - $("#history-name").text( new_value ); - } - }); - } - }); - $("#history-name").hide(); - $("#history-name-area").append( t ); - t.focus(); - return false; - }); - // Updater - updater({ - %for i, data in enumerate( reversed( datasets ) ): - %if data.visible and data.state not in [ "deleted", "empty", "error", "ok" ]: - %if i > 0: - , - %endif - "${data.id}": "${data.state}" - %endif - %endfor + } + else { + // Showing stuff here + body.slideDown( "fast", function() { + if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } + }); + + // Save setting + var stored = $.jStore.store("history_expand_state") + var prefs = stored ? JSON.parse(stored) : new Object; + prefs[id] = true; + $.jStore.store("history_expand_state", JSON.stringify(prefs)); + } + return false; }); - }) - //' Functionized so AJAX'd datasets can call them - // Get shown/hidden state from cookie - function initShowHide() { - // $( "div.historyItemBody" ).hide(); - // Load saved state and show as neccesary - var state = new CookieSet( "galaxy.history.expand_state" ); - for ( id in state.store ) { - if ( id ) { - $( "#" + id + " div.historyItemBody" ).show(); - } - } - // If Mozilla, hide scrollbars in hidden items since they cause animation bugs - if ( $.browser.mozilla ) { - $( "div.historyItemBody" ).each( function() { - if ( ! $(this).is( ":visible" ) ) $(this).find( "pre.peek" ).css( "overflow", "hidden" ); - }) - } - delete state; - } - // Add show/hide link and delete link to a history item - function setupHistoryItem( query ) { - query.each( function() { - var id = this.id; - var body = $(this).children( "div.historyItemBody" ); - var peek = body.find( "pre.peek" ) - $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { - if ( body.is(":visible") ) { - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } - body.slideUp( "fast" ); - ## other instances of this could be editing the cookie, refetch - var state = new CookieSet( "galaxy.history.expand_state" ); - state.remove( id ); state.save(); - delete state; - } - else { - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - var state = new CookieSet( "galaxy.history.expand_state" ); - state.add( id ); state.save(); - delete state; - } + // Delete link + $(this).find( "div.historyItemButtons > .delete" ).each( function() { + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#historyItem-' + data_id + "> div.historyItemTitleBar" ).addClass( "spinner" ); + $.ajax({ + url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Delete failed" ) }, + success: function() { + %if show_deleted: + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + %else: + $( "#historyItem-" + data_id ).fadeOut( "fast", function() { + $( "#historyItemContainer-" + data_id ).remove(); + if ( $( "div.historyItemContainer" ).length < 1 ) { + $( "#emptyHistoryMessage" ).show(); + } + }); + %endif + } + }); return false; }); - // Delete link - $(this).find( "div.historyItemButtons > .delete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#historyItem-' + data_id + "> div.historyItemTitleBar" ).addClass( "spinner" ); - $.ajax({ - url: "${h.url_for( action='delete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Delete failed" ) }, - success: function() { - %if show_deleted: - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - %else: - $( "#historyItem-" + data_id ).fadeOut( "fast", function() { - $( "#historyItemContainer-" + data_id ).remove(); - if ( $( "div.historyItemContainer" ).length < 1 ) { - $( "#emptyHistoryMessage" ).show(); - } - }); - %endif - } - }); - return false; + }); + // Undelete link + $(this).find( "a.historyItemUndelete" ).each( function() { + var data_id = this.id.split( "-" )[1]; + $(this).click( function() { + $( '#historyItem-' + data_id + " > div.historyItemTitleBar" ).addClass( "spinner" ); + $.ajax({ + url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), + error: function() { alert( "Undelete failed" ) }, + success: function() { + var to_update = {}; + to_update[data_id] = "none"; + updater( to_update ); + } }); - }); - // Undelete link - $(this).find( "a.historyItemUndelete" ).each( function() { - var data_id = this.id.split( "-" )[1]; - $(this).click( function() { - $( '#historyItem-' + data_id + " > div.historyItemTitleBar" ).addClass( "spinner" ); - $.ajax({ - url: "${h.url_for( controller='dataset', action='undelete_async', id='XXX' )}".replace( 'XXX', data_id ), - error: function() { alert( "Undelete failed" ) }, - success: function() { - var to_update = {}; - to_update[data_id] = "none"; - updater( to_update ); - } - }); - return false; - }); + return false; }); }); - }; - // Looks for changes in dataset state using an async request. Keeps - // calling itself (via setTimeout) until all datasets are in a terminal - // state. - var updater = function ( tracked_datasets ) { - // Check if there are any items left to track - var empty = true; - for ( i in tracked_datasets ) { - empty = false; - break; + }); +}; +// Looks for changes in dataset state using an async request. Keeps +// calling itself (via setTimeout) until all datasets are in a terminal +// state. +var updater = function ( tracked_datasets ) { + // Check if there are any items left to track + var empty = true; + for ( i in tracked_datasets ) { + empty = false; + break; + } + if ( ! empty ) { + // console.log( "Updater running in 3 seconds" ); + setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); + } else { + // console.log( "Updater finished" ); + } +}; +var updater_callback = function ( tracked_datasets ) { + // Build request data + var ids = [] + var states = [] + var force_history_refresh = false + $.each( tracked_datasets, function ( id, state ) { + ids.push( id ); + states.push( state ); + }); + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='root', action='history_item_updates' )}", + dataType: "json", + data: { ids: ids.join( "," ), states: states.join( "," ) }, + success : function ( data ) { + $.each( data, function( id, val ) { + // Replace HTML + var container = $("#historyItemContainer-" + id); + container.html( val.html ); + setupHistoryItem( container.children( ".historyItemWrapper" ) ); + initShowHide(); + // If new state was terminal, stop tracking + if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { + if ( val.force_history_refresh ){ + force_history_refresh = true; + } + delete tracked_datasets[ parseInt(id) ]; + } else { + tracked_datasets[ parseInt(id) ] = val.state; + } + }); + if ( force_history_refresh ) { + parent.frames.galaxy_history.location.reload(); + } + else { + // Keep going (if there are still any items to track) + updater( tracked_datasets ); + } + }, + error: function() { + // Just retry, like the old method, should try to be smarter + updater( tracked_datasets ); } - if ( ! empty ) { - // console.log( "Updater running in 3 seconds" ); - setTimeout( function() { updater_callback( tracked_datasets ) }, 3000 ); - } else { - // console.log( "Updater finished" ); - } - }; - var updater_callback = function ( tracked_datasets ) { - // Build request data - var ids = [] - var states = [] - var force_history_refresh = false - $.each( tracked_datasets, function ( id, state ) { - ids.push( id ); - states.push( state ); - }); - // Make ajax call - $.ajax( { - type: "POST", - url: "${h.url_for( controller='root', action='history_item_updates' )}", - dataType: "json", - data: { ids: ids.join( "," ), states: states.join( "," ) }, - success : function ( data ) { - $.each( data, function( id, val ) { - // Replace HTML - var container = $("#historyItemContainer-" + id); - container.html( val.html ); - setupHistoryItem( container.children( ".historyItemWrapper" ) ); - initShowHide(); - // If new state was terminal, stop tracking - if (( val.state == "ok") || ( val.state == "error") || ( val.state == "empty") || ( val.state == "deleted" ) || ( val.state == "discarded" )) { - if ( val.force_history_refresh ){ - force_history_refresh = true; - } - delete tracked_datasets[ parseInt(id) ]; - } else { - tracked_datasets[ parseInt(id) ] = val.state; - } - }); - if ( force_history_refresh ) { - parent.frames.galaxy_history.location.reload(); - } - else { - // Keep going (if there are still any items to track) - updater( tracked_datasets ); - } - }, - error: function() { - // Just retry, like the old method, should try to be smarter - updater( tracked_datasets ); - } - }); - }; + }); +}; </script> <style> diff -r 7df41ad788de -r 55c0eb35fad7 templates/workflow/editor.mako --- a/templates/workflow/editor.mako Tue Aug 11 15:46:23 2009 -0400 +++ b/templates/workflow/editor.mako Thu Aug 13 13:16:58 2009 -0400 @@ -31,9 +31,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.event.hover.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.form.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.json.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.cookie.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/json2.js')}"> </script> - <script type='text/javascript' src="${h.url_for('/static/scripts/json_cookie.js')}"> </script> + <script type='text/javascript' src="${h.url_for('/static/scripts/jquery.jstore-all.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.base.js')}"> </script> <script type='text/javascript' src="${h.url_for('/static/scripts/galaxy.workflow_editor.canvas.js')}"> </script> @@ -50,6 +48,7 @@ canvas_manager = null; // jQuery onReady $( function() { + if ( window.lt_ie_7 ) { show_modal( "Browser not supported", @@ -57,11 +56,13 @@ ); return; } + + // Load jStore for local storage + $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) + $.jStore.load(); // Auto-select best storage + // Canvas overview management canvas_manager = new CanvasManager( $("#canvas-viewport"), $("#overview") ); - - // Preferences cookie stored as JSON so that only one cookie is needed for multiple settings - var prefs_cookie = new JSONCookie("galaxy.workflow"); // Initialize workflow state reset(); @@ -128,39 +129,43 @@ canvas_manager.draw_overview(); }); - // Stores the size of the overview in a cookie when it's resized + $.jStore.ready(function(engine) { + engine.ready(function() { + // On load, set the size to the pref stored in local storage if it exists + overview_size = $.jStore.store("overview-size"); + if (overview_size) { + $("#overview-border").css( { + width: overview_size, + height: overview_size + }); + } + + // Show viewport on load unless pref says it's off + $.jStore.store("overview-off") ? hide_overview() : show_overview() + }); + }); + + // Stores the size of the overview into local storage when it's resized $("#overview-border").bind( "dragend", function( e ) { var op = $(this).offsetParent(); var opo = op.offset(); var new_size = Math.max( op.width() - ( e.offsetX - opo.left ), op.height() - ( e.offsetY - opo.top ) ); - prefs_cookie.set("overview-size", new_size); + $.jStore.store("overview-size", new_size + "px"); }); - // On load, set the size to the pref stored in cookie if it exists - overview_size = prefs_cookie.get("overview-size"); - if (overview_size) { - $("#overview-border").css( { - width: overview_size, - height: overview_size - }); - } - function show_overview() { - prefs_cookie.unset("overview-off"); + $.jStore.remove("overview-off"); $("#overview-border").css("right", "0px"); $("#close-viewport").css("background-position", "0px 0px"); } function hide_overview() { - prefs_cookie.set("overview-off", true); + $.jStore.store("overview-off", true); $("#overview-border").css("right", "20000px"); $("#close-viewport").css("background-position", "12px 0px"); } - // Show viewport on load unless pref says it's off - prefs_cookie.get("overview-off") == true ? hide_overview() : show_overview() - // Lets the overview be toggled visible and invisible, adjusting the arrows accordingly $("#close-viewport").click( function() { $("#overview-border").css("right") == "0px" ? hide_overview() : show_overview();

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[hg] galaxy 2569: Added sniff import statement to tabular.py so ...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7d48dc7e60b4 changeset: 2569:7d48dc7e60b4 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Aug 19 11:08:58 2009 -0400 description: Added sniff import statement to tabular.py so sam tests will pass 1 file(s) affected in this change: lib/galaxy/datatypes/tabular.py diffs (11 lines): diff -r 670f8800a2bf -r 7d48dc7e60b4 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Wed Aug 19 09:13:21 2009 -0400 +++ b/lib/galaxy/datatypes/tabular.py Wed Aug 19 11:08:58 2009 -0400 @@ -11,6 +11,7 @@ from cgi import escape from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement +from sniff import * log = logging.getLogger(__name__)

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[hg] galaxy 2573: Made workflow's "Input Dataset" name text fiel...
by Greg Von Kuster 24 Aug '09

24 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6b8e1ff3141a changeset: 2573:6b8e1ff3141a user: Kanwei Li <kanwei(a)gmail.com> date: Mon Aug 10 13:27:04 2009 -0400 description: Made workflow's "Input Dataset" name text field smaller to fit default size 1 file(s) affected in this change: templates/workflow/editor_generic_form.mako diffs (12 lines): diff -r a6be5c3955e9 -r 6b8e1ff3141a templates/workflow/editor_generic_form.mako --- a/templates/workflow/editor_generic_form.mako Mon Aug 10 12:09:50 2009 -0400 +++ b/templates/workflow/editor_generic_form.mako Mon Aug 10 13:27:04 2009 -0400 @@ -15,7 +15,7 @@ ${input.label}: </label> <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="${input.type}" name="${input.name}" value="${input.value}" size="40"> + <input type="${input.type}" name="${input.name}" value="${input.value}" size="30"> </div> %if input.error: <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">

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