June 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Update backbone-relational lib.
by Bitbucket 28 Jun '12

28 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/063a1d690724/ changeset: 063a1d690724 user: jgoecks date: 2012-06-28 19:31:20 summary: Update backbone-relational lib. affected #: 1 file diff -r adc8114131fa700da3b5800d7ba4568bd665c9b5 -r 063a1d690724b3485f41c620f664f11c7390ceef static/scripts/libs/backbone-relational.js --- a/static/scripts/libs/backbone-relational.js +++ b/static/scripts/libs/backbone-relational.js @@ -1,4 +1,4 @@ -/** +/** * Backbone-relational.js 0.5.0 * (c) 2011 Paul Uithol * @@ -19,15 +19,15 @@ exports = module.exports = Backbone; } else { - var _ = window._; + _ = window._; Backbone = window.Backbone; exports = window; } - + Backbone.Relational = { showWarnings: true }; - + /** * Semaphore mixin; can be used as both binary and counting. **/ @@ -116,37 +116,87 @@ * Backbone.Store keeps track of all created (and destruction of) Backbone.RelationalModel. * Handles lookup for relations. */ - Backbone.Store = function() { + Backbone.Store = function() { this._collections = []; this._reverseRelations = []; + this._subModels = []; + this._modelScopes = [ exports ]; }; _.extend( Backbone.Store.prototype, Backbone.Events, { - _collections: null, - _reverseRelations: null, + addModelScope: function( scope ) { + this._modelScopes.push( scope ); + }, + + /** + * Add a set of subModelTypes to the store, that can be used to resolve the '_superModel' + * for a model later in 'setupSuperModel'. + * + * @param {Backbone.RelationalModel} subModelTypes + * @param {Backbone.RelationalModel} superModelType + */ + addSubModels: function( subModelTypes, superModelType ) { + this._subModels.push({ + 'superModelType': superModelType, + 'subModels': subModelTypes + }); + }, + + /** + * Check if the given modelType is registered as another model's subModel. If so, add it to the super model's + * '_subModels', and set the modelType's '_superModel', '_subModelTypeName', and '_subModelTypeAttribute'. + * + * @param {Backbone.RelationalModel} modelType + */ + setupSuperModel: function( modelType ) { + _.find( this._subModels, function( subModelDef ) { + return _.find( subModelDef.subModels, function( subModelTypeName, typeValue ) { + var subModelType = this.getObjectByName( subModelTypeName ); + + if ( modelType === subModelType ) { + // Set 'modelType' as a child of the found superModel + subModelDef.superModelType._subModels[ typeValue ] = modelType; + + // Set '_superModel', '_subModelTypeValue', and '_subModelTypeAttribute' on 'modelType'. + modelType._superModel = subModelDef.superModelType; + modelType._subModelTypeValue = typeValue; + modelType._subModelTypeAttribute = subModelDef.superModelType.prototype.subModelTypeAttribute; + return true; + } + }, this ); + }, this ); + }, /** * Add a reverse relation. Is added to the 'relations' property on model's prototype, and to * existing instances of 'model' in the store as well. - * @param {object} relation + * @param {Object} relation * @param {Backbone.RelationalModel} relation.model * @param {String} relation.type * @param {String} relation.key - * @param {String|object} relation.relatedModel + * @param {String|Object} relation.relatedModel */ addReverseRelation: function( relation ) { var exists = _.any( this._reverseRelations, function( rel ) { - return _.all( relation, function( val, key ) { - return val === rel[ key ]; + return _.all( relation, function( val, key ) { + return val === rel[ key ]; + }); }); - }); if ( !exists && relation.model && relation.type ) { this._reverseRelations.push( relation ); - if ( !relation.model.prototype.relations ) { - relation.model.prototype.relations = []; - } - relation.model.prototype.relations.push( relation ); + var addRelation = function( model, relation ) { + if ( !model.prototype.relations ) { + model.prototype.relations = []; + } + model.prototype.relations.push( relation ); + + _.each( model._subModels, function( subModel ) { + addRelation( subModel, relation ); + }, this ); + }; + + addRelation( relation.model, relation ); this.retroFitRelation( relation ); } @@ -154,11 +204,15 @@ /** * Add a 'relation' to all existing instances of 'relation.model' in the store - * @param {object} relation + * @param {Object} relation */ retroFitRelation: function( relation ) { var coll = this.getCollection( relation.model ); coll.each( function( model ) { + if ( !( model instanceof relation.model ) ) { + return; + } + new relation.type( model, relation ); }, this); }, @@ -169,9 +223,17 @@ * @return {Backbone.Collection} A collection if found (or applicable for 'model'), or null */ getCollection: function( model ) { - var coll = _.detect( this._collections, function( c ) { - // Check if model is the type itself (a ref to the constructor), or is of type c.model - return model === c.model || model.constructor === c.model; + if ( model instanceof Backbone.RelationalModel ) { + model = model.constructor; + } + + var rootModel = model; + while ( rootModel._superModel ) { + rootModel = rootModel._superModel; + } + + var coll = _.detect( this._collections, function( c ) { + return c.model === rootModel; }); if ( !coll ) { @@ -187,22 +249,32 @@ * @return {Object} */ getObjectByName: function( name ) { - var type = _.reduce( name.split( '.' ), function( memo, val ) { - return memo[ val ]; - }, exports); - return type !== exports ? type: null; + var parts = name.split( '.' ), + type = null; + + _.find( this._modelScopes, function( scope ) { + type = _.reduce( parts, function( memo, val ) { + return memo[ val ]; + }, scope ); + + if ( type && type !== scope ) { + return true; + } + }, this ); + + return type; }, _createCollection: function( type ) { var coll; - // If 'type' is an instance, take it's constructor + // If 'type' is an instance, take its constructor if ( type instanceof Backbone.RelationalModel ) { type = type.constructor; } // Type should inherit from Backbone.RelationalModel. - if ( type.prototype instanceof Backbone.RelationalModel.prototype.constructor ) { + if ( type.prototype instanceof Backbone.RelationalModel ) { coll = new Backbone.Collection(); coll.model = type; @@ -213,7 +285,7 @@ }, /** - * Find an id + * Find the attribute that is to be used as the `id` on a given object * @param type * @param {String|Number|Object|Backbone.RelationalModel} item */ @@ -240,7 +312,18 @@ find: function( type, item ) { var id = this.resolveIdForItem( type, item ); var coll = this.getCollection( type ); - return coll && coll.get( id ); + + // Because the found object could be of any of the type's superModel + // types, only return it if it's actually of the type asked for. + if ( coll ) { + var obj = coll.get( id ); + + if ( obj instanceof type ) { + return obj; + } + } + + return null; }, /** @@ -281,19 +364,19 @@ * are used to regulate addition and removal of models from relations. * * @param {Backbone.RelationalModel} instance - * @param {object} options + * @param {Object} options * @param {string} options.key * @param {Backbone.RelationalModel.constructor} options.relatedModel - * @param {Boolean|String} [options.includeInJSON=true] Serialize the given attribute for related model(s)' in toJSON, or just their ids. + * @param {Boolean|String} [options.includeInJSON=true] Serialize the given attribute for related model(s)' in toJSON, or just their ids. * @param {Boolean} [options.createModels=true] Create objects from the contents of keys if the object is not found in Backbone.store. - * @param {object} [options.reverseRelation] Specify a bi-directional relation. If provided, Relation will reciprocate + * @param {Object} [options.reverseRelation] Specify a bi-directional relation. If provided, Relation will reciprocate * the relation to the 'relatedModel'. Required and optional properties match 'options', except that it also needs * {Backbone.Relation|String} type ('HasOne' or 'HasMany'). */ Backbone.Relation = function( instance, options ) { this.instance = instance; // Make sure 'options' is sane, and fill with defaults from subclasses and this object's prototype - options = ( typeof options === 'object' && options ) || {}; + options = _.isObject( options ) ? options : {}; this.reverseRelation = _.defaults( options.reverseRelation || {}, this.options.reverseRelation ); this.reverseRelation.type = !_.isString( this.reverseRelation.type ) ? this.reverseRelation.type : Backbone[ this.reverseRelation.type ] || Backbone.Relational.store.getObjectByName( this.reverseRelation.type ); @@ -302,7 +385,7 @@ this.key = this.options.key; this.keySource = this.options.keySource || this.key; - this.keyDestination = this.options.keyDestination || this.options.keySource || this.key; + this.keyDestination = this.options.keyDestination || this.keySource || this.key; // 'exports' should be the global object where 'relatedModel' can be found on if given as a string. this.relatedModel = this.options.relatedModel; @@ -340,7 +423,7 @@ _.bindAll( this, '_modelRemovedFromCollection', '_relatedModelAdded', '_relatedModelRemoved' ); - if( instance ) { + if ( instance ) { this.initialize(); // When a model in the store is destroyed, check if it is 'this.instance'. @@ -405,28 +488,28 @@ return false; } // Check if the type in 'relatedModel' inherits from Backbone.RelationalModel - if ( !( m.prototype instanceof Backbone.RelationalModel.prototype.constructor ) ) { + if ( !( m.prototype instanceof Backbone.RelationalModel ) ) { warn && console.warn( 'Relation=%o; model does not inherit from Backbone.RelationalModel (%o)', this, i ); return false; } // Check if the type in 'relatedModel' inherits from Backbone.RelationalModel - if ( !( rm.prototype instanceof Backbone.RelationalModel.prototype.constructor ) ) { + if ( !( rm.prototype instanceof Backbone.RelationalModel ) ) { warn && console.warn( 'Relation=%o; relatedModel does not inherit from Backbone.RelationalModel (%o)', this, rm ); return false; } // Check if this is not a HasMany, and the reverse relation is HasMany as well - if ( this instanceof Backbone.HasMany && this.reverseRelation.type === Backbone.HasMany.prototype.constructor ) { + if ( this instanceof Backbone.HasMany && this.reverseRelation.type === Backbone.HasMany ) { warn && console.warn( 'Relation=%o; relation is a HasMany, and the reverseRelation is HasMany as well.', this ); return false; } // Check if we're not attempting to create a duplicate relationship - if( i && i._relations.length ) { + if ( i && i._relations.length ) { var exists = _.any( i._relations, function( rel ) { - var hasReverseRelation = this.reverseRelation.key && rel.reverseRelation.key; - return rel.relatedModel === rm && rel.key === k && - ( !hasReverseRelation || this.reverseRelation.key === rel.reverseRelation.key ); - }, this ); + var hasReverseRelation = this.reverseRelation.key && rel.reverseRelation.key; + return rel.relatedModel === rm && rel.key === k && + ( !hasReverseRelation || this.reverseRelation.key === rel.reverseRelation.key ); + }, this ); if ( exists ) { warn && console.warn( 'Relation=%o between instance=%o.%s and relatedModel=%o.%s already exists', @@ -451,12 +534,6 @@ this.instance.release(); }, - createModel: function( item ) { - if ( this.options.createModels && typeof( item ) === 'object' ) { - return new this.relatedModel( item ); - } - }, - /** * Determine if a relation (on a different RelationalModel) is the reverse * relation of the current one. @@ -482,12 +559,12 @@ // Iterate over 'model', 'this.related.models' (if this.related is a Backbone.Collection), or wrap 'this.related' in an array. var models = !_.isUndefined( model ) ? [ model ] : this.related && ( this.related.models || [ this.related ] ); _.each( models , function( related ) { - _.each( related.getRelations(), function( relation ) { - if ( this._isReverseRelation( relation ) ) { - reverseRelations.push( relation ); - } + _.each( related.getRelations(), function( relation ) { + if ( this._isReverseRelation( relation ) ) { + reverseRelations.push( relation ); + } + }, this ); }, this ); - }, this ); return reverseRelations; }, @@ -501,7 +578,7 @@ sanitizeOptions: function( options ) { options = options ? _.clone( options ) : {}; if ( options.silent ) { - options = _.extend( {}, options, { silentChange: true } ); + options.silentChange = true; delete options.silent; } return options; @@ -516,7 +593,7 @@ unsanitizeOptions: function( options ) { options = options ? _.clone( options ) : {}; if ( options.silentChange ) { - options = _.extend( {}, options, { silent: true } ); + options.silent = true; delete options.silentChange; } return options; @@ -551,10 +628,9 @@ this.setRelated( model ); // Notify new 'related' object of the new relation. - var dit = this; - _.each( dit.getReverseRelations(), function( relation ) { - relation.addRelated( dit.instance ); - } ); + _.each( this.getReverseRelations(), function( relation ) { + relation.addRelated( this.instance ); + }, this ); }, findRelated: function( options ) { @@ -565,15 +641,7 @@ model = item; } else if ( item ) { - // Try to find an instance of the appropriate 'relatedModel' in the store, or create it - model = Backbone.Relational.store.find( this.relatedModel, item ); - - if ( model && _.isObject( item ) ) { - model.set( item, options ); - } - else if ( !model ) { - model = this.createModel( item ); - } + model = this.relatedModel.findOrCreate( item, { create: this.options.createModels } ); } return model; @@ -583,7 +651,7 @@ * If the key is changed, notify old & new reverse relations and initialize the new relation */ onChange: function( model, attr, options ) { - // Don't accept recursive calls to onChange (like onChange->findRelated->createModel->initializeRelations->addRelated->onChange) + // Don't accept recursive calls to onChange (like onChange->findRelated->findOrCreate->initializeRelations->addRelated->onChange) if ( this.isLocked() ) { return; } @@ -691,10 +759,10 @@ // Handle a custom 'collectionType' this.collectionType = this.options.collectionType; - if ( _( this.collectionType ).isString() ) { + if ( _.isString( this.collectionType ) ) { this.collectionType = Backbone.Relational.store.getObjectByName( this.collectionType ); } - if ( !this.collectionType.prototype instanceof Backbone.Collection.prototype.constructor ){ + if ( !this.collectionType.prototype instanceof Backbone.Collection ){ throw new Error( 'collectionType must inherit from Backbone.Collection' ); } @@ -710,7 +778,7 @@ }, _getCollectionOptions: function() { - return _.isFunction( this.options.collectionOptions ) ? + return _.isFunction( this.options.collectionOptions ) ? this.options.collectionOptions( this.instance ) : this.options.collectionOptions; }, @@ -737,12 +805,12 @@ if ( this.options.collectionKey ) { var key = this.options.collectionKey === true ? this.options.reverseRelation.key : this.options.collectionKey; - if (collection[ key ] && collection[ key ] !== this.instance ) { + if ( collection[ key ] && collection[ key ] !== this.instance ) { if ( Backbone.Relational.showWarnings && typeof console !== 'undefined' ) { console.warn( 'Relation=%o; collectionKey=%s already exists on collection=%o', this, key, this.options.collectionKey ); } } - else if (key) { + else if ( key ) { collection[ key ] = this.instance; } } @@ -768,19 +836,18 @@ // Try to find instances of the appropriate 'relatedModel' in the store _.each( this.keyContents, function( item ) { - var model = Backbone.Relational.store.find( this.relatedModel, item ); + var model = null; + if ( item instanceof this.relatedModel ) { + model = item; + } + else { + model = this.relatedModel.findOrCreate( item, { create: this.options.createModels } ); + } - if ( model && _.isObject( item ) ) { - model.set( item, options ); - } - else if ( !model ) { - model = this.createModel( item ); - } - - if ( model && !this.related.getByCid( model ) && !this.related.get( model ) ) { - models.push( model ); - } - }, this ); + if ( model && !this.related.getByCid( model ) && !this.related.get( model ) ) { + models.push( model ); + } + }, this ); } // Add all found 'models' in on go, so 'add' will only be called once (and thus 'sort', etc.) @@ -816,7 +883,7 @@ if ( this.related instanceof Backbone.Collection ) { coll = this.related; - coll.reset( [], { silent: true } ); + coll.remove( coll.models ); } else { coll = this._prepareCollection(); @@ -842,9 +909,9 @@ if ( !this.related.getByCid( model ) && !this.related.get( model ) ) { // Check if this new model was specified in 'this.keyContents' var item = _.any( this.keyContents, function( item ) { - var id = Backbone.Relational.store.resolveIdForItem( this.relatedModel, item ); - return id && id === model.id; - }, this ); + var id = Backbone.Relational.store.resolveIdForItem( this.relatedModel, item ); + return id && id === model.id; + }, this ); if ( item ) { this.related.add( model, options ); @@ -860,7 +927,7 @@ //console.debug('handleAddition called; args=%o', arguments); // Make sure the model is in fact a valid model before continuing. // (it can be invalid as a result of failing validation in Backbone.Collection._prepareModel) - if( !( model instanceof Backbone.Model ) ) { + if ( !( model instanceof Backbone.Model ) ) { return; } @@ -883,7 +950,7 @@ */ handleRemoval: function( model, coll, options ) { //console.debug('handleRemoval called; args=%o', arguments); - if( !( model instanceof Backbone.Model ) ) { + if ( !( model instanceof Backbone.Model ) ) { return; } @@ -940,6 +1007,9 @@ _deferProcessing: false, _queue: null, + subModelTypeAttribute: 'type', + subModelTypes: null, + constructor: function( attributes, options ) { // Nasty hack, for cases like 'model.get( <HasMany key> ).add( item )'. // Defer 'processQueue', so that when 'Relation.createModels' is used we: @@ -971,7 +1041,7 @@ this._queue.block(); Backbone.Relational.eventQueue.block(); - Backbone.Model.prototype.constructor.apply( this, arguments ); + Backbone.Model.apply( this, arguments ); // Try to run the global queue holding external events Backbone.Relational.eventQueue.unblock(); @@ -1004,7 +1074,7 @@ _.each( this.relations, function( rel ) { var type = !_.isString( rel.type ) ? rel.type : Backbone[ rel.type ] || Backbone.Relational.store.getObjectByName( rel.type ); - if ( type && type.prototype instanceof Backbone.Relation.prototype.constructor ) { + if ( type && type.prototype instanceof Backbone.Relation ) { new type( this, rel ); // Also pushes the new Relation into _relations } else { @@ -1016,17 +1086,18 @@ this.release(); this.processQueue(); }, - + /** * When new values are set, notify this model's relations (also if options.silent is set). * (Relation.setRelated locks this model before calling 'set' on it to prevent loops) */ updateRelations: function( options ) { - if( this._isInitialized && !this.isLocked() ) { + if ( this._isInitialized && !this.isLocked() ) { _.each( this._relations, function( rel ) { - var val = this.attributes[ rel.key ]; + // Update from data in `rel.keySource` if set, or `rel.key` otherwise + var val = this.attributes[ rel.keySource ] || this.attributes[ rel.key ]; if ( rel.related !== val ) { - this.trigger('relational:change:' + rel.key, this, val, options || {} ); + this.trigger( 'relational:change:' + rel.key, this, val, options || {} ); } }, this ); } @@ -1072,10 +1143,11 @@ /** * Retrieve related objects. * @param key {string} The relation key to fetch models for. - * @param options {object} Options for 'Backbone.Model.fetch' and 'Backbone.sync'. + * @param options {Object} Options for 'Backbone.Model.fetch' and 'Backbone.sync'. + * @param update {boolean} Whether to force a fetch from the server (updating existing models). * @return {jQuery.when[]} An array of request objects */ - fetchRelated: function( key, options ) { + fetchRelated: function( key, options, update ) { options || ( options = {} ); var setUrl, requests = [], @@ -1083,7 +1155,7 @@ keyContents = rel && rel.keyContents, toFetch = keyContents && _.select( _.isArray( keyContents ) ? keyContents : [ keyContents ], function( item ) { var id = Backbone.Relational.store.resolveIdForItem( rel.relatedModel, item ); - return id && !Backbone.Relational.store.find( rel.relatedModel, id ); + return id && ( update || !Backbone.Relational.store.find( rel.relatedModel, id ) ); }, this ); if ( toFetch && toFetch.length ) { @@ -1091,13 +1163,13 @@ var models = _.map( toFetch, function( item ) { var model; - if ( typeof( item ) === 'object' ) { - model = new rel.relatedModel( item ); + if ( _.isObject( item ) ) { + model = rel.relatedModel.build( item ); } else { var attrs = {}; attrs[ rel.relatedModel.prototype.idAttribute ] = item; - model = new rel.relatedModel( attrs ); + model = rel.relatedModel.build( attrs ); } return model; @@ -1117,9 +1189,9 @@ error: function() { var args = arguments; _.each( models, function( model ) { - model.trigger( 'destroy', model, model.collection, options ); - options.error && options.error.apply( model, args ); - }); + model.trigger( 'destroy', model, model.collection, options ); + options.error && options.error.apply( model, args ); + }); }, url: setUrl }, @@ -1153,7 +1225,7 @@ // Duplicate backbone's behavior to allow separate key/value parameters, instead of a single 'attributes' object var attributes; - if (_.isObject( key ) || key == null) { + if ( _.isObject( key ) || key == null ) { attributes = key; options = value; } @@ -1164,10 +1236,12 @@ var result = Backbone.Model.prototype.set.apply( this, arguments ); - // 'set' is called quite late in 'Backbone.Model.prototype.constructor', but before 'initialize'. // Ideal place to set up relations :) if ( !this._isInitialized && !this.isLocked() ) { + this.constructor.initializeModelHierarchy(); + Backbone.Relational.store.register( this ); + this.initializeRelations(); } // Update the 'idAttribute' in Backbone.store if; we don't want it to miss an 'id' update due to {silent:true} @@ -1227,8 +1301,8 @@ } _.each( this.getRelations(), function( rel ) { - delete attributes[ rel.key ]; - }); + delete attributes[ rel.key ]; + }); return new this.constructor( attributes ); }, @@ -1245,36 +1319,233 @@ this.acquire(); var json = Backbone.Model.prototype.toJSON.call( this ); + if ( this.constructor._superModel && !( this.constructor._subModelTypeAttribute in json ) ) { + json[ this.constructor._subModelTypeAttribute ] = this.constructor._subModelTypeValue; + } + _.each( this._relations, function( rel ) { - var value = json[ rel.key ]; + var value = json[ rel.key ]; - if ( rel.options.includeInJSON === true && value && _.isFunction( value.toJSON ) ) { - json[ rel.keyDestination ] = value.toJSON(); - } - else if ( _.isString( rel.options.includeInJSON ) ) { - if ( value instanceof Backbone.Collection ) { - json[ rel.keyDestination ] = value.pluck( rel.options.includeInJSON ); + if ( rel.options.includeInJSON === true) { + if ( value && _.isFunction( value.toJSON ) ) { + json[ rel.keyDestination ] = value.toJSON(); + } + else { + json[ rel.keyDestination ] = null; + } } - else if ( value instanceof Backbone.Model ) { - json[ rel.keyDestination ] = value.get( rel.options.includeInJSON ); + else if ( _.isString( rel.options.includeInJSON ) ) { + if ( value instanceof Backbone.Collection ) { + json[ rel.keyDestination ] = value.pluck( rel.options.includeInJSON ); + } + else if ( value instanceof Backbone.Model ) { + json[ rel.keyDestination ] = value.get( rel.options.includeInJSON ); + } + else { + json[ rel.keyDestination ] = null; + } } - } - else { - delete json[ rel.key ]; - } + else if ( _.isArray( rel.options.includeInJSON ) ) { + if ( value instanceof Backbone.Collection ) { + var valueSub = []; + value.each( function( model ) { + var curJson = {}; + _.each( rel.options.includeInJSON, function( key ) { + curJson[ key ] = model.get( key ); + }); + valueSub.push( curJson ); + }); + json[ rel.keyDestination ] = valueSub; + } + else if ( value instanceof Backbone.Model ) { + var valueSub = {}; + _.each( rel.options.includeInJSON, function( key ) { + valueSub[ key ] = value.get( key ); + }); + json[ rel.keyDestination ] = valueSub; + } + else { + json[ rel.keyDestination ] = null; + } + } + else { + delete json[ rel.key ]; + } - if ( rel.keyDestination !== rel.key ) { - delete json[ rel.key ]; - } - }, this ); + if ( rel.keyDestination !== rel.key ) { + delete json[ rel.key ]; + } + }); this.release(); return json; } + }, + { + setup: function( superModel ) { + // We don't want to share a relations array with a parent, as this will cause problems with + // reverse relations. + this.prototype.relations = ( this.prototype.relations || [] ).slice( 0 ); + + this._subModels = {}; + this._superModel = null; + + // If this model has 'subModelTypes' itself, remember them in the store + if ( this.prototype.hasOwnProperty( 'subModelTypes' ) ) { + Backbone.Relational.store.addSubModels( this.prototype.subModelTypes, this ); + } + // The 'subModelTypes' property should not be inherited, so reset it. + else { + this.prototype.subModelTypes = null; + } + + // Initialize all reverseRelations that belong to this new model. + _.each( this.prototype.relations, function( rel ) { + if ( !rel.model ) { + rel.model = this; + } + + if ( rel.reverseRelation && rel.model === this ) { + var preInitialize = true; + if ( _.isString( rel.relatedModel ) ) { + /** + * The related model might not be defined for two reasons + * 1. it never gets defined, e.g. a typo + * 2. it is related to itself + * In neither of these cases do we need to pre-initialize reverse relations. + */ + var relatedModel = Backbone.Relational.store.getObjectByName( rel.relatedModel ); + preInitialize = relatedModel && ( relatedModel.prototype instanceof Backbone.RelationalModel ); + } + + var type = !_.isString( rel.type ) ? rel.type : Backbone[ rel.type ] || Backbone.Relational.store.getObjectByName( rel.type ); + if ( preInitialize && type && type.prototype instanceof Backbone.Relation ) { + new type( null, rel ); + } + } + }, this ); + }, + + /** + * Create a 'Backbone.Model' instance based on 'attributes'. + * @param {Object} attributes + * @param {Object} [options] + * @return {Backbone.Model} + */ + build: function( attributes, options ) { + var model = this; + + // 'build' is a possible entrypoint; it's possible no model hierarchy has been determined yet. + this.initializeModelHierarchy(); + + // Determine what type of (sub)model should be built if applicable. + // Lookup the proper subModelType in 'this._subModels'. + if ( this._subModels && this.prototype.subModelTypeAttribute in attributes ) { + var subModelTypeAttribute = attributes[ this.prototype.subModelTypeAttribute ]; + var subModelType = this._subModels[ subModelTypeAttribute ]; + if ( subModelType ) { + model = subModelType; + } + } + + return new model( attributes, options ); + }, + + initializeModelHierarchy: function() { + // If we're here for the first time, try to determine if this modelType has a 'superModel'. + if ( _.isUndefined( this._superModel ) || _.isNull( this._superModel ) ) { + Backbone.Relational.store.setupSuperModel( this ); + + // If a superModel has been found, copy relations from the _superModel if they haven't been + // inherited automatically (due to a redefinition of 'relations'). + // Otherwise, make sure we don't get here again for this type by making '_superModel' false so we fail + // the isUndefined/isNull check next time. + if ( this._superModel ) { + // + if ( this._superModel.prototype.relations ) { + var supermodelRelationsExist = _.any( this.prototype.relations, function( rel ) { + return rel.model && rel.model !== this; + }, this ); + + if ( !supermodelRelationsExist ) { + this.prototype.relations = this._superModel.prototype.relations.concat( this.prototype.relations ); + } + } + } + else { + this._superModel = false; + } + } + + // If we came here through 'build' for a model that has 'subModelTypes', and not all of them have been resolved yet, try to resolve each. + if ( this.prototype.subModelTypes && _.keys( this.prototype.subModelTypes ).length !== _.keys( this._subModels ).length ) { + _.each( this.prototype.subModelTypes, function( subModelTypeName ) { + var subModelType = Backbone.Relational.store.getObjectByName( subModelTypeName ); + subModelType && subModelType.initializeModelHierarchy(); + }); + } + }, + + /** + * Find an instance of `this` type in 'Backbone.Relational.store'. + * - If `attributes` is a string or a number, `findOrCreate` will just query the `store` and return a model if found. + * - If `attributes` is an object, the model will be updated with `attributes` if found. + * Otherwise, a new model is created with `attributes` (unless `options.create` is explicitly set to `false`). + * @param {Object|String|Number} attributes Either a model's id, or the attributes used to create or update a model. + * @param {Object} [options] + * @param {Boolean} [options.create=true] + * @return {Backbone.RelationalModel} + */ + findOrCreate: function( attributes, options ) { + // Try to find an instance of 'this' model type in the store + var model = Backbone.Relational.store.find( this, attributes ); + + // If we found an instance, update it with the data in 'item'; if not, create an instance + // (unless 'options.create' is false). + if ( _.isObject( attributes ) ) { + if ( model ) { + model.set( attributes, options ); + } + else if ( !options || ( options && options.create !== false ) ) { + model = this.build( attributes, options ); + } + } + + return model; + } }); _.extend( Backbone.RelationalModel.prototype, Backbone.Semaphore ); /** + * Override Backbone.Collection._prepareModel, so objects will be built using the correct type + * if the collection.model has subModels. + */ + Backbone.Collection.prototype.__prepareModel = Backbone.Collection.prototype._prepareModel; + Backbone.Collection.prototype._prepareModel = function ( model, options ) { + options || (options = {}); + if ( !( model instanceof Backbone.Model ) ) { + var attrs = model; + options.collection = this; + + if ( typeof this.model.build !== 'undefined' ) { + model = this.model.build( attrs, options ); + } + else { + model = new this.model( attrs, options ); + } + + if ( !model._validate( model.attributes, options ) ) { + model = false; + } + } + else if ( !model.collection ) { + model.collection = this; + } + + return model; + } + + /** * Override Backbone.Collection.add, so objects fetched from the server multiple times will * update the existing Model. Also, trigger 'relational:add'. */ @@ -1289,22 +1560,22 @@ //console.debug( 'calling add on coll=%o; model=%o, options=%o', this, models, options ); _.each( models, function( model ) { - if ( !( model instanceof Backbone.Model ) ) { - // Try to find 'model' in Backbone.store. If it already exists, set the new properties on it. - var existingModel = Backbone.Relational.store.find( this.model, model[ this.model.prototype.idAttribute ] ); - if ( existingModel ) { - existingModel.set( existingModel.parse ? existingModel.parse( model ) : model, options ); - model = existingModel; + if ( !( model instanceof Backbone.Model ) ) { + // Try to find 'model' in Backbone.store. If it already exists, set the new properties on it. + var existingModel = Backbone.Relational.store.find( this.model, model[ this.model.prototype.idAttribute ] ); + if ( existingModel ) { + existingModel.set( existingModel.parse ? existingModel.parse( model ) : model, options ); + model = existingModel; + } + else { + model = Backbone.Collection.prototype._prepareModel.call( this, model, options ); + } } - else { - model = Backbone.Collection.prototype._prepareModel.call( this, model, options ); + + if ( model instanceof Backbone.Model && !this.get( model ) && !this.getByCid( model ) ) { + modelsToAdd.push( model ); } - } - - if ( model instanceof Backbone.Model && !this.get( model ) && !this.getByCid( model ) ) { - modelsToAdd.push( model ); - } - }, this ); + }, this ); // Add 'models' in a single batch, so the original add will only be called once (and thus 'sort', etc). @@ -1312,8 +1583,8 @@ add.call( this, modelsToAdd, options ); _.each( modelsToAdd, function( model ) { - this.trigger('relational:add', model, this, options); - }, this ); + this.trigger( 'relational:add', model, this, options ); + }, this ); } return this; @@ -1325,19 +1596,22 @@ var remove = Backbone.Collection.prototype.__remove = Backbone.Collection.prototype.remove; Backbone.Collection.prototype.remove = function( models, options ) { options || (options = {}); - if (!_.isArray( models ) ) { + if ( !_.isArray( models ) ) { models = [ models ]; } + else { + models = models.slice( 0 ); + } //console.debug('calling remove on coll=%o; models=%o, options=%o', this, models, options ); _.each( models, function( model ) { - model = this.getByCid( model ) || this.get( model ); + model = this.getByCid( model ) || this.get( model ); - if ( model instanceof Backbone.Model ) { - remove.call( this, model, options ); - this.trigger('relational:remove', model, this, options); - } - }, this ); + if ( model instanceof Backbone.Model ) { + remove.call( this, model, options ); + this.trigger('relational:remove', model, this, options); + } + }, this ); return this; }; @@ -1348,7 +1622,18 @@ var reset = Backbone.Collection.prototype.__reset = Backbone.Collection.prototype.reset; Backbone.Collection.prototype.reset = function( models, options ) { reset.call( this, models, options ); - this.trigger( 'relational:reset', models, options ); + this.trigger( 'relational:reset', this, options ); + + return this; + }; + + /** + * Override 'Backbone.Collection.sort' to trigger 'relational:reset'. + */ + var sort = Backbone.Collection.prototype.__sort = Backbone.Collection.prototype.sort; + Backbone.Collection.prototype.sort = function( options ) { + sort.call( this, options ); + this.trigger( 'relational:reset', this, options ); return this; }; @@ -1372,35 +1657,12 @@ return this; }; - // Override .extend() to check for reverseRelations to initialize. + // Override .extend() to automatically call .setup() Backbone.RelationalModel.extend = function( protoProps, classProps ) { var child = Backbone.Model.extend.apply( this, arguments ); - - var relations = ( protoProps && protoProps.relations ) || []; - _.each( relations, function( rel ) { - if( rel.reverseRelation ) { - rel.model = child; - - var preInitialize = true; - if ( _.isString( rel.relatedModel ) ) { - /** - * The related model might not be defined for two reasons - * 1. it never gets defined, e.g. a typo - * 2. it is related to itself - * In neither of these cases do we need to pre-initialize reverse relations. - */ - var relatedModel = Backbone.Relational.store.getObjectByName( rel.relatedModel ); - preInitialize = relatedModel && ( relatedModel.prototype instanceof Backbone.RelationalModel.prototype.constructor ); - } - - var type = !_.isString( rel.type ) ? rel.type : Backbone[ rel.type ] || Backbone.Relational.store.getObjectByName( rel.type ); - if ( preInitialize && type && type.prototype instanceof Backbone.Relation.prototype.constructor ) { - new type( null, rel ); - } - } - }); + + child.setup( this ); return child; }; - })(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Use url_for to generate logo URL.
by Bitbucket 27 Jun '12

27 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/adc8114131fa/ changeset: adc8114131fa user: jgoecks date: 2012-06-27 20:55:54 summary: Use url_for to generate logo URL. affected #: 3 files diff -r 8cd9f0ce913260795ee749536face3bd54f1bc62 -r adc8114131fa700da3b5800d7ba4568bd665c9b5 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -118,7 +118,7 @@ ## Logo, layered over tabs to be clickable <div class="title"> - <a href="${app.config.get( 'logo_url', '/' )}"> + <a href="${h.url_for( app.config.get( 'logo_url', '/' ) )}"><img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}"> Galaxy Tool Shed %if app.config.brand: diff -r 8cd9f0ce913260795ee749536face3bd54f1bc62 -r adc8114131fa700da3b5800d7ba4568bd665c9b5 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -184,7 +184,7 @@ ## Logo, layered over tabs to be clickable <div class="title"> - <a href="${app.config.get( 'logo_url', '/' )}"> + <a href="${h.url_for( app.config.get( 'logo_url', '/' ) )}"><img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}"> Galaxy %if app.config.brand: diff -r 8cd9f0ce913260795ee749536face3bd54f1bc62 -r adc8114131fa700da3b5800d7ba4568bd665c9b5 templates/webapps/reports/base_panels.mako --- a/templates/webapps/reports/base_panels.mako +++ b/templates/webapps/reports/base_panels.mako @@ -27,7 +27,7 @@ </div> ## Logo, layered over tabs to be clickable <div class="title" style="position: absolute; top: 0; left: 0;"> - <a href="${app.config.get( 'logo_url', '/' )}"> + <a href="${h.url_for( app.config.get( 'logo_url', '/' ) )}"><img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> Galaxy Reports %if app.config.brand: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Add tipsy config to icon buttons and add tipsy to paramamonster.
by Bitbucket 27 Jun '12

27 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8cd9f0ce9132/ changeset: 8cd9f0ce9132 user: jgoecks date: 2012-06-27 18:12:43 summary: Add tipsy config to icon buttons and add tipsy to paramamonster. affected #: 3 files diff -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 -r 8cd9f0ce913260795ee749536face3bd54f1bc62 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -8,10 +8,14 @@ * defines an icon button. Each dictionary must have the following * elements: icon_class, title, and on_click. */ -var create_icon_buttons_menu = function(config) { +var create_icon_buttons_menu = function(config, global_config) { + if (!global_config) { global_config = {}; } + // Create and initialize menu. var buttons = new IconButtonCollection( - _.map(config, function(button_config) { return new IconButton(button_config); }) + _.map(config, function(button_config) { + return new IconButton(_.extend(button_config, global_config)); + }) ); return new IconButtonMenuView( {collection: buttons} ); @@ -38,7 +42,8 @@ defaults: { title: "", icon_class: "", - on_click: null + on_click: null, + tipsy_config: {} } }); @@ -60,12 +65,17 @@ var self = this; this.collection.each(function(button) { // Create and add icon button to menu. - $("<a/>").attr('href', 'javascript:void(0)') + var elt = + $('<a/>').attr('href', 'javascript:void(0)') .attr('title', button.attributes.title) .addClass('icon-button menu-button') .addClass(button.attributes.icon_class) .appendTo(self.$el) .click(button.attributes.on_click); + + if (button.attributes.tipsy_config) { + elt.tipsy(button.attributes.tipsy_config); + } }); return this; } diff -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 -r 8cd9f0ce913260795ee749536face3bd54f1bc62 static/scripts/viz/paramamonster.js --- a/static/scripts/viz/paramamonster.js +++ b/static/scripts/viz/paramamonster.js @@ -294,7 +294,8 @@ icon_class: 'gear track-settings', on_click: function () { settings_div.toggle(); - } + }, + tipsy_config: { gravity: 's' } } ]); settings_td.prepend(icon_menu.$el); @@ -390,7 +391,7 @@ var self = this, menu = create_icon_buttons_menu([ { - title: 'Add', + title: 'Add parameter to tree', icon_class: 'plus-button', on_click: function () { input.set('in_ptree', true); @@ -400,7 +401,7 @@ }, { - title: 'Remove', + title: 'Remove parameter from tree', icon_class: 'toggle', on_click: function() { // Remove parameter from tree params where name matches clicked paramter. @@ -409,7 +410,10 @@ single_input_row.show(); } } - ]); + ], + { + tipsy_config: {gravity: 's'} + }); this.$el.prepend(menu.$el); // Update input's min, max, number of samples as values change. diff -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 -r 8cd9f0ce913260795ee749536face3bd54f1bc62 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -177,14 +177,14 @@ { icon_class: 'cross-circle', title: 'Close', on_click: function() { window.location = "${h.url_for( controller='visualization', action='list' )}"; } } - ]); + ], + { + tipsy_config: {gravity: 'n'} + }); menu.$el.attr("style", "float: right"); $("#center .unified-panel-header-inner").append(menu.$el); - // Manual tipsy config because default gravity is S and cannot be changed. - $(".menu-button").tipsy( {gravity: 'n'} ); - // Hide bookmarks by default right now. parent.force_right_panel("hide"); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: (a) Paramamonster implemention; (b) bug fixes and small additions to style sheets; and (c) bug fixes for rerunning tools on complete datasets.
by Bitbucket 27 Jun '12

27 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/27f54f28e9f1/ changeset: 27f54f28e9f1 user: jgoecks date: 2012-06-27 16:51:20 summary: (a) Paramamonster implemention; (b) bug fixes and small additions to style sheets; and (c) bug fixes for rerunning tools on complete datasets. affected #: 10 files diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 lib/galaxy/web/api/tools.py --- a/lib/galaxy/web/api/tools.py +++ b/lib/galaxy/web/api/tools.py @@ -133,8 +133,9 @@ # Run tool on region if region is specificied. run_on_regions = False - regions = from_json_string( payload.get( 'regions', None ) ) + regions = payload.get( 'regions', None ) if regions: + regions = from_json_string( regions ) if isinstance( regions, dict ): # Regions is a single region. regions = [ GenomeRegion.from_dict( regions ) ] @@ -256,7 +257,8 @@ # Set input datasets for tool. If running on regions, extract and use subset # when possible. # - regions_str = ",".join( [ str( r ) for r in regions ] ) + if run_on_regions: + regions_str = ",".join( [ str( r ) for r in regions ] ) for jida in original_job.input_datasets: # If param set previously by config actions, do nothing. if jida.name in params_set: diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -650,7 +650,7 @@ } div.form-row-input { - width: 300px; + width: 90%; float: left; } @@ -696,7 +696,7 @@ select, textarea, input[type="text"], input[type="file"], input[type="password"] { // -webkit-box-sizing: border-box; - max-width: 300px; + max-width: 90%; } textarea, input[type="text"], input[type="password"] { diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 static/june_2007_style/base_sprites.less.tmpl --- a/static/june_2007_style/base_sprites.less.tmpl +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -52,6 +52,10 @@ } .icon-button.toggle { -sprite-group: fugue; + -sprite-image: fugue/toggle-bw.png; +} +.icon-button.toggle:hover { + -sprite-group: fugue; -sprite-image: fugue/toggle.png; } .icon-button.arrow-circle { diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -742,23 +742,24 @@ .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} .icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} .icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} -.icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;} -.icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;} -.icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} -.icon-button.disk{background:url(fugue.png) no-repeat 0px -208px;} -.icon-button.information{background:url(fugue.png) no-repeat 0px -234px;} -.icon-button.annotate{background:url(fugue.png) no-repeat 0px -260px;} -.icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -286px;} -.icon-button.import{background:url(fugue.png) no-repeat 0px -312px;} -.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -338px;} -.icon-button.plus-button:hover{background:url(fugue.png) no-repeat 0px -364px;} -.icon-button.gear{background:url(fugue.png) no-repeat 0px -390px;} -.icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -416px;} -.icon-button.disk--arrow{background:url(fugue.png) no-repeat 0px -442px;} -.icon-button.disk--arrow:hover{background:url(fugue.png) no-repeat 0px -468px;} -.icon-button.cross-circle{background:url(fugue.png) no-repeat 0px -494px;} -.icon-button.cross-circle:hover{background:url(fugue.png) no-repeat 0px -520px;} -.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -546px;} +.icon-button.toggle:hover{background:url(fugue.png) no-repeat 0px -130px;} +.icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -156px;} +.icon-button.chevron{background:url(fugue.png) no-repeat 0px -182px;} +.icon-button.bug{background:url(fugue.png) no-repeat 0px -208px;} +.icon-button.disk{background:url(fugue.png) no-repeat 0px -234px;} +.icon-button.information{background:url(fugue.png) no-repeat 0px -260px;} +.icon-button.annotate{background:url(fugue.png) no-repeat 0px -286px;} +.icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -312px;} +.icon-button.import{background:url(fugue.png) no-repeat 0px -338px;} +.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -364px;} +.icon-button.plus-button:hover{background:url(fugue.png) no-repeat 0px -390px;} +.icon-button.gear{background:url(fugue.png) no-repeat 0px -416px;} +.icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -442px;} +.icon-button.disk--arrow{background:url(fugue.png) no-repeat 0px -468px;} +.icon-button.disk--arrow:hover{background:url(fugue.png) no-repeat 0px -494px;} +.icon-button.cross-circle{background:url(fugue.png) no-repeat 0px -520px;} +.icon-button.cross-circle:hover{background:url(fugue.png) no-repeat 0px -546px;} +.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -572px;} div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 static/june_2007_style/blue/fugue.png Binary file static/june_2007_style/blue/fugue.png has changed diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -52,6 +52,26 @@ ], urlRoot: galaxy_paths.get('tool_url'), + + /** + * Returns object copy, optionally including only inputs that can be sampled. + */ + copy: function(only_samplable_inputs) { + var copy = new Tool(this.toJSON()); + + // Return only samplable inputs if flag is set. + if (only_samplable_inputs) { + var valid_inputs = new Backbone.Collection(); + copy.get('inputs').each(function(input) { + if (input.get_samples()) { + valid_inputs.push(input); + } + }); + copy.set('inputs', valid_inputs); + } + + return copy; + }, apply_search_results: function(results) { ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); @@ -81,7 +101,7 @@ * Run tool; returns a Deferred that resolves to the tool's output(s). */ run: function() { - return this._run() + return this._run(); }, /** @@ -94,6 +114,17 @@ regions: JSON.stringify(regions) }); }, + + /** + * Returns input dict for tool's inputs. + */ + get_inputs_dict: function() { + var input_dict = {}; + this.get('inputs').each(function(input) { + input_dict[input.get('name')] = input.get('value'); + }); + return input_dict; + }, /** * Run tool; returns a Deferred that resolves to the tool's output(s). @@ -102,13 +133,9 @@ _run: function(additional_params) { // Create payload. var payload = _.extend({ - tool_id: this.id - }, additional_params), - input_dict = {}; - this.get('inputs').each(function(input) { - input_dict[input.get('name')] = input.get('value'); - }); - payload.inputs = input_dict; + tool_id: this.id, + inputs: this.get_inputs_dict() + }, additional_params); // Because job may require indexing datasets, use server-side // deferred to ensure that job is run. Also use deferred that @@ -145,21 +172,27 @@ label: null, type: null, value: null, + num_samples: 5 }, initialize: function() { this.attributes.html = unescape(this.attributes.html); }, + + copy: function() { + return new ToolInput(this.toJSON()); + }, /** * Returns samples from a tool input. */ - get_samples: function(num_samples) { - var - type = this.get('type'), - samples = [] + get_samples: function() { + var type = this.get('type'), + samples = null; if (type === 'number') { - samples = d3.scale.linear().domain([this.get('min'), this.get('max')]).ticks(num_samples); + samples = d3.scale.linear() + .domain([this.get('min'), this.get('max')]) + .ticks(this.get('num_samples')); } else if (type === 'select') { samples = _.map(this.get('options'), function(option) { @@ -167,24 +200,11 @@ }); } - return new ParamSamples({ - param: this, - samples: samples - }); + return samples; } }); /** - * A tool and parameter samples. - */ -var ParamSamples = Backbone.Model.extend({ - defaults: { - param: null, - samples: null - } -}) - -/** * Wrap collection of tools for fast access/manipulation. */ var ToolCollection = Backbone.Collection.extend({ diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -51,6 +51,10 @@ */ var IconButtonMenuView = Backbone.View.extend({ tagName: 'div', + + initialize: function() { + this.render(); + }, render: function() { var self = this; diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 static/scripts/viz/paramamonster.js --- a/static/scripts/viz/paramamonster.js +++ b/static/scripts/viz/paramamonster.js @@ -4,95 +4,230 @@ */ /** - * --- Models --- + * Tree for a tool's parameters. */ - var ToolParameterTree = Backbone.Model.extend({ defaults: { tool: null, - params: null, - num_samples: 4 - }, - - - initialize: function(options) { - // - // -- Create tree data from tool. -- - // - - // Valid inputs for tree are number, select parameters. - var tool = this.get('tool'), - num_samples = this.get('num_samples'), - params_samples = tool.get('inputs').map(function(input) { - return input.get_samples(num_samples); - }), - filtered_params_samples = _.filter(params_samples, function(param_sample) { - return param_sample.get('samples').length !== 0; - }); - - /** - * Returns tree data. Params_sampling is an array of - * - */ - var create_tree_data = function(params_samples, index) { - var - param_samples = params_samples[index], - param = param_samples.get('param'), - param_label = param.get('label'), - settings = param_samples.get('samples'); - - // Create leaves when last parameter setting is reached. - if (params_samples.length - 1 === index) { - return _.map(settings, function(setting) { - return { - name: param_label + '=' + setting, - param: param, - value: setting - } - }); - } - - // Recurse to handle other parameters. - return _.map(settings, function(setting) { - return { - name: param_label + '=' + setting, - param: param, - value: setting, - children: create_tree_data(filtered_params_samples, index + 1) - } - }); - }; - - var tree_data = { - name: 'Parameter Tree for ' + tool.get('name'), - children: create_tree_data(filtered_params_samples, 0) - }; - - // Set valid inputs, tree data for later use. - this.set('params', _.map(params_samples, function(s) { return s.get('param') })); - this.set('tree_data', tree_data); - } - -}); - -/** - * Tile of rendered genomic data. - */ -var Tile = Backbone.Model.extend({ - defaults: { - track: null, - index: null, - region: null, - resolution: null, - data: null, - stale: null, - html_elt: null + tree_data: null }, initialize: function(options) { + // Set up tool parameters to work with tree. + var self = this; + this.get('tool').get('inputs').each(function(input) { + if (!input.get_samples()) { return; } + + // All inputs are in tree to start. + self.add_param(input); + + // Listen for changes to input's attributes. + input.on('change:min change:max change:num_samples', function(input) { + if (input.get('in_ptree')) { + self.set_tree_data(); + } + }, self); + input.on('change:in_ptree', function(input) { + if (input.get('in_ptree')) { + self.add_param(input); + } + else { + self.remove_param(input); + } + self.set_tree_data(); + }, self); + }); + + self.set_tree_data(); + }, + + add_param: function(param) { + // If parameter already present, do not add it. + if (param.get('ptree_index')) { return; } + + param.set('in_ptree', true); + param.set('ptree_index', this.get_tree_params().length); + }, + + remove_param: function(param) { + // Remove param from tree. + param.set('in_ptree', false); + param.set('ptree_index', null); + + // Update ptree indices for remaining params. + _(this.get_tree_params()).each(function(input, index) { + // +1 to use 1-based indexing. + input.set('ptree_index', index + 1); + }); + }, + + /** + * Sets tree data using tool's inputs. + */ + set_tree_data: function() { + // Get samples for each parameter. + var params_samples = _.map(this.get_tree_params(), function(param) { + return { + param: param, + samples: param.get_samples() + }; + }); + var node_id = 0, + // Creates tree data recursively. + create_tree_data = function(params_samples, index) { + var param_samples = params_samples[index], + param = param_samples.param, + param_label = param.get('label'), + settings = param_samples.samples; + + // Create leaves when last parameter setting is reached. + if (params_samples.length - 1 === index) { + return _.map(settings, function(setting) { + return { + id: node_id++, + name: setting, + param: param, + value: setting + }; + }); + } + + // Recurse to handle other parameters. + return _.map(settings, function(setting) { + return { + id: node_id++, + name: setting, + param: param, + value: setting, + children: create_tree_data(params_samples, index + 1) + }; + }); + }; + + this.set('tree_data', { + name: 'Root', + children: (params_samples.length !== 0 ? create_tree_data(params_samples, 0) : null) + }); + }, + + get_tree_params: function() { + // Filter and sort parameters to get list in tree. + return _(this.get('tool').get('inputs').where( {in_ptree: true} )) + .sortBy( function(input) { return input.get('ptree_index'); } ); + }, + + /** + * Returns number of leaves in tree. + */ + get_num_leaves: function() { + return this.get_tree_params().reduce(function(memo, param) { return memo * param.get_samples().length; }, 1); + }, + + /** + * Returns array of settings based on a node and its subtree. + */ + get_node_settings: function(target_node) { + // -- Get fixed settings from tool and parent nodes. + + // Start with tool's settings. + var fixed_settings = this.get('tool').get_inputs_dict(); + + // Get fixed settings using node's parents. + var cur_node = target_node.parent; + if (cur_node) { + while(cur_node.depth !== 0) { + fixed_settings[cur_node.param.get('name')] = cur_node.value; + cur_node = cur_node.parent; + } + } + // Walk subtree starting at clicked node to get full list of settings. + var get_settings = function(node, settings) { + // Add setting for this node. + settings[node.param.get('name')] = node.value; + + if (!node.children) { + // At leaf node: add param setting and return. + return settings; + } + else { + // At interior node: return list of subtree settings. + return _.flatten( _.map(node.children, function(c) { return get_settings(c, _.clone(settings)); }) ); + } + }, + all_settings = get_settings(target_node, fixed_settings); + + // If user clicked on leaf, settings is a single dict. Convert to array for simplicity. + if (!_.isArray(all_settings)) { all_settings = [ all_settings ]; } + + return all_settings; + }, + + /** + * Returns all nodes connected a particular node; this includes parents and children of the node. + */ + get_connected_nodes: function(node) { + var get_subtree_nodes = function(a_node) { + if (!a_node.children) { + return a_node; + } + else { + // At interior node: return subtree nodes. + return _.flatten( [a_node, _.map(a_node.children, function(c) { return get_subtree_nodes(c); })] ); + } + }; + + // Get node's parents. + var parents = [], + cur_parent = node.parent; + while(cur_parent) { + parents.push(cur_parent); + cur_parent = cur_parent.parent; + } + + return _.flatten([parents, get_subtree_nodes(node)]); + }, + + /** + * Returns the leaf that corresponds to a settings collection. + */ + get_leaf: function(settings) { + var cur_node = this.get('tree_data'), + find_child = function(children) { + return _.find(children, function(child) { + return settings[child.param.get('name')] === child.value; + }); + }; + + while (cur_node.children) { + cur_node = find_child(cur_node.children); + } + return cur_node; } - +}); + +var ParamaMonsterTrack = Backbone.Model.extend({ + defaults: { + track: null, + settings: null, + regions: null + }, + + same_settings: function(a_track) { + var this_settings = this.get('settings'), + other_settings = a_track.get('settings'); + for (var prop in this_settings) { + if (!other_settings[prop] || + this_settings[prop] !== other_settings[prop]) { + return false; + } + } + return true; + } +}); + +var TrackCollection = Backbone.Collection.extend({ + model: ParamaMonsterTrack }); /** @@ -102,11 +237,24 @@ defaults: _.extend({}, Visualization.prototype.defaults, { tool: null, parameter_tree: null, - regions: null + regions: null, + tracks: null }), initialize: function(options) { - this.set('parameter_tree', new ToolParameterTree({ tool: this.get('tool') })); + var tool_with_samplable_inputs = this.get('tool').copy(true); + this.set('tool_with_samplable_inputs', tool_with_samplable_inputs); + + this.set('parameter_tree', new ToolParameterTree({ tool: tool_with_samplable_inputs })); + this.set('tracks', new TrackCollection()); + }, + + add_placeholder: function(settings) { + this.get('tracks').add(new PlaceholderTrack(settings)); + }, + + add_track: function(track) { + this.get('tracks').add(track); } }); @@ -114,87 +262,388 @@ * --- Views --- */ -var TileView = Backbone.View.extend({ - +/** + * ParamaMonster track view. + */ +var ParamaMonsterTrackView = Backbone.View.extend({ + tagName: 'tr', + + initialize: function(options) { + this.canvas_manager = options.canvas_manager; + this.render(); + this.model.on('change:track', this.draw_tiles, this); + }, + + render: function() { + // Render settings icon and popup. + // TODO: use template. + var settings = this.model.get('settings'), + settings_td = $('<td/>').addClass('settings').appendTo(this.$el), + settings_div = $('<div/>').addClass('track-info').hide().appendTo(settings_td); + settings_div.append( $('<div/>').css('font-weight', 'bold').text('Track Settings') ); + _.each(_.keys(settings), function(name) { + settings_div.append( name + ': ' + settings[name] + '<br/>'); + }); + var self = this, + run_on_dataset_button = $('<button/>').appendTo(settings_div).text('Run on complete dataset').click(function() { + self.trigger('run_on_dataset', settings); + }); + var icon_menu = create_icon_buttons_menu([ + { + title: 'Settings', + icon_class: 'gear track-settings', + on_click: function () { + settings_div.toggle(); + } + } + ]); + settings_td.prepend(icon_menu.$el); + + // Render tile placeholders. + _.each(this.model.get('regions'), function() { + self.$el.append($('<td/>').addClass('tile').html( + $('<img/>').attr('src', galaxy_paths.get('image_path') + '/loading_large_white_bg.gif') + )); + }); + + if (this.model.get('track')) { + this.draw_tiles(); + } + }, + + draw_tiles: function() { + // Display tiles for regions of interest. + var self = this, + track = this.model.get('track'), + regions = this.model.get('regions'), + tile_containers = this.$el.find('td.tile'); + + // When data is ready, draw tiles. + $.when(track.data_manager.data_is_ready()).then(function(data_ok) { + // Draw tile for each region. + _.each(regions, function(region, index) { + var resolution = region.length() / 300, + w_scale = 1/resolution, + mode = 'Pack'; + $.when(track.data_manager.get_data(region, mode, resolution, {})).then(function(tile_data) { + var canvas = self.canvas_manager.new_canvas(); + canvas.width = 300; + canvas.height = track.get_canvas_height(tile_data, mode, w_scale, canvas.width); + track.draw_tile(tile_data, canvas.getContext('2d'), mode, resolution, region, w_scale); + $(tile_containers[index]).empty().append(canvas); + }); + }); + }); + } }); +/** + * Tool input (parameter) that enables both value and sweeping inputs. View is unusual as + * it augments an existing input form row rather than creates a completely new HTML element. + */ +var ToolInputValOrSweepView = Backbone.View.extend({ + + // Template for rendering sweep inputs: + number_input_template: '<div class="form-row-input sweep">' + + '<input class="min" type="text" size="6" value="<%= min %>"> - ' + + '<input class="max" type="text" size="6" value="<%= max %>">' + + ' samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>">' + + '</div>', + + select_input_template: '<div class="form-row-input sweep"><%= options %></div>', + + initialize: function(options) { + this.$el = options.tool_row; + this.render(); + }, + + render: function() { + var input = this.model, + type = input.get('type'), + single_input_row = this.$el.find('.form-row-input'), + sweep_inputs_row = null; + + // Update tool inputs as single input changes. + single_input_row.find('input').change(function() { + input.set('value', $(this).val()); + }); + + // Add row for parameter sweep inputs. + if (type === 'number') { + sweep_inputs_row = $(_.template(this.number_input_template, this.model.toJSON())); + } + else if (type === 'select') { + var options = _.map(this.$el.find('select option'), function(option) { + return $(option).val(); + }), + options_text = options.join(', '); + sweep_inputs_row = $(_.template(this.select_input_template, { + options: options_text + })); + } + + // Fow now, assume parameter is included in tree to start. + sweep_inputs_row.insertAfter(single_input_row); + single_input_row.hide(); + + // Add buttons for adding/removing parameter. + var self = this, + menu = create_icon_buttons_menu([ + { + title: 'Add', + icon_class: 'plus-button', + on_click: function () { + input.set('in_ptree', true); + single_input_row.hide(); + sweep_inputs_row.show(); + } + + }, + { + title: 'Remove', + icon_class: 'toggle', + on_click: function() { + // Remove parameter from tree params where name matches clicked paramter. + input.set('in_ptree', false); + sweep_inputs_row.hide(); + single_input_row.show(); + } + } + ]); + this.$el.prepend(menu.$el); + + // Update input's min, max, number of samples as values change. + _.each(['min', 'max', 'num_samples'], function(attr) { + sweep_inputs_row.find('.' + attr).change(function() { + input.set(attr, parseFloat( $(this).val() )); + }); + }); + } +}); + +var ToolParameterTreeDesignView = Backbone.View.extend({ + className: 'tree-design', + + initialize: function(options) { + this.render(); + }, + + render: function() { + // Start with tool form view. + var tool_form_view = new ToolFormView({ + model: this.model.get('tool') + }); + tool_form_view.render(); + this.$el.append(tool_form_view.$el); + + // Set up views for each tool input. + var self = this, + inputs = self.model.get('tool').get('inputs'); + this.$el.find('.form-row').not('.form-actions').each(function(i) { + var input_view = new ToolInputValOrSweepView({ + model: inputs.at(i), + tool_row: $(this) + }); + }); + } +}); + +/** + * Displays and updates parameter tree. + */ var ToolParameterTreeView = Backbone.View.extend({ className: 'tool-parameter-tree', initialize: function(options) { + // When tree data changes, re-render. + this.model.on('change:tree_data', this.render, this); }, render: function() { - var width = 960, - height = 2000; + var tree_params = this.model.get_tree_params(); + // Start fresh. + this.$el.children().remove(); + + // Set width, height based on params and samples. + this.width = 100 * (2 + tree_params.length); + this.height = 15 * this.model.get_num_leaves(); + + var self = this; // Layout tree. var cluster = d3.layout.cluster() - .size([height, width - 160]); + .size([this.height - 10, this.width - 160]); var diagonal = d3.svg.diagonal() .projection(function(d) { return [d.y, d.x]; }); + // Layout nodes. + var nodes = cluster.nodes(this.model.get('tree_data')); + + // Setup and add labels for tree levels. + var param_depths = _.uniq(_.pluck(nodes, "y")); + _.each(tree_params, function(param, index) { + var x = param_depths[index+1]; + self.$el.append( $('<div>').addClass('label') + .text(param.get('label')) + // HACK: add 250 b/c in center panel. + .css('left', x + 250) ); + }); + // Set up vis element. var vis = d3.select(this.$el[0]) .append("svg") - .attr("width", width) - .attr("height", height) + .attr("width", this.width) + .attr("height", this.height) .append("g") - .attr("transform", "translate(80, 0)"); + .attr("transform", "translate(40, 10)"); - // Set up nodes, links. - var nodes = cluster.nodes(this.model.get('tree_data')); - + // Draw links. var link = vis.selectAll("path.link") .data(cluster.links(nodes)) .enter().append("path") .attr("class", "link") .attr("d", diagonal); + // Draw nodes. var node = vis.selectAll("g.node") .data(nodes) .enter().append("g") .attr("class", "node") - .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; }); + .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; }) + .on('mouseover', function(a_node) { + var connected_node_ids = _.pluck(self.model.get_connected_nodes(a_node), 'id'); + // TODO: probably can use enter() to do this more easily. + node.filter(function(d) { + return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined; + }).style('fill', '#f00'); + }) + .on('mouseout', function() { + node.style('fill', '#000'); + }); node.append("circle") - .attr("r", 4.5); + .attr("r", 9); node.append("text") - .attr("dx", function(d) { return d.children ? -8 : 8; }) + .attr("dx", function(d) { return d.children ? -12 : 12; }) .attr("dy", 3) .attr("text-anchor", function(d) { return d.children ? "end" : "start"; }) .text(function(d) { return d.name; }); } }); +/** + * ParamaMonster visualization view. View requires rendering in 3-panel setup for now. + */ var ParamaMonsterVisualizationView = Backbone.View.extend({ className: 'paramamonster', initialize: function(options) { - + this.canvas_manager = new CanvasManager(this.$el.parents('body')); + this.tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') }); + this.track_collection_container = $('<table/>').addClass('tracks'); + + // Handle node clicks for tree data. + this.model.get('parameter_tree').on('change:tree_data', this.handle_node_clicks, this); }, render: function() { - // Set up tool parameter tree. - var tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') }); - tool_param_tree_view.render(); - this.$el.append(tool_param_tree_view.$el); - - // When node clicked in tree, run tool and show tiles. - var node = d3.select(tool_param_tree_view.$el[0]).selectAll("g.node") + // Render tree design view in left panel. + var tree_design_view = new ToolParameterTreeDesignView({ + model: this.model.get('parameter_tree') + }); + + $('#left').append(tree_design_view.$el); + + // Render track collection container/view in right panel. + var self = this, + regions = self.model.get('regions'), + tr = $('<tr/>').appendTo(this.track_collection_container); + + _.each(regions, function(region) { + tr.append( $('<th>').text(region.toString()) ); + }); + tr.children().first().attr('colspan', 2); + + $('#right').append(this.track_collection_container); + + // Render tool parameter tree in center panel. + this.tool_param_tree_view.render(); + $('#center').append(this.tool_param_tree_view.$el); + + this.handle_node_clicks(); + }, + + run_tool_on_dataset: function(settings) { + var tool = this.model.get('tool'), + dataset = this.model.get('dataset'); + tool.set_input_values(settings); + $.when(tool.rerun(dataset)).then(function(outputs) { + // TODO: show modal with information about how to get to datasets. + }); + }, + + handle_node_clicks: function() { + // When node clicked in tree, run tool and add tracks to model. + var self = this, + param_tree = this.model.get('parameter_tree'), + regions = this.model.get('regions'), + node = d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node"); node.on("click", function(d, i) { - console.log(d, i); + // TODO: Show popup menu. - // Gather: (a) dataset of interest; (b) region(s) of interest and (c) sets of parameters based on node clicked. - - // Run job by submitting parameters + dataset as job inputs; get dataset ids as result. - - // Create tracks for all resulting dataset ids. - - // Display tiles for region(s) of interest. + // Get all settings corresponding to node. + var tool = self.model.get('tool'), + dataset = self.model.get('dataset'), + all_settings = param_tree.get_node_settings(d); + + // Create and add tracks for each settings group. + var tracks = _.map(all_settings, function(settings) { + var pm_track = new ParamaMonsterTrack({ + settings: settings, + regions: regions + }); + self.model.add_track(pm_track); + var track_view = new ParamaMonsterTrackView({ + model: pm_track, + canvas_manager: self.canvas_manager + }); + track_view.on('run_on_dataset', self.run_tool_on_dataset, self); + self.track_collection_container.append(track_view.$el); + track_view.$el.hover(function() { + var settings_leaf = param_tree.get_leaf(settings); + var connected_node_ids = _.pluck(param_tree.get_connected_nodes(settings_leaf), 'id'); + + // TODO: can do faster with enter? + d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node") + .filter(function(d) { + return _.find(connected_node_ids, function(id) { return id === d.id; }) !== undefined; + }).style('fill', '#f00'); + }, + function() { + d3.select(self.tool_param_tree_view.$el[0]).selectAll("g.node").style('fill', '#000'); + }); + return pm_track; + }); + + // For each track, run tool using track's settings and update track. + _.each(tracks, function(pm_track, index) { + setTimeout(function() { + // Set inputs and run tool. + //console.log('running with settings', pm_track.get('settings')); + tool.set_input_values(pm_track.get('settings')); + $.when(tool.rerun(dataset, regions)).then(function(output) { + // Create and add track for output dataset. + var track_config = _.extend({ + data_url: galaxy_paths.get('raw_data_url'), + converted_datasets_state_url: galaxy_paths.get('dataset_state_url') + }, output.first().get('track_config')), + track_obj = object_from_template(track_config, self, null); + pm_track.set('track', track_obj); + }); + }, index * 10000); + }); }); - - }, + } }); \ No newline at end of file diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -179,7 +179,6 @@ } } ]); - menu.render(); menu.$el.attr("style", "float: right"); $("#center .unified-panel-header-inner").append(menu.$el); diff -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 -r 27f54f28e9f1542e9681b8a4c238d856be7b9a34 templates/visualization/paramamonster.mako --- a/templates/visualization/paramamonster.mako +++ b/templates/visualization/paramamonster.mako @@ -2,8 +2,8 @@ <%def name="init()"><% - self.has_left_panel=False - self.has_right_panel=False + self.has_left_panel=True + self.has_right_panel=True self.active_view="visualization" self.message_box_visible=False %> @@ -12,7 +12,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} <style> - .unified-panel-body { + div#center { overflow: auto; } .link { @@ -27,6 +27,56 @@ fill: #fff; stroke: steelblue; stroke-width: 1.5px; + cursor: pointer; + } + .node:hover { + fill: #f00; + } + .node:hover circle { + fill: #ccc; + stroke: #f00; + } + table.tracks { + border-collapse: separate; + border-spacing: 5px; + } + .tile { + border: solid 1px #DDD; + margin: 2px; + border-radius: 10px; + margin: 3px; + } + .label { + position: fixed; + font: 10px sans-serif; + font-weight: bold; + background-color: #DDD; + border-radius: 5px; + padding: 1px; + } + th,td { + text-align: center; + } + td.settings { + vertical-align: top; + } + .icon-button.track-settings { + float: none; + } + .track-info { + text-align: left; + font: 10px sans-serif; + position: fixed; + background-color: #CCC; + border: solid 1px #AAA; + border-radius: 2px; + padding: 2px; + } + .btn-primary, .btn-primary:hover { + color: #EEE; + background-color: #DDD; + background-image: none; + border-radius: 12px; } </style></%def> @@ -34,28 +84,16 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.templates( "tool_link", "panel_section", "tool_search" )} - ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/paramamonster" )} + ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )} + ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/paramamonster", "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider" )} <script type="text/javascript"> - var tool; + var viz; $(function() { // -- Viz set up. -- - tool = new Tool(JSON.parse('${ h.to_json_string( tool ) }')); - // HACK: need to replace \ with \\ due to simplejson bug. - var dataset = new Dataset(JSON.parse('${ h.to_json_string( dataset.get_api_value() ).replace('\\', '\\\\' ) }')), - paramamonster_viz = new ParamaMonsterVisualization({ - tool: tool, - dataset: dataset - }); - viz_view = new ParamaMonsterVisualizationView({ model: paramamonster_viz }); - - viz_view.render(); - $('.unified-panel-body').append(viz_view.$el); - - // Tool testing. - var regions = [ + var tool = new Tool(JSON.parse('${ h.to_json_string( tool ) }')), + regions = [ new GenomeRegion({ chrom: 'chr19', start: '10000', @@ -63,25 +101,32 @@ }), new GenomeRegion({ chrom: 'chr19', - start: '30000', - end: '36000' + start: '150000', + end: '175000' }) - ]; + ], + // HACK: need to replace \ with \\ due to simplejson bug. + dataset = new Dataset(JSON.parse('${ h.to_json_string( dataset.get_api_value() ).replace('\\', '\\\\' ) }')); - $.when(tool.rerun(dataset, regions)).then(function(outputs) { - console.log(outputs); + + viz = new ParamaMonsterVisualization({ + tool: tool, + dataset: dataset, + regions: regions }); + var viz_view = new ParamaMonsterVisualizationView({ model: viz }); + + viz_view.render(); + $('.unified-panel-body').append(viz_view.$el); }); </script></%def><%def name="center_panel()"> - <div class="unified-panel-header" unselectable="on"> - <div class="unified-panel-header-inner"> - <div style="float:left;" id="title"></div> - </div> - <div style="clear: both"></div> - </div> - <div class="unified-panel-body"> - </div></%def> + +<%def name="left_panel()"> +</%def> + +<%def name="right_panel()"> +</%def> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Added remote authentication to the toolshed.
by Bitbucket 27 Jun '12

27 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/21ec1290ad02/ changeset: 21ec1290ad02 user: inithello date: 2012-06-27 15:47:32 summary: Added remote authentication to the toolshed. affected #: 3 files diff -r 9576fb8cd71e8ad16e9a6426c0c42dc6aba63716 -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -498,8 +498,10 @@ # remote user authenticates, we'll look for this information, and if missing, create it. if not self.app.security_agent.get_private_user_role( user ): self.app.security_agent.create_private_user_role( user ) - if not user.default_permissions: - self.app.security_agent.user_set_default_permissions( user, history=True, dataset=True ) + if 'webapp' not in self.environ or self.environ['webapp'] != 'community': + if not user.default_permissions: + self.app.security_agent.user_set_default_permissions( user ) + self.app.security_agent.user_set_default_permissions( user, history=True, dataset=True ) elif user is None: username = remote_user_email.split( '@', 1 )[0].lower() random.seed() @@ -520,7 +522,8 @@ self.sa_session.flush() self.app.security_agent.create_private_user_role( user ) # We set default user permissions, before we log in and set the default history permissions - self.app.security_agent.user_set_default_permissions( user ) + if 'webapp' not in self.environ or self.environ['webapp'] != 'community': + self.app.security_agent.user_set_default_permissions( user ) #self.log_event( "Automatically created account '%s'", user.email ) return user def __update_session_cookie( self, name='galaxysession' ): diff -r 9576fb8cd71e8ad16e9a6426c0c42dc6aba63716 -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 lib/galaxy/webapps/community/buildapp.py --- a/lib/galaxy/webapps/community/buildapp.py +++ b/lib/galaxy/webapps/community/buildapp.py @@ -17,6 +17,7 @@ import galaxy.webapps.community.model.mapping import galaxy.web.framework from galaxy.webapps.community.framework.middleware import hg +from galaxy import util log = logging.getLogger( __name__ ) @@ -102,6 +103,15 @@ # other middleware): app = httpexceptions.make_middleware( app, conf ) log.debug( "Enabling 'httpexceptions' middleware" ) + # If we're using remote_user authentication, add middleware that + # protects Galaxy from improperly configured authentication in the + # upstream server + if asbool(conf.get( 'use_remote_user', False )): + from galaxy.webapps.community.framework.middleware.remoteuser import RemoteUser + app = RemoteUser( app, maildomain = conf.get( 'remote_user_maildomain', None ), + display_servers = util.listify( conf.get( 'display_servers', '' ) ), + admin_users = conf.get( 'admin_users', '' ).split( ',' ) ) + log.debug( "Enabling 'remote user' middleware" ) # The recursive middleware allows for including requests in other # requests or forwarding of requests, all on the server side. if asbool(conf.get('use_recursive', True)): diff -r 9576fb8cd71e8ad16e9a6426c0c42dc6aba63716 -r 21ec1290ad02beb9c33516dcc4d5d4a732559414 lib/galaxy/webapps/community/framework/middleware/remoteuser.py --- /dev/null +++ b/lib/galaxy/webapps/community/framework/middleware/remoteuser.py @@ -0,0 +1,93 @@ +""" +Middleware for handling $REMOTE_USER if use_remote_user is enabled. +""" + +import socket + +errorpage = """ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<html lang="en"> + <head> + <title>Galaxy</title> + <style type="text/css"> + body { + min-width: 500px; + text-align: center; + } + .errormessage { + font: 75%% verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif; + padding: 10px; + margin: 100px auto; + min-height: 32px; + max-width: 500px; + border: 1px solid #AA6666; + background-color: #FFCCCC; + text-align: left; + } + </style> + </head> + <body> + <div class="errormessage"> + <h4>%s</h4> + <p>%s</p> + </div> + </body> +</html> +""" + +class RemoteUser( object ): + def __init__( self, app, maildomain=None, display_servers=None, admin_users=None ): + self.app = app + self.maildomain = maildomain + self.display_servers = display_servers or [] + self.admin_users = admin_users or [] + def __call__( self, environ, start_response ): + environ[ 'webapp' ] = 'community' + # Allow display servers + if self.display_servers and environ.has_key( 'REMOTE_ADDR' ): + try: + host = socket.gethostbyaddr( environ[ 'REMOTE_ADDR' ] )[0] + except( socket.error, socket.herror, socket.gaierror, socket.timeout ): + # in the event of a lookup failure, deny access + host = None + if host in self.display_servers: + environ[ 'HTTP_REMOTE_USER' ] = 'remote_display_server@%s' % ( self.maildomain or 'example.org' ) + return self.app( environ, start_response ) + # Apache sets REMOTE_USER to the string '(null)' when using the + # Rewrite* method for passing REMOTE_USER and a user is + # un-authenticated. Any other possible values need to go here as well. + path_info = environ.get('PATH_INFO', '') + if environ.has_key( 'HTTP_REMOTE_USER' ) and environ[ 'HTTP_REMOTE_USER' ] != '(null)': + if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ): + if self.maildomain is not None: + environ[ 'HTTP_REMOTE_USER' ] += '@' + self.maildomain + else: + title = "Access to Galaxy is denied" + message = """ + Galaxy is configured to authenticate users via an external + method (such as HTTP authentication in Apache), but only a + username (not an email address) was provided by the + upstream (proxy) server. Since Galaxy usernames are email + addresses, a default mail domain must be set.</p> + <p>Please contact your local Galaxy administrator. The + variable <code>remote_user_maildomain</code> must be set + before you may access Galaxy. + """ + return self.error( start_response, title, message ) + return self.app( environ, start_response ) + elif path_info.startswith( '/api/' ): + # The API handles its own authentication via keys + return self.app( environ, start_response ) + else: + title = "Access to Galaxy is denied" + message = """ + Galaxy is configured to authenticate users via an external + method (such as HTTP authentication in Apache), but a username + was not provided by the upstream (proxy) server. This is + generally due to a misconfiguration in the upstream server.</p> + <p>Please contact your local Galaxy administrator. + """ + return self.error( start_response, title, message ) + def error( self, start_response, title="Access denied", message="Please contact your local Galaxy administrator." ): + start_response( '403 Forbidden', [('Content-type', 'text/html')] ) + return [errorpage % (title, message)] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: scot...@gatech.edu: Generalized exit code and regex handling. TaskWrapper now uses the newly-generalized handling, too.
by Bitbucket 26 Jun '12

26 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9576fb8cd71e/ changeset: 9576fb8cd71e user: scot...(a)gatech.edu date: 2012-06-26 23:31:30 summary: Generalized exit code and regex handling. TaskWrapper now uses the newly-generalized handling, too. affected #: 2 files diff -r fb67f73df9a24cb9eba278e7c62ba996fa11a6be -r 9576fb8cd71e8ad16e9a6426c0c42dc6aba63716 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -306,78 +306,12 @@ #ERROR at this point means the job was deleted by an administrator. return self.fail( job.info ) - err_msg = "" - # Check exit codes and match regular expressions against stdout and - # stderr if this tool was configured to do so. - if ( len( self.tool.stdio_regexes ) > 0 or - len( self.tool.stdio_exit_codes ) > 0 ): - # We will check the exit code ranges in the order in which - # they were specified. Each exit_code is a ToolStdioExitCode - # that includes an applicable range. If the exit code was in - # that range, then apply the error level and add in a message. - # If we've reached a fatal error rule, then stop. - max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR - for stdio_exit_code in self.tool.stdio_exit_codes: - if ( tool_exit_code >= stdio_exit_code.range_start and - tool_exit_code <= stdio_exit_code.range_end ): - if None != stdio_exit_code.desc: - err_msg += stdio_exit_code.desc - # TODO: Find somewhere to stick the err_msg - possibly to - # the source (stderr/stdout), possibly in a new db column. - max_error_level = max( max_error_level, - stdio_exit_code.error_level ) - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - break - # If there is a regular expression for scanning stdout/stderr, - # then we assume that the tool writer overwrote the default - # behavior of just setting an error if there is *anything* on - # stderr. - if max_error_level < galaxy.tools.StdioErrorLevel.FATAL: - # We'll examine every regex. Each regex specifies whether - # it is to be run on stdout, stderr, or both. (It is - # possible for neither stdout nor stderr to be scanned, - # but those won't be scanned.) We record the highest - # error level, which are currently "warning" and "fatal". - # If fatal, then we set the job's state to ERROR. - # If warning, then we still set the job's state to OK - # but include a message. We'll do this if we haven't seen - # a fatal error yet - for regex in self.tool.stdio_regexes: - # If ( this regex should be matched against stdout ) - # - Run the regex's match pattern against stdout - # - If it matched, then determine the error level. - # o If it was fatal, then we're done - break. - # Repeat the stdout stuff for stderr. - # TODO: Collapse this into a single function. - if ( regex.stdout_match ): - regex_match = re.search( regex.match, stdout ) - if ( regex_match ): - err_msg += self.regex_err_msg( regex_match, regex ) - max_error_level = max( max_error_level, regex.error_level ) - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - break - if ( regex.stderr_match ): - regex_match = re.search( regex.match, stderr ) - if ( regex_match ): - err_msg += self.regex_err_msg( regex_match, regex ) - max_error_level = max( max_error_level, - regex.error_level ) - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - break - # If we encountered a fatal error, then we'll need to set the - # job state accordingly. Otherwise the job is ok: - if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: - job.state = job.states.ERROR - else: - job.state = job.states.OK - # When there are no regular expressions and no exit codes to check, - # default to the previous behavior: when there's anything on stderr - # the job has an error, and the job is ok otherwise. + # Check the + if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): + job.state = job.states.OK else: - if stderr: - job.state = job.states.ERROR - else: - job.state = job.states.OK + job.state = job.states.ERROR + if self.version_string_cmd: version_filename = self.get_version_string_path() if os.path.exists(version_filename): @@ -566,6 +500,107 @@ if self.app.config.cleanup_job == 'always' or ( not stderr and self.app.config.cleanup_job == 'onsuccess' ): self.cleanup() + def check_tool_output( self, stdout, stderr, tool_exit_code ): + """ + Check the output of a tool - given the stdout, stderr, and the tool's + exit code, return True if the tool exited succesfully and False + otherwise. No exceptions should be thrown. If this code encounters + an exception, it returns True so that the workflow can continue; + otherwise, a bug in this code could halt workflow progress. + Note that, if the tool did not define any exit code handling or + any stdio/stderr handling, then it reverts back to previous behavior: + if stderr contains anything, then False is returned. + """ + job = self.get_job() + err_msg = "" + # By default, the tool succeeded. This covers the case where the code + # has a bug but the tool was ok, and it lets a workflow continue. + success = True + + try: + # Check exit codes and match regular expressions against stdout and + # stderr if this tool was configured to do so. + if ( len( self.tool.stdio_regexes ) > 0 or + len( self.tool.stdio_exit_codes ) > 0 ): + # We will check the exit code ranges in the order in which + # they were specified. Each exit_code is a ToolStdioExitCode + # that includes an applicable range. If the exit code was in + # that range, then apply the error level and add in a message. + # If we've reached a fatal error rule, then stop. + max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR + for stdio_exit_code in self.tool.stdio_exit_codes: + if ( tool_exit_code >= stdio_exit_code.range_start and + tool_exit_code <= stdio_exit_code.range_end ): + if None != stdio_exit_code.desc: + err_msg += stdio_exit_code.desc + # TODO: Find somewhere to stick the err_msg - possibly to + # the source (stderr/stdout), possibly in a new db column. + max_error_level = max( max_error_level, + stdio_exit_code.error_level ) + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + break + + # If there is a regular expression for scanning stdout/stderr, + # then we assume that the tool writer overwrote the default + # behavior of just setting an error if there is *anything* on + # stderr. + if max_error_level < galaxy.tools.StdioErrorLevel.FATAL: + # We'll examine every regex. Each regex specifies whether + # it is to be run on stdout, stderr, or both. (It is + # possible for neither stdout nor stderr to be scanned, + # but those won't be scanned.) We record the highest + # error level, which are currently "warning" and "fatal". + # If fatal, then we set the job's state to ERROR. + # If warning, then we still set the job's state to OK + # but include a message. We'll do this if we haven't seen + # a fatal error yet + for regex in self.tool.stdio_regexes: + # If ( this regex should be matched against stdout ) + # - Run the regex's match pattern against stdout + # - If it matched, then determine the error level. + # o If it was fatal, then we're done - break. + # Repeat the stdout stuff for stderr. + # TODO: Collapse this into a single function. + if ( regex.stdout_match ): + regex_match = re.search( regex.match, stdout ) + if ( regex_match ): + err_msg += self.regex_err_msg( regex_match, regex ) + max_error_level = max( max_error_level, regex.error_level ) + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + break + if ( regex.stderr_match ): + regex_match = re.search( regex.match, stderr ) + if ( regex_match ): + err_msg += self.regex_err_msg( regex_match, regex ) + max_error_level = max( max_error_level, + regex.error_level ) + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + break + + # If we encountered a fatal error, then we'll need to set the + # job state accordingly. Otherwise the job is ok: + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + success = False + else: + success = True + + # When there are no regular expressions and no exit codes to check, + # default to the previous behavior: when there's anything on stderr + # the job has an error, and the job is ok otherwise. + else: + log.debug( "The tool did not define exit code or stdio handling; " + + "checking stderr for success" ) + if stderr: + success = False + else: + success = True + # On any exception, return True. + except: + log.warning( "Tool check encountered unexpected exception; " + + "assuming tool was successful" ) + success = True + return success + def regex_err_msg( self, match, regex ): """ Return a message about the match on tool output using the given @@ -970,7 +1005,7 @@ self.sa_session.add( task ) self.sa_session.flush() - def finish( self, stdout, stderr ): + def finish( self, stdout, stderr, tool_exit_code=0 ): # DBTODO integrate previous finish logic. # Simple finish for tasks. Just set the flag OK. log.debug( 'task %s for job %d ended' % (self.task_id, self.job_id) ) @@ -991,10 +1026,10 @@ # Job was deleted by an administrator self.fail( task.info ) return - if stderr: + if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): + task.state = task.states.OK + else: task.state = task.states.ERROR - else: - task.state = task.states.OK # Save stdout and stderr if len( stdout ) > 32768: log.error( "stdout for task %d is greater than 32K, only first part will be logged to database" % task.id ) diff -r fb67f73df9a24cb9eba278e7c62ba996fa11a6be -r 9576fb8cd71e8ad16e9a6426c0c42dc6aba63716 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -560,7 +560,7 @@ def fail_job( self, pbs_job_state ): """ - Seperated out so we can use the worker threads for it. + Separated out so we can use the worker threads for it. """ if pbs_job_state.stop_job: self.stop_job( self.sa_session.query( self.app.model.Job ).get( pbs_job_state.job_wrapper.job_id ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Also added missing publicbuilds.txt
by Bitbucket 26 Jun '12

26 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fb67f73df9a2/ changeset: fb67f73df9a2 user: inithello date: 2012-06-26 21:18:19 summary: Also added missing publicbuilds.txt affected #: 2 files diff -r e112508794a8585e96bc1ba15c2be1cce421393d -r fb67f73df9a24cb9eba278e7c62ba996fa11a6be .hgignore --- a/.hgignore +++ b/.hgignore @@ -51,6 +51,7 @@ tool-data/shared/rviewer/rviewer_build_sites.txt tool-data/shared/ucsc/builds.txt tool-data/shared/ensembl/builds.txt +tool-data/shared/ucsc/publicbuilds.txt tool-data/*.loc tool-data/genome/* diff -r e112508794a8585e96bc1ba15c2be1cce421393d -r fb67f73df9a24cb9eba278e7c62ba996fa11a6be tool-data/shared/ucsc/publicbuilds.txt --- /dev/null +++ b/tool-data/shared/ucsc/publicbuilds.txt @@ -0,0 +1,96 @@ +#Harvested from http://genome.cse.ucsc.edu/cgi-bin/das/dsn +? unspecified (?) +hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) +hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) +hg17 Human May 2004 (NCBI35/hg17) (hg17) +panTro3 Chimp Oct. 2010 (CGSC 2.1.3/panTro3) (panTro3) +panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) +gorGor3 Gorilla May 2011 (gorGor3.1/gorGor3) (gorGor3) +ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) +nomLeu1 Gibbon Jan. 2010 (GGSC Nleu1.0/nomLeu1) (nomLeu1) +rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) +calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) +calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) +mm10 Mouse Dec. 2011 (GRCm38/mm10) (mm10) +mm9 Mouse July 2007 (NCBI37/mm9) (mm9) +mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) +rn5 Rat Mar. 2012 (RGSC 5.0/rn5) (rn5) +rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) +hetGla1 Naked mole-rat Jul. 2011 (BGI HetGla_1.0/hetGla1) (hetGla1) +cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) +oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) +susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) +oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) +bosTau7 Cow Oct. 2011 (Baylor Btau_4.6.1/bosTau7) (bosTau7) +bosTau6 Cow Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) (bosTau6) +bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) +equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) +equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) +felCat4 Cat Dec. 2008 (NHGRI/GTB V17e/felCat4) (felCat4) +felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) +canFam3 Dog Sep. 2011 (Broad CanFam3.1/canFam3) (canFam3) +canFam2 Dog May 2005 (Broad/canFam2) (canFam2) +ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) +myoLuc2 Microbat Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) (myoLuc2) +loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) +monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) +monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) +macEug2 Wallaby Sep. 2009 (TWGS Meug_1.1/macEug2) (macEug2) +ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) +galGal4 Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) (galGal4) +galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) +melGal1 Turkey Dec. 2009 (TGC Turkey_2.01/melGal1) (melGal1) +taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) +anoCar2 Lizard May 2010 (Broad AnoCar2.0/anoCar2) (anoCar2) +anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) +chrPic1 Painted turtle Dec. 2011 (v3.0.1/chrPic1) (chrPic1) +xenTro3 X. tropicalis Nov. 2009 (JGI 4.2/xenTro3) (xenTro3) +xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) +danRer7 Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7) +danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) +tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) +tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) +fr3 Fugu Oct. 2011 (FUGU5/fr3) (fr3) +fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) +gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) +oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) +petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) +aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) +braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) +ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) +ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) +strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) +strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) +ce10 C. elegans Oct. 2010 (WS220/ce10) (ce10) +ce6 C. elegans May 2008 (WS190/ce6) (ce6) +ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) +caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) +caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) +cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) +cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) +caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) +caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) +caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) +priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) +dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) +dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) +droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) +droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) +droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) +droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) +droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) +droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) +droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) +dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) +dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) +droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) +droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) +droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) +droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) +droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) +droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) +anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) +apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) +apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) +sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) +sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Added missing builds.txt for Ensembl, fixed erroneous first line in output.
by Bitbucket 26 Jun '12

26 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e112508794a8/ changeset: e112508794a8 user: inithello date: 2012-06-26 21:10:25 summary: Added missing builds.txt for Ensembl, fixed erroneous first line in output. affected #: 2 files diff -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 -r e112508794a8585e96bc1ba15c2be1cce421393d cron/get_ensembl.py --- a/cron/get_ensembl.py +++ b/cron/get_ensembl.py @@ -17,6 +17,7 @@ for genome in genomes: builds[genome[0]] = dict( release=genome[3], species='%s (%s/%s)' % ( genome[1], genome[2], genome[0] ) ) for build in builds.items(): - lines.append( '\t'.join( [ build[0], '%d' % build[1]['release'], build[1]['species'] ] ) ) + if build[0]: + lines.append( '\t'.join( [ build[0], '%d' % build[1]['release'], build[1]['species'] ] ) ) -print '\n'.join( lines ) \ No newline at end of file +print '\n'.join( lines ) diff -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 -r e112508794a8585e96bc1ba15c2be1cce421393d tool-data/shared/ensembl/builds.txt --- /dev/null +++ b/tool-data/shared/ensembl/builds.txt @@ -0,0 +1,165 @@ + 67 Microcebus_murinus (Mouse lemur/) +MEDAKA1 67 Oryzias_latipes (Medaka/MEDAKA1) +Myoluc2.0 67 Myotis_lucifugus (Microbat/Myoluc2.0) +anoCar1 67 Anolis_carolinensis (Anole lizard/anoCar1) +WS220 67 Caenorhabditis_elegans (C.elegans/WS220) +WS180 67 Caenorhabditis_elegans (C.elegans/WS180) +MICROBAT1 67 Myotis_lucifugus (Microbat/MICROBAT1) +loxAfr3 67 Loxodonta_africana (Elephant/loxAfr3) +AgamP3 67 Anopheles_gambiae (Mosquito/AgamP3) +DROM3 67 Drosophila_melanogaster (Fly/DROM3) +LatCha1 67 Latimeria_chalumnae (Coelacanth/LatCha1) +vicPac1 67 Vicugna_pacos (Alpaca/vicPac1) +COMMON_SHREW1 67 Sorex_araneus (Shrew/COMMON_SHREW1) +MGSC3 67 Mus_musculus (Mouse/MGSC3) +MGSC1 67 Mus_musculus (Mouse/MGSC1) +JGI4.1 67 Xenopus_tropicalis (Xenopus/JGI4.1) +RGSC1 67 Rattus_norvegicus (Rat/RGSC1) +RGSC2 67 Rattus_norvegicus (Rat/RGSC2) +gadMor1 67 Gadus_morhua (Atlantic cod/gadMor1) +CSAV2.0 67 Ciona_savignyi (C.savignyi/CSAV2.0) +oryCun2 67 Oryctolagus_cuniculus (Rabbit/oryCun2) +ZFISH6 67 Danio_rerio (Zebrafish/ZFISH6) +ZFISH7 67 Danio_rerio (Zebrafish/ZFISH7) +ZFISH4 67 Danio_rerio (Zebrafish/ZFISH4) +ZFISH5 67 Danio_rerio (Zebrafish/ZFISH5) +ZFISH2 67 Danio_rerio (Zebrafish/ZFISH2) +ZFISH3 67 Danio_rerio (Zebrafish/ZFISH3) +MOZ2a 67 Anopheles_gambiae (Mosquito/MOZ2a) +EquCab2 67 Equus_caballus (Horse/EquCab2) +AMEL1.1 67 Apis_mellifera (Honeybee/AMEL1.1) +MMUL_1 67 Macaca_mulatta (Macaque/MMUL_1) +dasNov2 67 Dasypus_novemcinctus (Armadillo/dasNov2) +choHof1 67 Choloepus_hoffmanni (Sloth/choHof1) +lamPac1 50 Lama_pacos (Alpaca/lamPac1) +OANA5 67 Ornithorhynchus_anatinus (Platypus/OANA5) +CEL160 67 Caenorhabditis_elegans (C.elegans/CEL160) +WBcel215 67 Caenorhabditis_elegans (C.elegans/WBcel215) +gorGor3 67 Gorilla_gorilla (Gorilla/gorGor3) +SQUIRREL 67 Spermophilus_tridecemlineatus (Ground Squirrel/SQUIRREL) +gorGor1 67 Gorilla_gorilla (Gorilla/gorGor1) +pteVam1 67 Pteropus_vampyrus (Flying fox/pteVam1) +SGD1 67 Saccharomyces_cerevisiae (S.cerevisiae/SGD1) +micMur1 67 Microcebus_murinus (Mouse lemur/micMur1) +proCap1 67 Procavia_capensis (Rock hyrax/proCap1) +NCBIM30 67 Mus_musculus (Mouse/NCBIM30) +NCBIM33 67 Mus_musculus (Mouse/NCBIM33) +NCBIM32 67 Mus_musculus (Mouse/NCBIM32) +NCBIM35 67 Mus_musculus (Mouse/NCBIM35) +AaegL1 67 Aedes_aegypti (A.aegypti/AaegL1) +NCBIM37 67 Mus_musculus (Mouse/NCBIM37) +NCBIM36 67 Mus_musculus (Mouse/NCBIM36) +EF2 67 Saccharomyces_cerevisiae (S.cerevisiae/EF2) +EF3 67 Saccharomyces_cerevisiae (S.cerevisiae/EF3) +EF4 67 Saccharomyces_cerevisiae (S.cerevisiae/EF4) +BDGP5.4 67 Drosophila_melanogaster (Fly/BDGP5.4) +PPYG2 67 Pongo_abelii (Orangutan/PPYG2) +CEL150 67 Caenorhabditis_elegans (C.elegans/CEL150) +AMEL2.0 67 Apis_mellifera (Honeybee/AMEL2.0) +WASHUC1 67 Gallus_gallus (Chicken/WASHUC1) +WASHUC2 67 Gallus_gallus (Chicken/WASHUC2) +Btau_3.1 67 Bos_taurus (Cow/Btau_3.1) +gorGor3.1 67 Gorilla_gorilla (Gorilla/gorGor3.1) +CEL130 67 Caenorhabditis_elegans (C.elegans/CEL130) +Zv9 67 Danio_rerio (Zebrafish/Zv9) +BROADS1 67 Gasterosteus_aculeatus (Stickleback/BROADS1) +BROADD2 67 Canis_familiaris (Dog/BROADD2) +BROADD1 67 Canis_familiaris (Dog/BROADD1) +pika 67 Ochotona_princeps (Pika/pika) +ZFISH08 67 Danio_rerio (Zebrafish/ZFISH08) +ZFISH06 67 Danio_rerio (Zebrafish/ZFISH06) +calJac3 67 Callithrix_jacchus (Marmoset/calJac3) +CHIMP2.1.4 67 Pan_troglodytes (Chimp/CHIMP2.1.4) +JGI2 67 Ciona_intestinalis (C.intestinalis/JGI2) +JGI3 67 Xenopus_tropicalis (Xenopus/JGI3) +UCSC 67 Homo_sapiens (Human/UCSC) +Zv8 67 Danio_rerio (Zebrafish/Zv8) +JGI4 67 Xenopus_tropicalis (Xenopus/JGI4) +CEL140 67 Caenorhabditis_elegans (C.elegans/CEL140) +HEDGEHOG 67 Erinaceus_europaeus (Hedgehog/HEDGEHOG) +callJacc3 67 Callithrix_jacchus (Marmoset/callJacc3) +WS210 67 Caenorhabditis_elegans (C.elegans/WS210) +BDGP4 67 Drosophila_melanogaster (Fly/BDGP4) +BDGP5 67 Drosophila_melanogaster (Fly/BDGP5) +CHIMP1 67 Pan_troglodytes (Chimp/CHIMP1) +OtoGar3 67 Otolemur_garnettii (Bushbaby/OtoGar3) +MOZ2 67 Anopheles_gambiae (Mosquito/MOZ2) +FUGU4 67 Takifugu_rubripes (Fugu/FUGU4) +MOZ1 67 Anopheles_gambiae (Mosquito/MOZ1) +GUINEAPIG 67 Cavia_porcellus (Guinea Pig/GUINEAPIG) +BROADE1 67 Loxodonta_africana (Elephant/BROADE1) +RABBIT 67 Oryctolagus_cuniculus (Rabbit/RABBIT) +TETRAODON7 67 Tetraodon_nigroviridis (Tetraodon/TETRAODON7) +TETRAODON8 67 Tetraodon_nigroviridis (Tetraodon/TETRAODON8) +gorGor2 67 Gorilla_gorilla (Gorilla/gorGor2) +SGD1.01 67 Saccharomyces_cerevisiae (S.cerevisiae/SGD1.01) +ailMel1 67 Ailuropoda_melanoleuca (Panda/ailMel1) +Sscrofa9 67 Sus_scrofa (Pig/Sscrofa9) +cavPor3 67 Cavia_porcellus (Guinea Pig/cavPor3) +Orenil1.0 67 Oreochromis_niloticus (Nile tilapia/Orenil1.0) +BDGP4.2 67 Drosophila_melanogaster (Fly/BDGP4.2) +BDGP4.3 67 Drosophila_melanogaster (Fly/BDGP4.3) +Petromyzon_marin 64 Petromyzon_marinus (Lamprey/Petromyzon_marin) +RGSC3.4 67 Rattus_norvegicus (Rat/RGSC3.4) +Pmarinus_7.0 67 Petromyzon_marinus (Lamprey/Pmarinus_7.0) +RGSC3.1 67 Rattus_norvegicus (Rat/RGSC3.1) +BDGP5.25 67 Drosophila_melanogaster (Fly/BDGP5.25) +ARMA 67 Dasypus_novemcinctus (Armadillo/ARMA) +CINT1.95 67 Ciona_intestinalis (C.intestinalis/CINT1.95) +Btau_1.0 67 Bos_taurus (Cow/Btau_1.0) +JGI_4.2 67 Xenopus_tropicalis (Xenopus/JGI_4.2) +CEL116 67 Caenorhabditis_elegans (C.elegans/CEL116) +BUSHBABY1 67 Otolemur_garnettii (Bushbaby/BUSHBABY1) +Sscrofa10.2 67 Sus_scrofa (Pig/Sscrofa10.2) +BDGP3.2.1 67 Drosophila_melanogaster (Fly/BDGP3.2.1) +taeGut3.2.4 67 Taeniopygia_guttata (Zebra finch/taeGut3.2.4) +KH 67 Ciona_intestinalis (C.intestinalis/KH) +JGI4_1 67 Xenopus_tropicalis (Xenopus/JGI4_1) +spetri2 67 Spermophilus_tridecemlineatus (Ground Squirrel/spetri2) +Btau_4.0 67 Bos_taurus (Cow/Btau_4.0) +UMD2 67 Meleagris_gallopavo (Turkey/UMD2) +NCBI28 67 Homo_sapiens (Human/NCBI28) +NCBI29 67 Homo_sapiens (Human/NCBI29) +Btau_2.0 67 Bos_taurus (Cow/Btau_2.0) +NCBI26 67 Homo_sapiens (Human/NCBI26) +CAT 67 Felis_catus (Cat/CAT) +TENREC 67 Echinops_telfairi (Tenrec/TENREC) +WS200 67 Caenorhabditis_elegans (C.elegans/WS200) +AnoCar1.0 67 Anolis_carolinensis (Anole lizard/AnoCar1.0) +Nleu1.0 67 Nomascus_leucogenys (Gibbon/Nleu1.0) +Meug_1.0 67 Macropus_eugenii (Wallaby/Meug_1.0) +C_jacchus3.2.1 67 Callithrix_jacchus (Marmoset/C_jacchus3.2.1) +CHIMP2.1 67 Pan_troglodytes (Chimp/CHIMP2.1) +WS190 67 Caenorhabditis_elegans (C.elegans/WS190) +dipOrd1 67 Dipodomys_ordii (Kangaroo rat/dipOrd1) +AnoCar2.0 67 Anolis_carolinensis (Anole lizard/AnoCar2.0) +ACME0.1 67 None (None/ACME0.1) +CEL95 67 Caenorhabditis_elegans (C.elegans/CEL95) +CEL93 67 Caenorhabditis_elegans (C.elegans/CEL93) +DEVIL7.0 67 Sarcophilus_harrisii (Tasmanian Devil/DEVIL7.0) +CEL98 67 Caenorhabditis_elegans (C.elegans/CEL98) +CEL102 67 Caenorhabditis_elegans (C.elegans/CEL102) +TREESHREW 67 Tupaia_belangeri (Tree Shrew/TREESHREW) +NCBI31 67 Homo_sapiens (Human/NCBI31) +NCBI30 67 Homo_sapiens (Human/NCBI30) +NCBI33 67 Homo_sapiens (Human/NCBI33) +NCBI35 67 Homo_sapiens (Human/NCBI35) +NCBI34 67 Homo_sapiens (Human/NCBI34) +turTru1 67 Tursiops_truncatus (Bottlenose dolphin/turTru1) +NCBI36 67 Homo_sapiens (Human/NCBI36) +UMD3.1 67 Bos_taurus (Cow/UMD3.1) +speTri1 67 Spermophilus_tridecemlineatus (Ground Squirrel/speTri1) +GRCh37 67 Homo_sapiens (Human/GRCh37) +CHIMP1A 67 Pan_troglodytes (Chimp/CHIMP1A) +WB170 67 Caenorhabditis_elegans (C.elegans/WB170) +FUGU1 67 Takifugu_rubripes (Fugu/FUGU1) +FUGU2 67 Takifugu_rubripes (Fugu/FUGU2) +NCBIM34 67 Mus_musculus (Mouse/NCBIM34) +DROM3A 67 Drosophila_melanogaster (Fly/DROM3A) +tarSyr1 67 Tarsius_syrichta (Tarsier/tarSyr1) +CBR25 67 Caenorhabditis_briggsae (C.briggsae/CBR25) +BROADO5 67 Monodelphis_domestica (Opossum/BROADO5) +BROADO2 67 Monodelphis_domestica (Opossum/BROADO2) +BROADO3 67 Monodelphis_domestica (Opossum/BROADO3) +BDGP5.13 67 Drosophila_melanogaster (Fly/BDGP5.13) +MMUL_0_1 67 Macaca_mulatta (Macaque/MMUL_0_1) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Add share_string option to cloud_launch.
by Bitbucket 26 Jun '12

26 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/40ff9b0e1549/ changeset: 40ff9b0e1549 user: dannon date: 2012-06-26 17:07:09 summary: Add share_string option to cloud_launch. affected #: 2 files diff -r 2e0254547b09bfccbd0834524a0fb4919b6a6efd -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 lib/galaxy/web/controllers/cloudlaunch.py --- a/lib/galaxy/web/controllers/cloudlaunch.py +++ b/lib/galaxy/web/controllers/cloudlaunch.py @@ -25,11 +25,11 @@ BaseUIController.__init__(self, app) @web.expose - def index(self, trans): - return trans.fill_template("cloud/index.mako") + def index(self, trans, share_string=None): + return trans.fill_template("cloud/index.mako", share_string=share_string) @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type): + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string): ec2_error = None try: # Create security group & key pair used when starting an instance @@ -47,6 +47,8 @@ 'instance_type':instance_type} if password: user_provided_data['password'] = password + if share_string: + user_provided_data['share_string'] = share_string rs = run_instance(ec2_conn=ec2_conn, user_provided_data=user_provided_data, key_name=kp_name, diff -r 2e0254547b09bfccbd0834524a0fb4919b6a6efd -r 40ff9b0e1549c1b083a3822b25b8337808ad8995 templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -59,7 +59,7 @@ <form action="${h.url_for( controller='cloudlaunch', action='launch_instance' )}" method="post"><div class="form-row"><label for="id_cluster_name">Cluster Name</label> - <input type="text" size="80" name="cluster_name" id="id_cluster_name"/><br/> + <input type="text" size="40" name="cluster_name" id="id_cluster_name"/><br/></div><div class="form-row"><label for="id_password">Password</label> @@ -73,6 +73,14 @@ <label for="id_secret">Secret Key</label><input type="password" size="120" name="secret" id="id_secret"/><br/></div> + %if share_string: + <input type='hidden' name='share_string' value='${share_string}'/> + %else: + <div class="form-row"> + <label for="id_share_string">Instance Share String (optional)</label> + <input type="text" size="120" name="share_string" id="id_share_string"/><br/> + </div> + %endif <div class="form-row"><label for="id_instance_type">Instance Type</label><select name="instance_type" id="id_instance_type"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: smcmanus: Recommit of PBS and DRMAA fixes
by Bitbucket 25 Jun '12

25 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2e0254547b09/ changeset: 2e0254547b09 user: smcmanus date: 2012-06-25 23:16:49 summary: Recommit of PBS and DRMAA fixes affected #: 3 files diff -r 319b2b0e832c8ea5ef520c76722f7ad6270507c3 -r 2e0254547b09bfccbd0834524a0fb4919b6a6efd lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -291,8 +291,6 @@ the output datasets based on stderr and stdout from the command, and the contents of the output files. """ - # TODO: Eliminate debugging code after testing all runners - log.debug( "JobWrapper.finish: exit code:" + str(tool_exit_code) ) # default post job setup self.sa_session.expunge_all() job = self.get_job() diff -r 319b2b0e832c8ea5ef520c76722f7ad6270507c3 -r 2e0254547b09bfccbd0834524a0fb4919b6a6efd lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -39,6 +39,11 @@ drmaa.JobState.FAILED: 'job finished, but failed', } +# The last four lines (following the last fi) will: +# - setup the env +# - move to the job wrapper's working directory +# - execute the command +# - take the command's exit code ($?) and write it to a file. drm_template = """#!/bin/sh GALAXY_LIB="%s" if [ "$GALAXY_LIB" != "None" ]; then @@ -52,6 +57,7 @@ %s cd %s %s +echo $? > %s """ def __lineno__(): """Returns the current line number in our program.""" @@ -77,7 +83,7 @@ self.job_file = None self.ofile = None self.efile = None - self.rcfile = None + self.ecfile = None self.runner_url = None class DRMAAJobRunner( BaseJobRunner ): @@ -169,7 +175,7 @@ # define job attributes ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) - rcfile = "%s.drmrc" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) + ecfile = "%s.drmec" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) job_name = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) @@ -178,7 +184,7 @@ jt.jobName = job_name jt.outputPath = ":%s" % ofile jt.errorPath = ":%s" % efile - jt.returnCodePath = ":%s" % rcfile + # Avoid a jt.exitCodePath for now - it's only used when finishing. native_spec = self.get_native_spec( runner_url ) if native_spec is not None: jt.nativeSpecification = native_spec @@ -187,7 +193,8 @@ script = drm_template % ( job_wrapper.galaxy_lib_dir, job_wrapper.get_env_setup_clause(), os.path.abspath( job_wrapper.working_directory ), - command_line ) + command_line, + ecfile ) try: fh = file( jt.remoteCommand, "w" ) @@ -231,7 +238,7 @@ drm_job_state.job_id = job_id drm_job_state.ofile = ofile drm_job_state.efile = efile - drm_job_state.rcfile = rcfile + drm_job_state.ecfile = ecfile drm_job_state.job_file = jt.remoteCommand drm_job_state.old_state = 'new' drm_job_state.running = False @@ -316,17 +323,22 @@ """ ofile = drm_job_state.ofile efile = drm_job_state.efile - rcfile = drm_job_state.rcfile + ecfile = drm_job_state.ecfile job_file = drm_job_state.job_file # collect the output # wait for the files to appear which_try = 0 + # By default, the exit code is 0, which typically indicates success. + exit_code = 0 while which_try < (self.app.config.retry_job_output_collection + 1): try: ofh = file(ofile, "r") efh = file(efile, "r") + ecfh = file(ecfile, "r") stdout = ofh.read( 32768 ) stderr = efh.read( 32768 ) + # The exit code should only be 8 bits, but read more anyway + exit_code_str = ecfh.read(32) which_try = (self.app.config.retry_job_output_collection + 1) except: if which_try == self.app.config.retry_job_output_collection: @@ -337,8 +349,15 @@ time.sleep(1) which_try += 1 + # Decode the exit code. If it's bogus, then just use 0. try: - drm_job_state.job_wrapper.finish( stdout, stderr ) + exit_code = int(exit_code_str) + except: + log.warning( "Exit code " + exit_code_str + " invalid. Using 0." ) + exit_code = 0 + + try: + drm_job_state.job_wrapper.finish( stdout, stderr, exit_code ) except: log.exception("Job wrapper finish method failed") @@ -382,7 +401,7 @@ drm_job_state = DRMAAJobState() drm_job_state.ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) - drm_job_state.rcfile = "%s.drmrc" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + drm_job_state.ecfile = "%s.drmec" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) drm_job_state.job_file = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job.id) drm_job_state.job_id = str( job.job_runner_external_id ) drm_job_state.runner_url = job_wrapper.get_job_runner() diff -r 319b2b0e832c8ea5ef520c76722f7ad6270507c3 -r 2e0254547b09bfccbd0834524a0fb4919b6a6efd lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -532,16 +532,22 @@ stdout = ofh.read( 32768 ) stderr = efh.read( 32768 ) # This should be an 8-bit exit code, but read ahead anyway: - exit_code = ecfh.read(32) + exit_code_str = ecfh.read(32) except: stdout = '' stderr = 'Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error.' # By default, the exit code is 0, which usually indicates success # (although clearly some error happened). + exit_code_str = "" + + # Translate the exit code string to an integer; use 0 on failure. + try: + exit_code = int( exit_code_str ) + except: + log.warning( "Exit code " + exit_code_str + " was invalid. Using 0." ) exit_code = 0 - log.debug(stderr) - log.debug( "Job exit code: " + exit_code ) + # Call on the job wrapper to complete the call: try: pbs_job_state.job_wrapper.finish( stdout, stderr, exit_code ) except: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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