galaxy-commits August 2014

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commit/galaxy-central: dannon: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456)
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/18e8ddfb9c3c/ Changeset: 18e8ddfb9c3c User: dannon Date: 2014-08-12 17:25:22 Summary: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456) tool_list.py should now use tool_conf.xml not tool_conf.xml.sample Affected #: 1 file diff -r a94473459ebb4749a375420492d6da9a948ccd3a -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -3,7 +3,7 @@ #--------read tool_conf.xml.sample to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml.sample", "r"): +for line in open("tool_conf.xml", "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: 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: 3 new changesets
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82a9821e0fbb/ Changeset: 82a9821e0fbb Branch: tool_list_fix User: peterjc Date: 2014-08-12 17:13:05 Summary: Created new branch tool_list_fix Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/24d8995c3568/ Changeset: 24d8995c3568 Branch: tool_list_fix User: peterjc Date: 2014-08-12 17:15:04 Summary: tool_list.py should now use tool_conf.xml not tool_conf.xml.sample See a94473459ebb4749a375420492d6da9a948ccd3a where the rest of the run_functional_tests.sh system was updated. Affected #: 1 file diff -r 82a9821e0fbb3b4c9387152e48be189cc2829a45 -r 24d8995c35689fc42e96d6f02dc222cbf75531ed tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -3,7 +3,7 @@ #--------read tool_conf.xml.sample to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml.sample", "r"): +for line in open("tool_conf.xml", "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: https://bitbucket.org/galaxy/galaxy-central/commits/18e8ddfb9c3c/ Changeset: 18e8ddfb9c3c User: dannon Date: 2014-08-12 17:25:22 Summary: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456) tool_list.py should now use tool_conf.xml not tool_conf.xml.sample Affected #: 1 file diff -r a94473459ebb4749a375420492d6da9a948ccd3a -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -3,7 +3,7 @@ #--------read tool_conf.xml.sample to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml.sample", "r"): +for line in open("tool_conf.xml", "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: History panel: clean up and documentation
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a94473459ebb/ Changeset: a94473459ebb User: carlfeberhard Date: 2014-08-12 16:45:26 Summary: History panel: clean up and documentation Affected #: 19 files diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-li-edit.js --- a/static/scripts/mvc/collection/collection-li-edit.js +++ b/static/scripts/mvc/collection/collection-li-edit.js @@ -13,7 +13,8 @@ var _super = DC_LI.DCListItemView; /** @class Editing view for DatasetCollectionElement. */ -var DCEListItemEdit = _super.extend({ +var DCEListItemEdit = _super.extend( +/** @lends DCEListItemEdit.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -8,7 +8,8 @@ var ListItemView = BASE_MVC.ListItemView; /** @class Read only view for DatasetCollection. */ -var DCListItemView = ListItemView.extend({ +var DCListItemView = ListItemView.extend( +/** @lends DCListItemView.prototype */{ //TODO: may not be needed /** logger used to record this.log messages, commonly set to console */ @@ -26,7 +27,7 @@ ListItemView.prototype.initialize.call( this, attributes ); }, - /** In this override, don't show`or render any details (no need to do anything here) + /** In this override, don't show or render any details (no need to do anything here) * - currently the parent control will load a panel for this collection over itself * @fires expanded when a body has been expanded */ @@ -87,7 +88,8 @@ //============================================================================== /** @class Read only view for DatasetCollectionElement. */ -var DCEListItemView = ListItemView.extend({ +var DCEListItemView = ListItemView.extend( +/** @lends DCEListItemView.prototype */{ //TODO: this might be expendable - compacted with HDAListItemView /** logger used to record this.log messages, commonly set to console */ @@ -99,7 +101,7 @@ /** jq fx speed for this view */ fxSpeed : 'fast', - /** */ + /** set up */ initialize : function( attributes ){ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } this.log( 'DCEListItemView.initialize:', attributes ); @@ -138,14 +140,15 @@ /** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation * (a dataset contained in a dataset collection). */ -var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend({ +var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend( +/** @lends DatasetDCEListItemView.prototype */{ className : DATASET_LI.DatasetListItemView.prototype.className + " dataset-collection-element", /** logger used to record this.log messages, commonly set to console */ //logger : console, - /** */ + /** set up */ initialize : function( attributes ){ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } this.log( 'DatasetDCEListItemView.initialize:', attributes ); @@ -185,7 +188,8 @@ /** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection * (a nested DC). */ -var NestedDCDCEListItemView = DCListItemView.extend({ +var NestedDCDCEListItemView = DCListItemView.extend( +/** @lends NestedDCDCEListItemView.prototype */{ className : DCListItemView.prototype.className + " dataset-collection-element", diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-model.js --- a/static/scripts/mvc/collection/collection-model.js +++ b/static/scripts/mvc/collection/collection-model.js @@ -47,7 +47,7 @@ * When collection elements are passed from the API, the underlying element is * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object). * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues - * effectively changing a DCE from a container to a subclass. + * effectively changing a DCE from a container to a subclass (has a --> is a). */ var DatasetCollectionElementMixin = { @@ -82,7 +82,7 @@ }; //TODO: unused? -/** Concrete class of Generic DatasetCollectionElement */ +/** @class Concrete class of Generic DatasetCollectionElement */ var DatasetCollectionElement = Backbone.Model .extend( BASE_MVC.LoggableMixin ) .extend( DatasetCollectionElementMixin ); @@ -94,7 +94,6 @@ /** @lends DCECollection.prototype */{ model: DatasetCollectionElement, - // comment this out to suppress log output /** logger used to record this.log messages, commonly set to console */ //logger : console, @@ -124,7 +123,10 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, - defaults : _.extend( {}, DATASET_MODEL.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ), + defaults : _.extend( {}, + DATASET_MODEL.DatasetAssociation.prototype.defaults, + DatasetCollectionElementMixin.defaults + ), // because all objects have constructors (as this hashmap would even if this next line wasn't present) // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model @@ -162,7 +164,7 @@ //logger : console, //TODO: unused? - /** */ + /** set up */ initialize : function( attributes, options ){ this.debug( this + '(DatasetDCECollection).initialize:', attributes, options ); DCECollection.prototype.initialize.call( this, attributes, options ); @@ -203,7 +205,7 @@ /** Which class to use for elements */ collectionClass : DCECollection, - /** */ + /** set up: create elements instance var and (on changes to elements) update them */ initialize : function( model, options ){ this.debug( this + '(DatasetCollection).initialize:', model, options, this ); //historyContent.HistoryContent.prototype.initialize.call( this, attrs, options ); @@ -269,6 +271,7 @@ }, // ........................................................................ searchable + /** searchable attributes for collections */ searchAttributes : [ 'name' ], @@ -291,6 +294,7 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + /** override since we know the collection will only contain datasets */ collectionClass : DatasetDCECollection, //TODO: unused? @@ -368,10 +372,11 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + /** This is a collection of nested collections */ model: NestedDCDCE, //TODO: unused? - /** */ + /** set up */ initialize : function( attrs, options ){ this.debug( this + '(NestedDCDCECollection).initialize:', attrs, options ); DCECollection.prototype.initialize.call( this, attrs, options ); @@ -394,7 +399,10 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, - /** */ + // because all objects have constructors (as this hashmap would even if this next line wasn't present) + // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model + // - re-apply manually it now + /** This is both a collection and a collection element - call the constructor */ constructor : function( attributes, options ){ this.debug( '\t NestedPairDCDCE.constructor:', attributes, options ); //DatasetCollection.constructor.call( this, attributes, options ); @@ -418,10 +426,11 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + /** We know this collection is composed of only nested pair collections */ model: NestedPairDCDCE, //TODO: unused? - /** */ + /** set up */ initialize : function( attrs, options ){ this.debug( this + '(NestedPairDCDCECollection).initialize:', attrs, options ); NestedDCDCECollection.prototype.initialize.call( this, attrs, options ); @@ -443,11 +452,11 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, - // list:paired is the only collection that itself contains collections + /** list:paired is the only collection that itself contains collections */ collectionClass : NestedPairDCDCECollection, //TODO: unused? - /** */ + /** set up */ initialize : function( attributes, options ){ this.debug( this + '(ListPairedDatasetCollection).initialize:', attributes, options ); DatasetCollection.prototype.initialize.call( this, attributes, options ); diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -24,7 +24,9 @@ /** (in ms) that jquery effects will use */ fxSpeed : 'fast', + /** sub view class used for datasets */ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, + /** sub view class used for nested collections */ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, // ......................................................................... SET UP @@ -229,7 +231,7 @@ } }, - /** */ + /** When a sub-collection is clicked, hide the current panel and render the sub-collection in its own panel */ _addCollectionPanel : function( collectionView ){ //TODO: a bit hackish var currPanel = this, @@ -333,9 +335,11 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var ListCollectionPanel = CollectionPanel.extend({ +var ListCollectionPanel = CollectionPanel.extend( +/** @lends ListCollectionPanel.prototype */{ //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass + /** sub view class used for datasets */ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, // ........................................................................ misc @@ -348,7 +352,8 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var PairCollectionPanel = ListCollectionPanel.extend({ +var PairCollectionPanel = ListCollectionPanel.extend( +/** @lends PairCollectionPanel.prototype */{ // ........................................................................ misc /** string rep */ @@ -360,9 +365,11 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var ListOfPairsCollectionPanel = CollectionPanel.extend({ +var ListOfPairsCollectionPanel = CollectionPanel.extend( +/** @lends ListOfPairsCollectionPanel.prototype */{ //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass + /** sub view class used for nested collections */ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, // ........................................................................ misc diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/dataset/dataset-model.js --- a/static/scripts/mvc/dataset/dataset-model.js +++ b/static/scripts/mvc/dataset/dataset-model.js @@ -10,7 +10,7 @@ * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin. */ var DatasetAssociation = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( - BASE_MVC.mixin( searchableMixin, { + BASE_MVC.mixin( searchableMixin, /** @lends DatasetAssociation.prototype */{ /** default attributes for a model */ defaults : { @@ -43,8 +43,10 @@ //annotation : '' }, - initialize : function( attrs, options ){ - this.debug( 'Dataset.initialize', attrs, options ); + /** instance vars and listeners */ + initialize : function( attributes, options ){ + this.debug( this + '(Dataset).initialize', attributes, options ); + //!! this state is not in trans.app.model.Dataset.states - set it here - if( !this.get( 'accessible' ) ){ this.set( 'state', STATES.NOT_VIEWABLE ); @@ -62,7 +64,6 @@ var id = this.get( 'id' ); if( !id ){ return {}; } var urls = { -//TODO: how many of these are still used? 'purge' : 'datasets/' + id + '/purge_async', 'display' : 'datasets/' + id + '/display/?preview=True', 'edit' : 'datasets/' + id + '/edit', @@ -146,6 +147,7 @@ return this.save( { deleted: false }, options ); }, + /** remove the file behind this dataset from the filesystem (if permitted) */ purge : function _purge( options ){ //TODO: use, override model.destroy, HDA.delete({ purge: true }) if( this.get( 'purged' ) ){ return jQuery.when(); } @@ -160,7 +162,7 @@ // }, options )); // //xhr.done( function( response ){ - // console.debug( 'response', response ); + // hda.debug( 'response', response ); // //hda.set({ deleted: true, purged: true }); // hda.set( response ); //}); diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/dataset/states.js --- a/static/scripts/mvc/dataset/states.js +++ b/static/scripts/mvc/dataset/states.js @@ -27,8 +27,9 @@ PAUSED : 'paused', /** metadata discovery/setting failed or errored (but otherwise ok) */ FAILED_METADATA : 'failed_metadata', +//TODO: not in trans.app.model.Dataset.states - is in database /** not accessible to the current user (i.e. due to permissions) */ - NOT_VIEWABLE : 'noPermission', // not in trans.app.model.Dataset.states + NOT_VIEWABLE : 'noPermission', /** deleted while uploading */ DISCARDED : 'discarded', /** the tool producing this dataset failed */ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-li-edit.js --- a/static/scripts/mvc/history/hdca-li-edit.js +++ b/static/scripts/mvc/history/hdca-li-edit.js @@ -7,7 +7,8 @@ var _super = HDCA_LI.HDCAListItemView; /** @class Editing view for HistoryDatasetCollectionAssociation. */ -var HDCAListItemEdit = _super.extend({ +var HDCAListItemEdit = _super.extend( +/** @lends HDCAListItemEdit.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-li.js --- a/static/scripts/mvc/history/hdca-li.js +++ b/static/scripts/mvc/history/hdca-li.js @@ -9,13 +9,12 @@ var _super = DC_LI.DCListItemView; /** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history). */ -var HDCAListItemView = _super.extend({ +var HDCAListItemView = _super.extend( +/** @lends HDCAListItemView.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, -//TODO: not a dataset - /** */ className : _super.prototype.className + " history-content", /** In this override, add the state as a class for use with state-based CSS */ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-model.js --- a/static/scripts/mvc/history/hdca-model.js +++ b/static/scripts/mvc/history/hdca-model.js @@ -19,7 +19,6 @@ //============================================================================== /** @class Backbone model for List Dataset Collection within a History. - * @constructs */ var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( /** @lends HistoryListDatasetCollection.prototype */{ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-content-model.js --- a/static/scripts/mvc/history/history-content-model.js +++ b/static/scripts/mvc/history/history-content-model.js @@ -34,20 +34,24 @@ // Build a new id (type_id) that prefixes the history_content_type so the bbone collection can differentiate idAttribute : 'type_id', + /** override constructor to build type_id and insert into original attributes */ constructor : function( attrs, options ){ attrs.type_id = typeIdStr( attrs.history_content_type, attrs.id ); this.debug( 'HistoryContentMixin.constructor:', attrs.type_id ); Backbone.Model.apply( this, arguments ); }, + /** object level fn for building the type_id string */ _typeIdStr : function(){ return typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) ); }, + /** add listener to re-create type_id when the id changes */ initialize : function( attrs, options ){ this.on( 'change:id', this._createTypeId ); }, + /** set the type_id in the model attributes */ _createTypeId : function(){ this.set( 'type_id', this._typeIdStr() ); }, @@ -90,12 +94,12 @@ return url; }, - /** save this HDA as not visible */ + /** save this content as not visible */ hide : function( options ){ if( !this.get( 'visible' ) ){ return jQuery.when(); } return this.save( { visible: false }, options ); }, - /** save this HDA as visible */ + /** save this content as visible */ unhide : function( options ){ if( this.get( 'visible' ) ){ return jQuery.when(); } return this.save( { visible: true }, options ); @@ -114,6 +118,7 @@ //============================================================================== +//TODO: needed? /** @class (Concrete/non-mixin) base model for content items. */ var HistoryContent = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( HistoryContentMixin ); diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -26,7 +26,6 @@ /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ model : function( attrs, options ) { - //console.debug( 'HistoryContents.model:', attrs, options ); //TODO: can we move the type_id stuff here? //attrs.type_id = typeIdStr( attrs ); @@ -70,24 +69,25 @@ }, // ........................................................................ common queries - /** Get the ids of every hda in this collection + /** Get the ids of every item in this collection * @returns array of encoded ids */ ids : function(){ - return this.map( function( hda ){ return hda.get('id'); }); +//TODO: is this still useful since type_id + return this.map( function( item ){ return item.get('id'); }); }, - /** Get hdas that are not ready - * @returns array of HDAs + /** Get contents that are not ready + * @returns array of content models */ notReady : function(){ - return this.filter( function( hda ){ - return !hda.inReadyState(); + return this.filter( function( content ){ + return !content.inReadyState(); }); }, - /** Get the id of every hda in this collection not in a 'ready' state (running). - * @returns an array of hda ids + /** Get the id of every model in this collection not in a 'ready' state (running). + * @returns an array of model ids * @see HistoryDatasetAssociation#inReadyState */ running : function(){ @@ -95,24 +95,26 @@ this.each( function( item ){ var isRunning = !item.inReadyState(); if( isRunning ){ +//TODO: is this still correct since type_id idList.push( item.get( 'id' ) ); } }); return idList; }, - /** Get the hda with the given hid + /** Get the model with the given hid * @param {Int} hid the hid to search for - * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found + * @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found */ getByHid : function( hid ){ - return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); + return _.first( this.filter( function( content ){ return content.get( 'hid' ) === hid; }) ); }, - /** Get every 'shown' hda in this collection based on show_deleted/hidden - * @param {Boolean} show_deleted are we showing deleted hdas? - * @param {Boolean} show_hidden are we showing hidden hdas? - * @returns array of hda models + //TODO:?? this may belong in the containing view + /** Get every 'shown' model in this collection based on show_deleted/hidden + * @param {Boolean} show_deleted are we showing deleted content? + * @param {Boolean} show_hidden are we showing hidden content? + * @returns array of content models * @see HistoryDatasetAssociation#isVisible */ getVisible : function( show_deleted, show_hidden, filters ){ @@ -131,13 +133,13 @@ return filteredHdas; }, - /** return true if any hdas don't have details */ + /** return true if any contents don't have details */ haveDetails : function(){ - return this.all( function( hda ){ return hda.hasDetails(); }); + return this.all( function( content ){ return content.hasDetails(); }); }, // ........................................................................ ajax - /** fetch detailed model data for all HDAs in this collection */ + /** fetch detailed model data for all contents in this collection */ fetchAllDetails : function( options ){ options = options || {}; var detailsFlag = { details: 'all' }; @@ -145,8 +147,8 @@ return this.fetch( options ); }, - /** using a queue, perform hdaAjaxFn on each of the hdas in this collection */ - ajaxQueue : function( hdaAjaxFn, options ){ + /** using a queue, perform ajaxFn on each of the models in this collection */ + ajaxQueue : function( ajaxFn, options ){ var deferred = jQuery.Deferred(), startingLength = this.length, responses = []; @@ -157,12 +159,12 @@ } // use reverse order (stylistic choice) - var ajaxFns = this.chain().reverse().map( function( hda, i ){ + var ajaxFns = this.chain().reverse().map( function( content, i ){ return function(){ - var xhr = hdaAjaxFn.call( hda, options ); + var xhr = ajaxFn.call( content, options ); // if successful, notify using the deferred to allow tracking progress xhr.done( function( response ){ - deferred.notify({ curr: i, total: startingLength, response: response, model: hda }); + deferred.notify({ curr: i, total: startingLength, response: response, model: content }); }); // (regardless of previous error or success) if not last ajax call, shift and call the next // if last fn, resolve deferred @@ -183,17 +185,18 @@ }, // ........................................................................ sorting/filtering - /** return a new collection of HDAs whose attributes contain the substring matchesWhat */ + /** return a new collection of contents whose attributes contain the substring matchesWhat */ matches : function( matchesWhat ){ - return this.filter( function( hda ){ - return hda.matches( matchesWhat ); + return this.filter( function( content ){ + return content.matches( matchesWhat ); }); }, // ........................................................................ misc + /** override to get a correct/smarter merge when incoming data is partial */ set : function( models, options ){ // arrrrrrrrrrrrrrrrrg... - // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone) + // (e.g. stupid backbone) // w/o this partial models from the server will fill in missing data with model defaults // and overwrite existing data on the client // see Backbone.Collection.set and _prepareModel @@ -213,7 +216,7 @@ Backbone.Collection.prototype.set.call( this, models, options ); }, - /** Convert this ad-hoc collection of HDAs to a formal collection tracked + /** Convert this ad-hoc collection of hdas to a formal collection tracked by the server. **/ promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-annotated.js --- a/static/scripts/mvc/history/history-panel-annotated.js +++ b/static/scripts/mvc/history/history-panel-annotated.js @@ -23,7 +23,7 @@ * @constructs */ var AnnotatedHistoryPanel = _super.extend( -/** @lends HistoryPanel.prototype */{ +/** @lends AnnotatedHistoryPanel.prototype */{ /** logger used to record this.log messages, commonly set to console */ // comment this out to suppress log output diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -7,7 +7,8 @@ // ============================================================================ /** session storage for history panel preferences (and to maintain state) */ -var HistoryPanelPrefs = BASE_MVC.SessionStorageModel.extend({ +var HistoryPanelPrefs = BASE_MVC.SessionStorageModel.extend( +/** @lends HistoryPanelPrefs.prototype */{ defaults : { /** is the panel currently showing the search/filter controls? */ searching : false, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -333,9 +333,9 @@ // maintain a list of hdas that are selected hdaView.on( 'selected', function( hdaView, event ){ if( !event ){ return; } - //console.debug( 'selected', event ); + //this.debug( 'selected', event ); var selectedIds = []; - //console.debug( historyView.lastSelectedViewId, historyView.hdaViews[ historyView.lastSelectedViewId ] ); + //this.debug( historyView.lastSelectedViewId, historyView.hdaViews[ historyView.lastSelectedViewId ] ); // shift will select a range, but not set lastSelectedViewId if( ( event.shiftKey ) @@ -348,19 +348,19 @@ } else { var id = hdaView.model.id; historyView.lastSelectedViewId = id; - //console.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId ); + //this.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId ); selectedIds = [ id ]; } - //console.debug( 'selectedIds:', selectedIds ); + //this.debug( 'selectedIds:', selectedIds ); historyView.selectedHdaIds = _.union( historyView.selectedHdaIds, selectedIds ); //TODO: might want to use getSelectedHdaViews instead managing these lists with ops - //console.debug( 'selected', historyView.selectedHdaIds ); + //this.debug( 'selected', historyView.selectedHdaIds ); }); hdaView.on( 'de-selected', function( hdaView, event ){ - //console.debug( 'de-selected', event ); + //this.debug( 'de-selected', event ); var id = hdaView.model.id; historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id ); - //console.debug( 'de-selected', historyView.selectedHdaIds ); + //this.debug( 'de-selected', historyView.selectedHdaIds ); }); }, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -8,7 +8,9 @@ ], function( HISTORY_MODEL, HDA_LI, HDCA_LI, USER, BASE_MVC, _l ){ // ============================================================================ /** session storage for individual history preferences */ -var HistoryPrefs = BASE_MVC.SessionStorageModel.extend({ +var HistoryPrefs = BASE_MVC.SessionStorageModel.extend( +/** @lends HistoryPrefs.prototype */{ + defaults : { //TODO:?? expandedHdas to array? expandedHdas : {}, @@ -85,6 +87,7 @@ /** class to use for constructing the HDA views */ HDAViewClass : HDA_LI.HDAListItemView, + /** class to use for constructing the HDCA views */ HDCAViewClass : HDCA_LI.HDCAListItemView, tagName : 'div', @@ -753,17 +756,17 @@ this.storage.get( 'show_hidden' ), this.filters ).each( function( hda ){ - //console.debug( 'checking: ', hda.get( 'name' ) ); + //panel.debug( 'checking: ', hda.get( 'name' ) ); if( withinSet ){ - //console.debug( '\t\t adding: ', hda.get( 'name' ) ); + //panel.debug( '\t\t adding: ', hda.get( 'name' ) ); set.push( panel.hdaViews[ hda.id ] ); if( hda === viewA.model || hda === viewB.model ){ - //console.debug( '\t found last: ', hda.get( 'name' ) ); + //panel.debug( '\t found last: ', hda.get( 'name' ) ); withinSet = false; } } else { if( hda === viewA.model || hda === viewB.model ){ - //console.debug( 'found first: ', hda.get( 'name' ) ); + //panel.debug( 'found first: ', hda.get( 'name' ) ); withinSet = true; set.push( panel.hdaViews[ hda.id ] ); } diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/collection/collection-panel.js --- a/static/scripts/packed/mvc/collection/collection-panel.js +++ b/static/scripts/packed/mvc/collection/collection-panel.js @@ -1,1 +1,1 @@ -define(["mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(h,f,a,e){var d=Backbone.View.extend(a.LoggableMixin).extend({tagName:"div",className:"dataset-collection-panel",fxSpeed:"fast",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.hasUser=i.hasUser;this.panelStack=[];this.parentName=i.parentName;window.collectionPanel=this},_setUpListeners:function(){this.on("all",function(i){this.log(this+"",arguments)},this);return this},_setUpModelEventHandlers:function(){return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(!this.model){return this}j=this.renderModel();$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderModel:function(){var k=this.model.get("collection_type")||this.model.object.get("collection_type"),j=_.extend(this.model.toJSON(),{parentName:this.parentName,type:k}),i=$("<div/>").append(this.templates.panel(j));this._setUpBehaviours(i);this.renderContents(i);return i},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},renderContents:function(j){j=j||this.$el;this.warn(this+".renderContents:, model:",this.model);var i=this,l={},k=this.model.getVisibleContents();this.$datasetsList(j).empty();if(k&&k.length){k.each(function(n){var o=n.id,m=i._createContentView(n);l[o]=m;i._attachContentView(m.render(),j)})}this.contentViews=l;return this.contentViews},_createContentView:function(k){var j=null,i=this._getContentClass(k);j=new i({model:k,linkTarget:this.linkTarget,hasUser:this.hasUser,logger:this.logger});this._setUpContentListeners(j);return j},_getContentClass:function(i){switch(i.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",i.get("element_type"))},_setUpContentListeners:function(j){var i=this;if(j.model.get("element_type")==="dataset_collection"){j.on("expanded",function(k){i.info("expanded",k);i._addCollectionPanel(k)})}},_addCollectionPanel:function(k){var l=this,i=k.model;var j=new c({model:i,parentName:this.model.get("name"),linkTarget:this.linkTarget});l.panelStack.push(j);l.$(".controls").add(".datasets-list").hide();l.$el.append(j.$el);j.on("close",function(){l.render();k.collapse();l.panelStack.pop()});if(!j.model.hasDetails()){var m=j.model.fetch();m.done(function(){j.render()})}else{j.render()}},_attachContentView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.append(k.$el);return this},events:{"click .navigation .back":"close"},close:function(i){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates=d.prototype.templates=(function(){var i=_.template(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- collection.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.type === "list:paired" ){ %>',e("a list of paired datasets"),"<% } %>","</div>","</div>","</div>",'<div class="datasets-list"></div>'].join(""));return{panel:function(j){return i({_l:e,collection:j})}}}());var b=d.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=b.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var g=d.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:d,ListCollectionPanel:b,PairCollectionPanel:c,ListOfPairsCollectionPanel:g}}); \ No newline at end of file +define(["mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(h,f,a,e){var d=Backbone.View.extend(a.LoggableMixin).extend({tagName:"div",className:"dataset-collection-panel",fxSpeed:"fast",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.hasUser=i.hasUser;this.panelStack=[];this.parentName=i.parentName},_setUpListeners:function(){this.on("all",function(i){this.log(this+"",arguments)},this);return this},_setUpModelEventHandlers:function(){return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(!this.model){return this}j=this.renderModel();$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderModel:function(){var k=this.model.get("collection_type")||this.model.object.get("collection_type"),j=_.extend(this.model.toJSON(),{parentName:this.parentName,type:k}),i=$("<div/>").append(this.templates.panel(j));this._setUpBehaviours(i);this.renderContents(i);return i},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},renderContents:function(j){j=j||this.$el;this.warn(this+".renderContents:, model:",this.model);var i=this,l={},k=this.model.getVisibleContents();this.$datasetsList(j).empty();if(k&&k.length){k.each(function(n){var o=n.id,m=i._createContentView(n);l[o]=m;i._attachContentView(m.render(),j)})}this.contentViews=l;return this.contentViews},_createContentView:function(k){var j=null,i=this._getContentClass(k);j=new i({model:k,linkTarget:this.linkTarget,hasUser:this.hasUser,logger:this.logger});this._setUpContentListeners(j);return j},_getContentClass:function(i){switch(i.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",i.get("element_type"))},_setUpContentListeners:function(j){var i=this;if(j.model.get("element_type")==="dataset_collection"){j.on("expanded",function(k){i.info("expanded",k);i._addCollectionPanel(k)})}},_addCollectionPanel:function(k){var l=this,i=k.model;var j=new c({model:i,parentName:this.model.get("name"),linkTarget:this.linkTarget});l.panelStack.push(j);l.$(".controls").add(".datasets-list").hide();l.$el.append(j.$el);j.on("close",function(){l.render();k.collapse();l.panelStack.pop()});if(!j.model.hasDetails()){var m=j.model.fetch();m.done(function(){j.render()})}else{j.render()}},_attachContentView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.append(k.$el);return this},events:{"click .navigation .back":"close"},close:function(i){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates=d.prototype.templates=(function(){var i=_.template(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- collection.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.type === "list:paired" ){ %>',e("a list of paired datasets"),"<% } %>","</div>","</div>","</div>",'<div class="datasets-list"></div>'].join(""));return{panel:function(j){return i({_l:e,collection:j})}}}());var b=d.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=b.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var g=d.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:d,ListCollectionPanel:b,PairCollectionPanel:c,ListOfPairsCollectionPanel:g}}); \ No newline at end of file diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/dataset/dataset-model.js --- a/static/scripts/packed/mvc/dataset/dataset-model.js +++ b/static/scripts/packed/mvc/dataset/dataset-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var f=b.SearchableModelMixin;var e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(f,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(h,g){this.debug("Dataset.initialize",h,g);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var i=this.get("id");if(!i){return{}}var h={purge:"datasets/"+i+"/purge_async",display:"datasets/"+i+"/display/?preview=True",edit:"datasets/"+i+"/edit",download:"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+i,rerun:"tool_runner/rerun?id="+i,show_params:"datasets/"+i+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};var g=(galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(h,function(k,j){h[j]=g+k});this.urls=h;return h},_setUpListeners:function(){this.on("change:state",function(h,g){this.log(this+" has changed state:",h,g);if(this.inReadyState()){this.trigger("state:ready",h,g,this.previous("state"))}});this.on("change:id change:file_ext",function(g){this._generateUrls()})},toJSON:function(){var g=Backbone.Model.prototype.toJSON.call(this);return _.extend(g,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var g=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||g)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(g){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},g)},undelete:function(g){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},g)},purge:function d(g){if(this.get("purged")){return jQuery.when()}g=g||{};g.url=this.urls.purge;var h=this,i=jQuery.ajax(g);i.done(function(l,j,k){h.set({deleted:true,purged:true})});i.fail(function(n,j,m){var k=c("Unable to purge dataset");var l=("Removal of datasets by users is not allowed in this Galaxy instance");if(n.responseJSON&&n.responseJSON.error){k=n.responseJSON.error}else{if(n.responseText.indexOf(l)!==-1){k=l}}n.responseText=k;h.trigger("error",h,n,g,c(k),{error:k})});return i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var g=this.get("id")||"";if(this.get("name")){g='"'+this.get("name")+'",'+g}return"Dataset("+g+")"}}));return{DatasetAssociation:e}}); \ No newline at end of file +define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var f=b.SearchableModelMixin;var e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(f,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(g,h){this.debug(this+"(Dataset).initialize",g,h);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var i=this.get("id");if(!i){return{}}var h={purge:"datasets/"+i+"/purge_async",display:"datasets/"+i+"/display/?preview=True",edit:"datasets/"+i+"/edit",download:"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+i,rerun:"tool_runner/rerun?id="+i,show_params:"datasets/"+i+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};var g=(galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(h,function(k,j){h[j]=g+k});this.urls=h;return h},_setUpListeners:function(){this.on("change:state",function(h,g){this.log(this+" has changed state:",h,g);if(this.inReadyState()){this.trigger("state:ready",h,g,this.previous("state"))}});this.on("change:id change:file_ext",function(g){this._generateUrls()})},toJSON:function(){var g=Backbone.Model.prototype.toJSON.call(this);return _.extend(g,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var g=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||g)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(g){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},g)},undelete:function(g){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},g)},purge:function d(g){if(this.get("purged")){return jQuery.when()}g=g||{};g.url=this.urls.purge;var h=this,i=jQuery.ajax(g);i.done(function(l,j,k){h.set({deleted:true,purged:true})});i.fail(function(n,j,m){var k=c("Unable to purge dataset");var l=("Removal of datasets by users is not allowed in this Galaxy instance");if(n.responseJSON&&n.responseJSON.error){k=n.responseJSON.error}else{if(n.responseText.indexOf(l)!==-1){k=l}}n.responseText=k;h.trigger("error",h,n,g,c(k),{error:k})});return i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var g=this.get("id")||"";if(this.get("name")){g='"'+this.get("name")+'",'+g}return"Dataset("+g+")"}}));return{DatasetAssociation:e}}); \ No newline at end of file diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/history/history-contents.js --- a/static/scripts/packed/mvc/history/history-contents.js +++ b/static/scripts/packed/mvc/history/history-contents.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file +define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/history/history-panel-annotated.js --- a/static/scripts/packed/mvc/history/history-panel-annotated.js +++ b/static/scripts/packed/mvc/history/history-panel-annotated.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-panel","mvc/history/hda-li","utils/localization"],function(e,b,a){var d=e.ReadOnlyHistoryPanel;var c=d.extend({className:"annotated-history-panel",HDAViewClass:b.HDAReadonlyListItemView,renderModel:function(){this.$el.addClass(this.className);var h=d.prototype.renderModel.call(this),f=this.$datasetsList(h),g=$("<table/>").addClass("datasets-list datasets-table");g.append(f.children());f.replaceWith(g);h.find(".history-subtitle").after(this.renderHistoryAnnotation());h.find(".history-search-btn").hide();h.find(".history-controls").after(h.find(".history-search-controls").show());return h},renderHistoryAnnotation:function(){var f=this.model.get("annotation");if(!f){return null}return $(['<div class="history-annotation">',f,"</div>"].join(""))},renderHdas:function(g){g=g||this.$el;var f=d.prototype.renderHdas.call(this,g);this.$datasetsList(g).prepend($("<tr/>").addClass("headers").append([$("<th/>").text(a("Dataset")),$("<th/>").text(a("Annotation"))]));return f},attachContentView:function(i,g){g=g||this.$el;var j=_.find(i.el.classList,function(k){return(/^state\-/).test(k)}),f=i.model.get("annotation")||"",h=$("<tr/>").addClass("dataset-row").append([$("<td/>").addClass("dataset-container").append(i.$el).addClass(j?j.replace("-","-color-"):""),$("<td/>").addClass("additional-info").text(f)]);this.$datasetsList(g).append(h)},events:_.extend(_.clone(d.prototype.events),{"click tr":function(f){$(f.currentTarget).find(".dataset-title-bar").click()},"click .icon-btn":function(f){f.stopPropagation()}}),toString:function(){return"AnnotatedHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{AnnotatedHistoryPanel:c}}); \ No newline at end of file +define(["mvc/history/history-panel","mvc/history/hda-li","utils/localization"],function(e,b,a){var d=e.ReadOnlyHistoryPanel;var c=d.extend({className:"annotated-history-panel",renderModel:function(){this.$el.addClass(this.className);var h=d.prototype.renderModel.call(this),f=this.$datasetsList(h),g=$("<table/>").addClass("datasets-list datasets-table");g.append(f.children());f.replaceWith(g);h.find(".history-subtitle").after(this.renderHistoryAnnotation());h.find(".history-search-btn").hide();h.find(".history-controls").after(h.find(".history-search-controls").show());return h},renderHistoryAnnotation:function(){var f=this.model.get("annotation");if(!f){return null}return $(['<div class="history-annotation">',f,"</div>"].join(""))},renderHdas:function(g){g=g||this.$el;var f=d.prototype.renderHdas.call(this,g);this.$datasetsList(g).prepend($("<tr/>").addClass("headers").append([$("<th/>").text(a("Dataset")),$("<th/>").text(a("Annotation"))]));return f},attachContentView:function(i,g){g=g||this.$el;var j=_.find(i.el.classList,function(k){return(/^state\-/).test(k)}),f=i.model.get("annotation")||"",h=$("<tr/>").addClass("dataset-row").append([$("<td/>").addClass("dataset-container").append(i.$el).addClass(j?j.replace("-","-color-"):""),$("<td/>").addClass("additional-info").text(f)]);this.$datasetsList(g).append(h)},events:_.extend(_.clone(d.prototype.events),{"click tr":function(f){$(f.currentTarget).find(".dataset-title-bar").click()},"click .icon-btn":function(f){f.stopPropagation()}}),toString:function(){return"AnnotatedHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{AnnotatedHistoryPanel:c}}); \ 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: natefoo: Updated tag latest_2014.08.11 for changeset 7e4d21621ce1
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7e81cbc2603f/ Changeset: 7e81cbc2603f Branch: stable User: natefoo Date: 2014-08-12 15:58:36 Summary: Updated tag latest_2014.08.11 for changeset 7e4d21621ce1 Affected #: 1 file diff -r 7e4d21621ce12e13ebbdf9fd3259df58c3ef124c -r 7e81cbc2603f0695802ab49dcd65f6dda7b42322 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -52b5cc75a1757eddfb94ee373193c9d8fa2ec442 latest_2014.08.11 +7e4d21621ce12e13ebbdf9fd3259df58c3ef124c latest_2014.08.11 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: 3 new changesets
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e30d65cf25e8/ Changeset: e30d65cf25e8 Branch: stable User: BjoernGruening Date: 2014-08-12 10:33:27 Summary: install_repository_manager do not need trans.app anymore. Affected #: 1 file diff -r b6d2c77d8bce44cdaba188ce949ed69f94be6bc4 -r e30d65cf25e8e28677d971c19faaae0eb390e6af lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -239,8 +239,7 @@ tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True ) self.__ensure_can_install_repos( trans ) install_repository_manager = InstallRepositoryManager( trans.app ) - installed_tool_shed_repositories = install_repository_manager.install( trans.app, - tool_shed_url, + installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url, name, owner, changeset_revision, https://bitbucket.org/galaxy/galaxy-central/commits/fa1a6a494166/ Changeset: fa1a6a494166 Branch: stable User: BjoernGruening Date: 2014-08-12 10:38:24 Summary: First argument to __install_repositories is the Tool Shed URL (tool_shed_url) Affected #: 1 file diff -r e30d65cf25e8e28677d971c19faaae0eb390e6af -r fa1a6a4941664d9f2cf6dfbb816911778b7c9dcb lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -694,7 +694,8 @@ name, owner, changeset_revision ) - installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict, + installed_tool_shed_repositories = self.__install_repositories( tool_shed_url, + repository_revision_dict, repo_info_dicts, install_options ) return installed_tool_shed_repositories https://bitbucket.org/galaxy/galaxy-central/commits/7e4d21621ce1/ Changeset: 7e4d21621ce1 Branch: stable User: BjoernGruening Date: 2014-08-12 10:41:45 Summary: initiate_repository_installation was not updated in the recent code restructuring efforts Affected #: 1 file diff -r fa1a6a4941664d9f2cf6dfbb816911778b7c9dcb -r 7e4d21621ce12e13ebbdf9fd3259df58c3ef124c lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -789,7 +789,7 @@ # at this point because repository dependencies may have added additional repositories for installation # along with the single specified repository. encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ - initiate_repository_installation( self.app, installation_dict ) + self.initiate_repository_installation( installation_dict ) # Some repositories may have repository dependencies that are required to be installed before the # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in # the required order. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History & collections: client-side file and class renaming: - li: readonly list item view, - li-edit: editable list item view, - primary identity first (eg. hda-*), - moved hda/hdca into history directory; Fix bug for dataset URLs
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/588c52157560/ Changeset: 588c52157560 User: carlfeberhard Date: 2014-08-12 15:38:08 Summary: History & collections: client-side file and class renaming: - li: readonly list item view, - li-edit: editable list item view, - primary identity first (eg. hda-*), - moved hda/hdca into history directory; Fix bug for dataset URLs Affected #: 74 files diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-li-edit.js --- /dev/null +++ b/static/scripts/mvc/collection/collection-li-edit.js @@ -0,0 +1,33 @@ +define([ + "mvc/collection/collection-li", + "utils/localization" +], function( DC_LI, _l ){ +//============================================================================== +/* + +NOTE: not much going on here. Until we find out what operations a user will need + to perform on their own DC's, we'll leave this empty. + +*/ +//============================================================================== +var _super = DC_LI.DCListItemView; +/** @class Editing view for DatasetCollectionElement. + */ +var DCEListItemEdit = _super.extend({ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + // ......................................................................... misc + /** string rep */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'DCEListItemEdit(' + modelString + ')'; + } +}); + +//============================================================================== + return { + DCEListItemEdit : DCEListItemEdit + }; +}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-li.js --- /dev/null +++ b/static/scripts/mvc/collection/collection-li.js @@ -0,0 +1,223 @@ +define([ + "mvc/dataset/dataset-li", + "mvc/base-mvc", + "utils/localization" +], function( DATASET_LI, BASE_MVC, _l ){ +/* global Backbone, LoggableMixin */ +//============================================================================== +var ListItemView = BASE_MVC.ListItemView; +/** @class Read only view for DatasetCollection. + */ +var DCListItemView = ListItemView.extend({ +//TODO: may not be needed + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + className : ListItemView.prototype.className + " dataset-collection", + /** */ + fxSpeed : 'fast', + +//TODO: ununsed + /** set up */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( this + '(DCListItemView).initialize:', attributes ); + ListItemView.prototype.initialize.call( this, attributes ); + }, + + /** In this override, don't show`or render any details (no need to do anything here) + * - currently the parent control will load a panel for this collection over itself + * @fires expanded when a body has been expanded + */ + expand : function(){ + var view = this; + return view._fetchModelDetails() + .always(function(){ + view.trigger( 'expanded', view ); + }); + }, + + // ......................................................................... rendering + //TODO:?? possibly move to listItem + /** render a subtitle to show the user what sort of collection this is */ + _renderSubtitle : function(){ + var $subtitle = $( '<div class="subtitle"></div>' ); + //TODO: would be good to get this in the subtitle + //var len = this.model.elements.length; + switch( this.model.get( 'collection_type' ) ){ + case 'list': + return $subtitle.text( _l( 'a list of datasets' ) ); + case 'paired': + return $subtitle.text( _l( 'a pair of datasets' ) ); + case 'list:paired': + return $subtitle.text( _l( 'a list of paired datasets' ) ); + } + return $subtitle; + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'DCListItemView(' + modelString + ')'; + } +}); + +// ............................................................................ TEMPLATES +/** underscore templates */ +DCListItemView.prototype.templates = (function(){ + + // use element identifier + var titleBarTemplate = BASE_MVC.wrapTemplate([ + '<div class="title-bar clear" tabindex="0">', + '<div class="title">', + '<span class="name"><%- collection.element_identifier || collection.name %></span>', + '</div>', + '<div class="subtitle"></div>', + '</div>' + ], 'collection' ); + + return _.extend( {}, ListItemView.prototype.templates, { + titleBar : titleBarTemplate + }); +}()); + + +//============================================================================== +/** @class Read only view for DatasetCollectionElement. + */ +var DCEListItemView = ListItemView.extend({ +//TODO: this might be expendable - compacted with HDAListItemView + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + logger : console, + + /** add the DCE class to the list item */ + className : ListItemView.prototype.className + " dataset-collection-element", + /** jq fx speed for this view */ + fxSpeed : 'fast', + + /** */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( 'DCEListItemView.initialize:', attributes ); + ListItemView.prototype.initialize.call( this, attributes ); + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'DCEListItemView(' + modelString + ')'; + } +}); + +// ............................................................................ TEMPLATES +/** underscore templates */ +DCEListItemView.prototype.templates = (function(){ + + // use the element identifier here - since that will persist and the user will need it + var titleBarTemplate = BASE_MVC.wrapTemplate([ + '<div class="title-bar clear" tabindex="0">', + '<div class="title">', + '<span class="name"><%- element.element_identifier %></span>', + '</div>', + '<div class="subtitle"></div>', + '</div>' + ], 'element' ); + + return _.extend( {}, ListItemView.prototype.templates, { + titleBar : titleBarTemplate + }); +}()); + + +//============================================================================== +/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation + * (a dataset contained in a dataset collection). + */ +var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend({ + + className : DATASET_LI.DatasetListItemView.prototype.className + " dataset-collection-element", + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( 'DatasetDCEListItemView.initialize:', attributes ); + DATASET_LI.DatasetListItemView.prototype.initialize.call( this, attributes ); + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'DatasetDCEListItemView(' + modelString + ')'; + } +}); + +// ............................................................................ TEMPLATES +/** underscore templates */ +DatasetDCEListItemView.prototype.templates = (function(){ + + // use the element identifier here and not the dataset name + //TODO:?? can we steal the DCE titlebar? + var titleBarTemplate = BASE_MVC.wrapTemplate([ + '<div class="title-bar clear" tabindex="0">', + '<span class="state-icon"></span>', + '<div class="title">', + '<span class="name"><%- element.element_identifier %></span>', + '</div>', + '</div>' + ], 'element' ); + + return _.extend( {}, DATASET_LI.DatasetListItemView.prototype.templates, { + titleBar : titleBarTemplate + }); +}()); + + +//============================================================================== +/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection + * (a nested DC). + */ +var NestedDCDCEListItemView = DCListItemView.extend({ + + className : DCListItemView.prototype.className + " dataset-collection-element", + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + /** In this override, add the state as a class for use with state-based CSS */ + _swapNewRender : function( $newRender ){ + DCListItemView.prototype._swapNewRender.call( this, $newRender ); +//TODO: model currently has no state + var state = this.model.get( 'state' ) || 'ok'; + //if( this.model.has( 'state' ) ){ + this.$el.addClass( 'state-' + state ); + //} + return this.$el; + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'NestedDCDCEListItemView(' + modelString + ')'; + } +}); + + +//============================================================================== + return { + DCListItemView : DCListItemView, + DCEListItemView : DCEListItemView, + DatasetDCEListItemView : DatasetDCEListItemView, + NestedDCDCEListItemView : NestedDCDCEListItemView + }; +}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-model.js --- a/static/scripts/mvc/collection/collection-model.js +++ b/static/scripts/mvc/collection/collection-model.js @@ -2,7 +2,7 @@ "mvc/dataset/dataset-model", "mvc/base-mvc", "utils/localization" -], function( DATASET, BASE_MVC, _l ){ +], function( DATASET_MODEL, BASE_MVC, _l ){ //============================================================================== /* Notes: @@ -118,13 +118,13 @@ //============================================================================== /** @class Backbone model for a dataset collection element that is a dataset (HDA). */ -var DatasetDCE = DATASET.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin, +var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin, /** @lends DatasetDCE.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, - defaults : _.extend( {}, DATASET.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ), + defaults : _.extend( {}, DATASET_MODEL.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ), // because all objects have constructors (as this hashmap would even if this next line wasn't present) // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model @@ -132,7 +132,7 @@ /** call the mixin constructor */ constructor : function( attributes, options ){ this.debug( '\t DatasetDCE.constructor:', attributes, options ); - //DATASET.DatasetAssociation.prototype.constructor.call( this, attributes, options ); + //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options ); DatasetCollectionElementMixin.constructor.call( this, attributes, options ); }, @@ -140,7 +140,7 @@ /** set up */ initialize : function( attributes, options ){ this.debug( this + '(DatasetDCE).initialize:', attributes, options ); - DATASET.DatasetAssociation.prototype.initialize.call( this, attributes, options ); + DATASET_MODEL.DatasetAssociation.prototype.initialize.call( this, attributes, options ); }, /** String representation. */ diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -1,20 +1,15 @@ define([ - "mvc/collection/dataset-collection-base", + "mvc/collection/collection-model", + "mvc/collection/collection-li", "mvc/base-mvc", "utils/localization" -], function( DC_BASE, BASE_MVC, _l ){ +], function( DC_MODEL, DC_LI, BASE_MVC, _l ){ /* ============================================================================= TODO: ============================================================================= */ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. - * @name CollectionPanel - * - * @augments Backbone.View - * @borrows LoggableMixin#logger as #logger - * @borrows LoggableMixin#log as #log - * @constructs */ var CollectionPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( /** @lends CollectionPanel.prototype */{ @@ -29,8 +24,8 @@ /** (in ms) that jquery effects will use */ fxSpeed : 'fast', - DatasetDCEViewClass : DC_BASE.DatasetDCEBaseView, - NestedDCEViewClass : DC_BASE.NestedDCEBaseView, + DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, + NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events @@ -44,9 +39,13 @@ } this.log( this + '.initialize:', attributes ); + this.linkTarget = attributes.linkTarget || '_blank'; + this.hasUser = attributes.hasUser; this.panelStack = []; this.parentName = attributes.parentName; + + //window.collectionPanel = this; }, /** create any event listeners for the panel @@ -70,7 +69,7 @@ }, // ------------------------------------------------------------------------ panel rendering - /** Render urls, historyPanel body, and hdas (if any are shown) + /** Render panel * @fires: rendered when the panel is attached and fully visible * @see Backbone.View#render */ @@ -122,7 +121,7 @@ return this; }, - /** render with history data + /** render with collection data * @returns {jQuery} dom fragment as temporary container to be swapped out later */ renderModel : function( ){ @@ -139,7 +138,7 @@ return $newRender; }, - /** Set up HistoryPanel js/widget behaviours */ + /** Set up js/widget behaviours */ _setUpBehaviours : function( $where ){ //TODO: these should be either sub-MVs, or handled by events $where = $where || this.$el; @@ -152,16 +151,16 @@ $container : function(){ return ( this.findContainerFn )?( this.findContainerFn.call( this ) ):( this.$el.parent() ); }, - /** where hdaViews are attached */ + /** where list content views are attached */ $datasetsList : function( $where ){ return ( $where || this.$el ).find( '.datasets-list' ); }, // ------------------------------------------------------------------------ sub-views - /** Set up/render a view for each HDA to be shown, init with model and listeners. - * HDA views are cached to the map this.hdaViews (using the model.id as key). - * @param {jQuery} $whereTo what dom element to prepend the HDA views to - * @returns the number of visible hda views + /** Set up/render a view for each DCE to be shown, init with model and listeners. + * DCE views are cached to the map this.contentViews (using the model.id as key). + * @param {jQuery} $whereTo what dom element to prepend the DCE views to + * @returns the number of visible DCE views */ renderContents : function( $whereTo ){ //this.debug( 'renderContents, elements:', this.model.elements ); @@ -172,7 +171,7 @@ contentViews = {}, //NOTE: no filtering here visibleContents = this.model.getVisibleContents(); - this.log( 'renderContents, visibleContents:', visibleContents, $whereTo ); + //this.debug( 'renderContents, visibleContents:', visibleContents, $whereTo ); this.$datasetsList( $whereTo ).empty(); if( visibleContents && visibleContents.length ){ @@ -192,8 +191,8 @@ //this.debug( 'content json:', JSON.stringify( content, null, ' ' ) ); var contentView = null, ContentClass = this._getContentClass( content ); - this.debug( 'ContentClass:', ContentClass ); - this.debug( 'content:', content ); + //this.debug( 'content:', content ); + //this.debug( 'ContentClass:', ContentClass ); contentView = new ContentClass({ model : content, linkTarget : this.linkTarget, @@ -201,20 +200,20 @@ hasUser : this.hasUser, logger : this.logger }); - this.debug( 'contentView:', contentView ); + //this.debug( 'contentView:', contentView ); this._setUpContentListeners( contentView ); return contentView; }, /** */ _getContentClass : function( content ){ - this.debug( this + '._getContentClass:', content ); - this.debug( 'DCEViewClass:', this.DCEViewClass ); + //this.debug( this + '._getContentClass:', content ); +//TODO: subclasses use DCEViewClass - but are currently unused - decide switch( content.get( 'element_type' ) ){ case 'hda': - return this.DCEViewClass; + return this.DatasetDCEViewClass; case 'dataset_collection': - return this.DCEViewClass; + return this.NestedDCDCEViewClass; } throw new TypeError( 'Unknown element type:', content.get( 'element_type' ) ); }, @@ -232,14 +231,16 @@ /** */ _addCollectionPanel : function( collectionView ){ +//TODO: a bit hackish var currPanel = this, collectionModel = collectionView.model; - this.debug( 'collection panel (stack), collectionView:', collectionView ); - this.debug( 'collection panel (stack), collectionModel:', collectionModel ); + //this.debug( 'collection panel (stack), collectionView:', collectionView ); + //this.debug( 'collection panel (stack), collectionModel:', collectionModel ); var panel = new PairCollectionPanel({ model : collectionModel, - parentName : this.model.get( 'name' ) + parentName : this.model.get( 'name' ), + linkTarget : this.linkTarget }); currPanel.panelStack.push( panel ); @@ -277,7 +278,7 @@ 'click .navigation .back' : 'close' }, - /** */ + /** close/remove this collection panel */ close : function( event ){ this.$el.remove(); this.trigger( 'close' ); @@ -334,7 +335,8 @@ /** @class non-editable, read-only View/Controller for a dataset collection. */ var ListCollectionPanel = CollectionPanel.extend({ - DCEViewClass : DC_BASE.DatasetDCEBaseView, + //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass + DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, // ........................................................................ misc /** string rep */ @@ -360,7 +362,8 @@ /** @class non-editable, read-only View/Controller for a dataset collection. */ var ListOfPairsCollectionPanel = CollectionPanel.extend({ - DCEViewClass : DC_BASE.NestedDCDCEBaseView, + //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass + NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, // ........................................................................ misc /** string rep */ diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/dataset-collection-base.js --- a/static/scripts/mvc/collection/dataset-collection-base.js +++ /dev/null @@ -1,222 +0,0 @@ -define([ - "mvc/dataset/dataset-list-element", - "mvc/base-mvc", - "utils/localization" -], function( DATASET_LI, BASE_MVC, _l ){ -/* global Backbone, LoggableMixin */ -//============================================================================== -var ListItemView = BASE_MVC.ListItemView; -/** @class Read only view for DatasetCollection. - */ -var DCBaseView = ListItemView.extend({ -//TODO: may not be needed - - /** logger used to record this.log messages, commonly set to console */ - //logger : console, - - className : ListItemView.prototype.className + " dataset-collection", - /** */ - fxSpeed : 'fast', - -//TODO: ununsed - /** set up */ - initialize : function( attributes ){ - if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } - this.log( 'DCBaseView.initialize:', attributes ); - ListItemView.prototype.initialize.call( this, attributes ); - }, - - /** In this override, don't show`or render any details (no need to do anything here) - * - currently the parent control will load a panel for this collection over itself - * @fires expanded when a body has been expanded - */ - expand : function(){ - var view = this; - return view._fetchModelDetails() - .always(function(){ - view.trigger( 'expanded', view ); - }); - }, - - // ......................................................................... rendering - //TODO:?? possibly move to listItem - /** render a subtitle to show the user what sort of collection this is */ - _renderSubtitle : function(){ - var $subtitle = $( '<div class="subtitle"></div>' ); - //TODO: would be good to get this in the subtitle - //var len = this.model.elements.length; - switch( this.model.get( 'collection_type' ) ){ - case 'list': - return $subtitle.text( _l( 'a list of datasets' ) ); - case 'paired': - return $subtitle.text( _l( 'a pair of datasets' ) ); - case 'list:paired': - return $subtitle.text( _l( 'a list of paired datasets' ) ); - } - return $subtitle; - }, - - // ......................................................................... misc - /** String representation */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'DCBaseView(' + modelString + ')'; - } -}); - -// ............................................................................ TEMPLATES -/** underscore templates */ -DCBaseView.prototype.templates = (function(){ - - // use element identifier - var titleBarTemplate = BASE_MVC.wrapTemplate([ - '<div class="title-bar clear" tabindex="0">', - '<div class="title">', - '<span class="name"><%- collection.element_identifier || collection.name %></span>', - '</div>', - '<div class="subtitle"></div>', - '</div>' - ], 'collection' ); - - return _.extend( {}, ListItemView.prototype.templates, { - titleBar : titleBarTemplate - }); -}()); - - -//============================================================================== -/** @class Read only view for DatasetCollectionElement. - */ -var DCEBaseView = ListItemView.extend({ -//TODO: this might be expendable - compacted with HDADCEBaseView - - /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output - logger : console, - - /** add the DCE class to the list item */ - className : ListItemView.prototype.className + " dataset-collection-element", - /** jq fx speed for this view */ - fxSpeed : 'fast', - - /** */ - initialize : function( attributes ){ - if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } - this.log( 'DCEBaseView.initialize:', attributes ); - ListItemView.prototype.initialize.call( this, attributes ); - }, - - // ......................................................................... misc - /** String representation */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'DCEBaseView(' + modelString + ')'; - } -}); - -// ............................................................................ TEMPLATES -/** underscore templates */ -DCEBaseView.prototype.templates = (function(){ - - // use the element identifier here - since that will persist and the user will need it - var titleBarTemplate = BASE_MVC.wrapTemplate([ - '<div class="title-bar clear" tabindex="0">', - '<div class="title">', - '<span class="name"><%- element.element_identifier %></span>', - '</div>', - '<div class="subtitle"></div>', - '</div>' - ], 'element' ); - - return _.extend( {}, ListItemView.prototype.templates, { - titleBar : titleBarTemplate - }); -}()); - - -//============================================================================== -/** @class Read only view for a DatasetCollectionElement that is also an HDA. - */ -var DatasetDCEBaseView = DATASET_LI.DatasetListItemView.extend({ - - className : DATASET_LI.DatasetListItemView.prototype.className + " dataset-collection-element", - - /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output - //logger : console, - - /** */ - initialize : function( attributes ){ - if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } - this.log( 'DatasetDCEBaseView.initialize:', attributes ); - DATASET_LI.DatasetListItemView.prototype.initialize.call( this, attributes ); - }, - - // ......................................................................... misc - /** String representation */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'DatasetDCEBaseView(' + modelString + ')'; - } -}); - -// ............................................................................ TEMPLATES -/** underscore templates */ -DatasetDCEBaseView.prototype.templates = (function(){ - - // use the element identifier here and not the dataset name - //TODO:?? can we steal the DCE titlebar? - var titleBarTemplate = BASE_MVC.wrapTemplate([ - '<div class="title-bar clear" tabindex="0">', - '<span class="state-icon"></span>', - '<div class="title">', - '<span class="name"><%- element.element_identifier %></span>', - '</div>', - '</div>' - ], 'element' ); - - return _.extend( {}, DATASET_LI.DatasetListItemView.prototype.templates, { - titleBar : titleBarTemplate - }); -}()); - -//============================================================================== -/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection - * (a nested DC). - */ -var NestedDCDCEBaseView = DCBaseView.extend({ - - className : DCBaseView.prototype.className + " dataset-collection-element", - - /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output - //logger : console, - - /** In this override, add the state as a class for use with state-based CSS */ - _swapNewRender : function( $newRender ){ - DATASET_LI.DatasetListItemView.prototype._swapNewRender.call( this, $newRender ); -//TODO: model currently has no state - var state = this.model.get( 'state' ) || 'ok'; - //if( this.model.has( 'state' ) ){ - this.$el.addClass( 'state-' + state ); - //} - return this.$el; - }, - - // ......................................................................... misc - /** String representation */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'NestedDCDCEBaseView(' + modelString + ')'; - } -}); - - -//============================================================================== - return { - DCBaseView : DCBaseView, - DCEBaseView : DCEBaseView, - DatasetDCEBaseView : DatasetDCEBaseView, - NestedDCDCEBaseView : NestedDCDCEBaseView - }; -}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/dataset-collection-edit.js --- a/static/scripts/mvc/collection/dataset-collection-edit.js +++ /dev/null @@ -1,39 +0,0 @@ -define([ - "mvc/dataset/states", - "mvc/collection/dataset-collection-base", - "utils/localization" -], function( STATES, DC_BASE_VIEW, _l ){ -//============================================================================== -/* - -NOTE: not much going on here. Until we find out what operations a user will need - to perform on their own DC's, we'll leave this empty. - -*/ -//============================================================================== -var _super = DC_BASE_VIEW.DCBaseView; -/** @class Editing view for DatasetCollection. - * @name DatasetCollectionEditView - * - * @augments DCBaseView - * @constructs - */ -var DCEditView = _super.extend({ - - /** logger used to record this.log messages, commonly set to console */ - // comment this out to suppress log output - //logger : console, - - // ......................................................................... misc - /** string rep */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'DCEditView(' + modelString + ')'; - } -}); - -//============================================================================== - return { - DCEditView : DCEditView - }; -}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/hdca-base.js --- a/static/scripts/mvc/collection/hdca-base.js +++ /dev/null @@ -1,67 +0,0 @@ -define([ - "mvc/dataset/states", - "mvc/collection/dataset-collection-base", - "mvc/base-mvc", - "utils/localization" -], function( STATES, DC_BASE, BASE_MVC, _l ){ -/* global Backbone */ -//============================================================================== -var _super = DC_BASE.DCBaseView; -/** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history). - */ -var HDCABaseView = _super.extend({ - - /** logger used to record this.log messages, commonly set to console */ - //logger : console, - -//TODO: not a dataset - /** */ - className : _super.prototype.className + " history-content", - - /** In this override, add the state as a class for use with state-based CSS */ - _swapNewRender : function( $newRender ){ - _super.prototype._swapNewRender.call( this, $newRender ); -//TODO: model currently has no state - var state = this.model.get( 'state' ) || STATES.OK; - //if( this.model.has( 'state' ) ){ - this.$el.addClass( 'state-' + state ); - //} - return this.$el; - }, - - // ......................................................................... misc - /** String representation */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HDCABaseView(' + modelString + ')'; - } -}); - -/** underscore templates */ -HDCABaseView.prototype.templates = (function(){ - -// could steal this from hda-base (or use mixed content) - var titleBarTemplate = BASE_MVC.wrapTemplate([ - // adding the hid display to the title - '<div class="title-bar clear" tabindex="0">', - '<span class="state-icon"></span>', - '<div class="title">', - //TODO: remove whitespace and use margin-right - '<span class="hid"><%- collection.hid %></span> ', - '<span class="name"><%- collection.name %></span>', - '</div>', - '<div class="subtitle"></div>', - '</div>' - ], 'collection' ); - - return _.extend( {}, _super.prototype.templates, { - titleBar : titleBarTemplate - }); -}()); - - -//============================================================================== - return { - HDCABaseView : HDCABaseView - }; -}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/hdca-edit.js --- a/static/scripts/mvc/collection/hdca-edit.js +++ /dev/null @@ -1,55 +0,0 @@ -define([ - "mvc/dataset/states", - "mvc/collection/hdca-base", - "utils/localization" -], function( STATES, HDCA_BASE, _l ){ -//============================================================================== -var _super = HDCA_BASE.HDCABaseView; -/** @class Editing view for HistoryDatasetCollectionAssociation. - */ -var HDCAEditView = _super.extend({ - - /** logger used to record this.log messages, commonly set to console */ - //logger : console, - - // ......................................................................... delete - /** In this override, add the delete button. */ - _renderPrimaryActions : function(){ - this.log( this + '._renderPrimaryActions' ); - // render the display, edit attr and delete icon-buttons - return _super.prototype._renderPrimaryActions.call( this ) - .concat([ - this._renderDeleteButton() - ]); - }, - - /** Render icon-button to delete this collection. */ - _renderDeleteButton : function(){ - var self = this, - deleted = this.model.get( 'deleted' ); - return faIconButton({ - title : deleted? _l( 'Dataset collection is already deleted' ): _l( 'Delete' ), - classes : 'delete-btn', - faIcon : 'fa-times', - disabled : deleted, - onclick : function() { - // ...bler... tooltips being left behind in DOM (hover out never called on deletion) - self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' ); - self.model[ 'delete' ](); - } - }); - }, - - // ......................................................................... misc - /** string rep */ - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HDCAEditView(' + modelString + ')'; - } -}); - -//============================================================================== - return { - HDCAEditView : HDCAEditView - }; -}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/collection/hdca-model.js --- a/static/scripts/mvc/collection/hdca-model.js +++ /dev/null @@ -1,83 +0,0 @@ -define([ - "mvc/history/history-content-base", - "mvc/collection/collection-model", - "utils/localization" -], function( HISTORY_CONTENT, DC_MODEL, _l ){ -/*============================================================================== - -Models for DatasetCollections contained within a history. - -TODO: - these might be compactable to one class if some duplication with - collection-model is used. - -==============================================================================*/ -var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin, - ListDC = DC_MODEL.ListDatasetCollection, - PairDC = DC_MODEL.PairDatasetCollection, - ListPairedDC = DC_MODEL.ListPairedDatasetCollection; - -//============================================================================== -/** @class Backbone model for List Dataset Collection within a History. - * @constructs - */ -var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( -/** @lends HistoryListDatasetCollection.prototype */{ - - initialize : function( model, options ){ - ListDC.prototype.initialize.call( this, model, options ); - hcontentMixin.initialize.call( this, model, options ); - }, - - /** String representation. */ - toString : function(){ - return ([ 'HistoryListDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); - } -}); - - -//============================================================================== -/** @class Backbone model for Pair Dataset Collection within a History. - * @constructs - */ -var HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend( -/** @lends HistoryPairDatasetCollection.prototype */{ - - initialize : function( model, options ){ - PairDC.prototype.initialize.call( this, model, options ); - hcontentMixin.initialize.call( this, model, options ); - }, - - /** String representation. */ - toString : function(){ - return ([ 'HistoryPairDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); - } -}); - - -//============================================================================== -/** @class Backbone model for List of Pairs Dataset Collection within a History. - * @constructs - */ -var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend( -/** @lends HistoryListPairedDatasetCollection.prototype */{ - - initialize : function( model, options ){ - ListPairedDC.prototype.initialize.call( this, model, options ); - hcontentMixin.initialize.call( this, model, options ); - }, - - /** String representation. */ - toString : function(){ - return ([ 'HistoryListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); - } -}); - - -//============================================================================== - return { - HistoryListDatasetCollection : HistoryListDatasetCollection, - HistoryPairDatasetCollection : HistoryPairDatasetCollection, - HistoryListPairedDatasetCollection : HistoryListPairedDatasetCollection - }; -}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/dataset/dataset-li-edit.js --- /dev/null +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -0,0 +1,351 @@ +define([ + "mvc/dataset/states", + "mvc/dataset/dataset-li", + "mvc/tags", + "mvc/annotations", + "mvc/base-mvc", + "utils/localization" +], function( STATES, DATASET_LI, TAGS, ANNOTATIONS, BASE_MVC, _l ){ +//============================================================================== +var _super = DATASET_LI.DatasetListItemView; +/** @class Editing view for DatasetAssociation. + */ +var DatasetListItemEdit = _super.extend( +/** @lends DatasetListItemEdit.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** set up: options */ + initialize : function( attributes ){ + _super.prototype.initialize.call( this, attributes ); +//TODO: shouldn't this err if false? + this.hasUser = attributes.hasUser; + + /** allow user purge of dataset files? */ + this.purgeAllowed = attributes.purgeAllowed || false; + + //TODO: move to HiddenUntilActivatedViewMixin + /** should the tags editor be shown or hidden initially? */ + this.tagsEditorShown = attributes.tagsEditorShown || false; + /** should the tags editor be shown or hidden initially? */ + this.annotationEditorShown = attributes.annotationEditorShown || false; + }, + + // ......................................................................... titlebar actions + /** In this override, add the other two primary actions: edit and delete */ + _renderPrimaryActions : function(){ + var actions = _super.prototype._renderPrimaryActions.call( this ); + if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){ + return actions; + } + // render the display, edit attr and delete icon-buttons + return _super.prototype._renderPrimaryActions.call( this ).concat([ + this._renderEditButton(), + this._renderDeleteButton() + ]); + }, + +//TODO: move titleButtons into state renderers, remove state checks in the buttons + + /** Render icon-button to edit the attributes (format, permissions, etc.) this dataset. */ + _renderEditButton : function(){ + // don't show edit while uploading, in-accessible + // DO show if in error (ala previous history panel) + if( ( this.model.get( 'state' ) === STATES.DISCARDED ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } + + var purged = this.model.get( 'purged' ), + deleted = this.model.get( 'deleted' ), + editBtnData = { + title : _l( 'Edit attributes' ), + href : this.model.urls.edit, + target : this.linkTarget, + faIcon : 'fa-pencil', + classes : 'edit-btn' + }; + + // disable if purged or deleted and explain why in the tooltip + if( deleted || purged ){ + editBtnData.disabled = true; + if( purged ){ + editBtnData.title = _l( 'Cannot edit attributes of datasets removed from disk' ); + } else if( deleted ){ + editBtnData.title = _l( 'Undelete dataset to edit attributes' ); + } + + // disable if still uploading or new + } else if( _.contains( [ STATES.UPLOAD, STATES.NEW ], this.model.get( 'state' ) ) ){ + editBtnData.disabled = true; + editBtnData.title = _l( 'This dataset is not yet editable' ); + } + return faIconButton( editBtnData ); + }, + + /** Render icon-button to delete this hda. */ + _renderDeleteButton : function(){ + // don't show delete if... + if( ( !this.model.get( 'accessible' ) ) ){ + return null; + } + + var self = this, + deletedAlready = this.model.isDeletedOrPurged(); + return faIconButton({ + title : !deletedAlready? _l( 'Delete' ) : _l( 'Dataset is already deleted' ), + disabled : deletedAlready, + faIcon : 'fa-times', + classes : 'delete-btn', + onclick : function() { + // ...bler... tooltips being left behind in DOM (hover out never called on deletion) + self.$el.find( '.icon-btn.delete-btn' ).trigger( 'mouseout' ); + self.model[ 'delete' ](); + } + }); + }, + + // ......................................................................... details + /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */ + _renderDetails : function(){ + //TODO: generalize to be allow different details for each state + var $details = _super.prototype._renderDetails.call( this ), + state = this.model.get( 'state' ); + + if( !this.model.isDeletedOrPurged() && _.contains([ STATES.OK, STATES.FAILED_METADATA ], state ) ){ + this._renderTags( $details ); + this._renderAnnotation( $details ); + this._makeDbkeyEditLink( $details ); + } + +//TODO: TRIPLE tap, ugh. + this._setUpBehaviors( $details ); + return $details; + }, + + /** Add less commonly used actions in the details section based on state */ + _renderSecondaryActions : function(){ + var actions = _super.prototype._renderSecondaryActions.call( this ); + switch( this.model.get( 'state' ) ){ + case STATES.UPLOAD: + case STATES.NEW: + case STATES.NOT_VIEWABLE: + return actions; + case STATES.ERROR: + // error button comes first + actions.unshift( this._renderErrButton() ); + return actions.concat([ this._renderRerunButton() ]); + case STATES.OK: + case STATES.FAILED_METADATA: + return actions.concat([ this._renderRerunButton(), this._renderVisualizationsButton() ]); + } + return actions.concat([ this._renderRerunButton() ]); + }, + + /** Render icon-button to report an error on this dataset to the galaxy admin. */ + _renderErrButton : function(){ + return faIconButton({ + title : _l( 'View or report this error' ), + href : this.model.urls.report_error, + classes : 'report-error-btn', + target : this.linkTarget, + faIcon : 'fa-bug' + }); + }, + + /** Render icon-button to re-run the job that created this dataset. */ + _renderRerunButton : function(){ + return faIconButton({ + title : _l( 'Run this job again' ), + href : this.model.urls.rerun, + classes : 'rerun-btn', + target : this.linkTarget, + faIcon : 'fa-refresh' + }); + }, + + /** Render an icon-button or popupmenu of links based on the applicable visualizations */ + _renderVisualizationsButton : function(){ + //TODO: someday - lazyload visualizations + var visualizations = this.model.get( 'visualizations' ); + if( ( this.model.isDeletedOrPurged() ) + || ( !this.hasUser ) + || ( !this.model.hasData() ) + || ( _.isEmpty( visualizations ) ) ){ + return null; + } + if( !_.isObject( visualizations[0] ) ){ + this.warn( 'Visualizations have been switched off' ); + return null; + } + + var $visualizations = $( this.templates.visualizations( visualizations, this ) ); + // use addBack here to include the root $visualizations elem (for the case of 1 visualization) + this._addScratchBookFn( $visualizations.find( '.visualization-link' ).addBack( '.visualization-link' ) ); + return $visualizations; + }, + + /** add scratchbook functionality to visualization links */ + _addScratchBookFn : function( $links ){ + $links.click( function( ev ){ + if( Galaxy.frame && Galaxy.frame.active ){ + Galaxy.frame.add({ + title : "Visualization", + type : "url", + content : $( this ).attr( 'href' ) + }); + ev.preventDefault(); + ev.stopPropagation(); + } + }); + }, + +//TODO: if possible move these to readonly view - but display the owner's tags/annotation (no edit) + /** Render the tags list/control */ + _renderTags : function( $where ){ + if( !this.hasUser ){ return; } + var view = this; + this.tagsEditor = new TAGS.TagsEditor({ + model : this.model, + el : $where.find( '.tags-display' ), + onshowFirstTime : function(){ this.render(); }, + // persist state on the hda view (and not the editor) since these are currently re-created each time + onshow : function(){ view.tagsEditorShown = true; }, + onhide : function(){ view.tagsEditorShown = false; }, + $activator : faIconButton({ + title : _l( 'Edit dataset tags' ), + classes : 'tag-btn', + faIcon : 'fa-tags' + }).appendTo( $where.find( '.actions .right' ) ) + }); + if( this.tagsEditorShown ){ this.tagsEditor.toggle( true ); } + }, + + /** Render the annotation display/control */ + _renderAnnotation : function( $where ){ + if( !this.hasUser ){ return; } + var view = this; + this.annotationEditor = new ANNOTATIONS.AnnotationEditor({ + model : this.model, + el : $where.find( '.annotation-display' ), + onshowFirstTime : function(){ this.render(); }, + // persist state on the hda view (and not the editor) since these are currently re-created each time + onshow : function(){ view.annotationEditorShown = true; }, + onhide : function(){ view.annotationEditorShown = false; }, + $activator : faIconButton({ + title : _l( 'Edit dataset annotation' ), + classes : 'annotate-btn', + faIcon : 'fa-comment' + }).appendTo( $where.find( '.actions .right' ) ) + }); + if( this.annotationEditorShown ){ this.annotationEditor.toggle( true ); } + }, + + /** If the format/dbkey/genome_build isn't set, make the display a link to the edit page */ + _makeDbkeyEditLink : function( $details ){ + // make the dbkey a link to editing + if( this.model.get( 'metadata_dbkey' ) === '?' + && !this.model.isDeletedOrPurged() ){ + var editableDbkey = $( '<a class="value">?</a>' ) + .attr( 'href', this.model.urls.edit ) + .attr( 'target', this.linkTarget ); + $details.find( '.dbkey .value' ).replaceWith( editableDbkey ); + } + }, + + // ......................................................................... events + /** event map */ + events : _.extend( _.clone( _super.prototype.events ), { + 'click .undelete-link' : function( ev ){ this.model.undelete(); return false; }, + 'click .purge-link' : '_confirmPurge' + }), + + /** listener for item purge */ + _confirmPurge : function _confirmPurge( ev ){ +//TODO: confirm dialog + this.model.purge(); + return false; + }, + + // ......................................................................... misc + /** string rep */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'HDAEditView(' + modelString + ')'; + } +}); + + +// ............................................................................ TEMPLATES +/** underscore templates */ +DatasetListItemEdit.prototype.templates = (function(){ +//TODO: move to require text! plugin + + var warnings = _.extend( {}, _super.prototype.templates.warnings, { + failed_metadata : BASE_MVC.wrapTemplate([ + // in this override, provide a link to the edit page + '<% if( dataset.state === "failed_metadata" ){ %>', + '<div class="failed_metadata-warning warningmessagesmall">', + _l( 'An error occurred setting the metadata for this dataset' ), + '<br /><a href="<%= dataset.urls.edit %>" target="<%= view.linkTarget %>">', + _l( 'Set it manually or retry auto-detection' ), + '</a>', + '</div>', + '<% } %>' + ], 'dataset' ), + + deleted : BASE_MVC.wrapTemplate([ + // in this override, provide links to undelete or purge the dataset + '<% if( dataset.deleted && !dataset.purged ){ %>', + // deleted not purged + '<div class="deleted-msg warningmessagesmall">', + _l( 'This dataset has been deleted' ), + '<br /><a class="undelete-link" href="javascript:void(0);">', _l( 'Undelete it' ), '</a>', + '<% if( view.purgeAllowed ){ %>', + '<br /><a class="purge-link" href="javascript:void(0);">', + _l( 'Permanently remove it from disk' ), + '</a>', + '<% } %>', + '</div>', + '<% } %>' + ], 'dataset' ) + }); + + var visualizationsTemplate = BASE_MVC.wrapTemplate([ + '<% if( visualizations.length === 1 ){ %>', + '<a class="visualization-btn visualization-link icon-btn" href="<%= visualizations[0].href %>"', + ' target="<%= visualizations[0].target %>" title="', _l( 'Visualize in' ), + ' <%= visualizations[0].html %>">', + '<span class="fa fa-bar-chart-o"></span>', + '</a>', + + '<% } else { %>', + '<div class="visualizations-dropdown dropdown">', + '<a class="visualization-btn icon-btn" data-toggle="dropdown" title="', _l( 'Visualize' ), '">', + '<span class="fa fa-bar-chart-o"></span>', + '</a>', + '<ul class="dropdown-menu" role="menu">', + '<% _.each( visualizations, function( visualization ){ %>', + '<li><a class="visualization-link" href="<%= visualization.href %>"', + ' target="<%= visualization.target %>">', + '<%= visualization.html %>', + '</a></li>', + '<% }); %>', + '</ul>', + '</div>', + '<% } %>' + ], 'visualizations' ); + + return _.extend( {}, _super.prototype.templates, { + warnings : warnings, + visualizations : visualizationsTemplate + }); +}()); + + +//============================================================================== + return { + DatasetListItemEdit : DatasetListItemEdit + }; +}); diff -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 -r 588c521575605b698ee15376f3b919f6a2cda20c static/scripts/mvc/dataset/dataset-li.js --- /dev/null +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -0,0 +1,464 @@ +define([ + "mvc/dataset/states", + "mvc/base-mvc", + "utils/localization" +], function( STATES, BASE_MVC, _l ){ +/* global Backbone */ +//============================================================================== +var _super = BASE_MVC.ListItemView; +/** @class Read only list view for either LDDAs, HDAs, or HDADCEs. + * Roughly, any DatasetInstance (and not a raw Dataset). + */ +var DatasetListItemView = _super.extend( +/** @lends DatasetListItemView.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + className : _super.prototype.className + " dataset", + + /** Set up: instance vars, options, and event handlers */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( this + '.initialize:', attributes ); + _super.prototype.initialize.call( this, attributes ); + + /** where should pages from links be displayed? (default to new tab/window) */ + this.linkTarget = attributes.linkTarget || '_blank'; + + this._setUpListeners(); + }, + + /** event listeners */ + _setUpListeners : function(){ + // hide the primary actions in the title bar when selectable + this.on( 'selectable', function( isSelectable ){ + if( isSelectable ){ + this.$( '.primary-actions' ).hide(); + } else { + this.$( '.primary-actions' ).show(); + } + }); + + // re-rendering on any model changes + this.model.on( 'change', function( model, options ){ + // if the model moved into the ready state and is expanded without details, fetch those details now + if( this.model.changedAttributes().state && this.model.inReadyState() + && this.expanded && !this.model.hasDetails() ){ + // will render automatically (due to fetch -> change) + this.model.fetch(); + + } else { + this.render(); + } + }, this ); + + this.on( 'all', function( event ){ + this.log( event ); + }, this ); + }, + + // ......................................................................... expandable + /** In this override, only get details if in the ready state. + * Note: fetch with no 'change' event triggering to prevent automatic rendering. + */ + _fetchModelDetails : function(){ + var view = this; + if( view.model.inReadyState() && !view.model.hasDetails() ){ + return view.model.fetch({ silent: true }); + } + return jQuery.when(); + }, + + // ......................................................................... removal + /** Remove this view's html from the DOM and remove all event listeners. + * @param {Number or String} speed jq effect speed + * @param {Function} callback an optional function called when removal is done (scoped to this view) + */ + remove : function( speed, callback ){ + var view = this; + speed = speed || this.fxSpeed; + this.$el.fadeOut( speed, function(){ + Backbone.View.prototype.remove.call( view ); + if( callback ){ callback.call( view ); } + }); + }, + + // ......................................................................... rendering + /* TODO: + dataset states are the issue primarily making dataset rendering complex + each state should have it's own way of displaying/set of details + often with different actions that can be applied + throw in deleted/purged/visible and things get complicated easily + I've considered (a couple of times) - creating a view for each state + - but recreating the view during an update...seems wrong + */ + /** Render this HDA, set up ui. + * @param {Number or String} speed jq fx speed + * @returns {Object} this + */ + render : function( speed ){ + //HACK: hover exit doesn't seem to be called on prev. tooltips when RE-rendering - so: no tooltip hide + // handle that here by removing previous view's tooltips + //this.$el.find("[title]").tooltip( "destroy" ); + return _super.prototype.render.call( this, speed ); + }, + + /** In this override, add the dataset state as a class for use with state-based CSS */ + _swapNewRender : function( $newRender ){ + _super.prototype._swapNewRender.call( this, $newRender ); + if( this.model.has( 'state' ) ){ + this.$el.addClass( 'state-' + this.model.get( 'state' ) ); + } + return this.$el; + }, + + // ................................................................................ titlebar + /** In this override, add the dataset display button. */ + _renderPrimaryActions : function(){ + // render just the display for read-only + return [ this._renderDisplayButton() ]; + }, + + /** Render icon-button to display dataset data */ + _renderDisplayButton : function(){ +//TODO:?? too complex - possibly move into template + // don't show display if not viewable or not accessible + var state = this.model.get( 'state' ); + if( ( state === STATES.NOT_VIEWABLE ) + || ( state === STATES.DISCARDED ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } + + var displayBtnData = { + target : this.linkTarget, + classes : 'display-btn' + }; + + // show a disabled display if the data's been purged + if( this.model.get( 'purged' ) ){ + displayBtnData.disabled = true; + displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); + + // disable if still uploading + } else if( state === STATES.UPLOAD ){ + displayBtnData.disabled = true; + displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' ); + + // disable if still new + } else if( state === STATES.NEW ){ + displayBtnData.disabled = true; + displayBtnData.title = _l( 'This dataset is not yet viewable' ); + + } else { + displayBtnData.title = _l( 'View data' ); + + // default link for dataset + displayBtnData.href = this.model.urls.display; + + // add frame manager option onclick event + var self = this; + displayBtnData.onclick = function( ev ){ + if( Galaxy.frame && Galaxy.frame.active ){ + // Create frame with TabularChunkedView. + Galaxy.frame.add({ + title : "Data Viewer: " + self.model.get( 'name' ), + type : "other", + content : function( parent_elt ){ + var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); + $.when( new_dataset.fetch() ).then( function(){ + DATA.createTabularDatasetChunkedView({ + model: new_dataset, + parent_elt: parent_elt, + embedded: true, + height: '100%' + }); + }); + } + }); + ev.preventDefault(); + } + }; + } + displayBtnData.faIcon = 'fa-eye'; + return faIconButton( displayBtnData ); + }, + + // ......................................................................... rendering details + /** Render the enclosing div of the hda body and, if expanded, the html in the body + * @returns {jQuery} rendered DOM + */ + _renderDetails : function(){ + //TODO: generalize to be allow different details for each state + var $details = _super.prototype._renderDetails.call( this ); + $details.find( '.actions .left' ).empty().append( this._renderSecondaryActions() ); + $details.find( '.summary' ).html( this._renderSummary() ); + $details.find( '.display-applications' ).html( this._renderDisplayApplications() ); + +//TODO: double tap + this._setUpBehaviors( $details ); + return $details; + }, + + /** Defer to the appropo summary rendering fn based on state */ + _renderSummary : function(){ + var summaryRenderFn = this.templates.summaries[ this.model.get( 'state' ) ]; + summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown; + return summaryRenderFn( this.model.toJSON(), this ); + }, + + /** Render the external display application links */ + _renderDisplayApplications : function(){ + if( this.model.isDeletedOrPurged() ){ return ''; } + // render both old and new display apps using the same template + return [ + this.templates.displayApplications( this.model.get( 'display_apps' ), this ), + this.templates.displayApplications( this.model.get( 'display_types' ), this ) + ].join( '' ); + }, + + // ......................................................................... secondary/details actions + /** A series of links/buttons for less commonly used actions: re-run, info, etc. */ + _renderSecondaryActions : function(){ + this.debug( '_renderSecondaryActions' ); + switch( this.model.get( 'state' ) ){ + case STATES.NOT_VIEWABLE: + return []; + case STATES.OK: + case STATES.FAILED_METADATA: + case STATES.ERROR: + return [ this._renderDownloadButton(), this._renderShowParamsButton() ]; + } + return [ this._renderShowParamsButton() ]; + }, + + /** Render icon-button to show the input and output (stdout/err) for the job that created this. + * @returns {jQuery} rendered DOM + */ + _renderShowParamsButton : function(){ + // gen. safe to show in all cases + return faIconButton({ + title : _l( 'View details' ), + classes : 'dataset-params-btn', + href : this.model.urls.show_params, + target : this.linkTarget, + faIcon : 'fa-info-circle' + }); + }, + + /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this. + * @returns {jQuery} rendered DOM + */ + _renderDownloadButton : function(){ +//TODO: to (its own) template fn + // don't show anything if the data's been purged + if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; } + + // return either: a popupmenu with links to download assoc. meta files (if there are meta files) + // or a single download icon-button (if there are no meta files) + if( !_.isEmpty( this.model.get( 'meta_files' ) ) ){ + return this._renderMetaFileDownloadButton(); + } + + return $([ + '<a class="download-btn icon-btn" href="', this.model.urls.download, '" title="' + _l( 'Download' ) + '">', + '<span class="fa fa-floppy-o"></span>', + '</a>' + ].join( '' )); + }, + + /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */ + _renderMetaFileDownloadButton : function(){ + var urls = this.model.urls; + return $([ + '<div class="metafile-dropdown dropdown">', + '<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"', + ' title="' + _l( 'Download' ) + '">', + '<span class="fa fa-floppy-o"></span>', + '</a>', + '<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">', + '<li><a href="' + urls.download + '">', _l( 'Download dataset' ), '</a></li>', + _.map( this.model.get( 'meta_files' ), function( meta_file ){ + return [ + '<li><a href="', urls.meta_download + meta_file.file_type, '">', + _l( 'Download' ), ' ', meta_file.file_type, + '</a></li>' + ].join( '' ); + }).join( '\n' ), + '</ul>', + '</div>' + ].join( '\n' )); + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'DatasetListItemView(' + modelString + ')'; + } +}); + +// ............................................................................ TEMPLATES +/** underscore templates */ +DatasetListItemView.prototype.templates = (function(){ +//TODO: move to require text! plugin + + var warnings = _.extend( {}, _super.prototype.templates.warnings, { + failed_metadata : BASE_MVC.wrapTemplate([ + // failed metadata is rendered as a warning on an otherwise ok dataset view + '<% if( model.state === "failed_metadata" ){ %>', + '<div class="warningmessagesmall">', + _l( 'An error occurred setting the metadata for this dataset' ), + '</div>', + '<% } %>' + ]), + error : BASE_MVC.wrapTemplate([ + // error during index fetch - show error on dataset + '<% if( model.error ){ %>', + '<div class="errormessagesmall">', + _l( 'There was an error getting the data for this dataset' ), ': <%- model.error %>', + '</div>', + '<% } %>' + ]), + purged : BASE_MVC.wrapTemplate([ + '<% if( model.purged ){ %>', + '<div class="purged-msg warningmessagesmall">', + _l( 'This dataset has been deleted and removed from disk' ), + '</div>', + '<% } %>' + ]), + deleted : BASE_MVC.wrapTemplate([ + // deleted not purged + '<% if( model.deleted && !model.purged ){ %>', + '<div class="deleted-msg warningmessagesmall">', + _l( 'This dataset has been deleted' ), + '</div>', + '<% } %>' + ]) + + //NOTE: hidden warning is only needed for HDAs + }); + + var detailsTemplate = BASE_MVC.wrapTemplate([ + '<div class="details">', + '<div class="summary"></div>', + + '<div class="actions clear">', + '<div class="left"></div>', + '<div class="right"></div>', + '</div>', + + // do not display tags, annotation, display apps, or peek when deleted + '<% if( !dataset.deleted && !dataset.purged ){ %>', + '<div class="tags-display"></div>', + '<div class="annotation-display"></div>', + + '<div class="display-applications"></div>', + + '<% if( dataset.peek ){ %>', + '<pre class="dataset-peek"><%= dataset.peek %></pre>', + '<% } %>', + '<% } %>', + '</div>' + ], 'dataset' ); + +//TODO: still toooooooooooooo complex - rework + var summaryTemplates = {}; + summaryTemplates[ STATES.OK ] = summaryTemplates[ STATES.FAILED_METADATA ] = BASE_MVC.wrapTemplate([ + '<% if( dataset.misc_blurb ){ %>', + '<div class="blurb">', + '<span class="value"><%- dataset.misc_blurb %></span>', + '</div>', + '<% } %>', + + '<% if( dataset.data_type ){ %>', + '<div class="datatype">', + '<label class="prompt">', _l( 'format' ), '</label>', + '<span class="value"><%- dataset.data_type %></span>', + '</div>', + '<% } %>', + + '<% if( dataset.metadata_dbkey ){ %>', + '<div class="dbkey">', + '<label class="prompt">', _l( 'database' ), '</label>', + '<span class="value">', + '<%- dataset.metadata_dbkey %>', + '</span>', + '</div>', + '<% } %>', + + '<% if( dataset.misc_info ){ %>', + '<div class="info">', + '<span class="value"><%- dataset.misc_info %></span>', + '</div>', + '<% } %>' + ], 'dataset' ); + summaryTemplates[ STATES.NEW ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'This is a new dataset and not all of its data are available yet' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.NOT_VIEWABLE ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'You do not have permission to view this dataset' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.DISCARDED ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'The job creating this dataset was cancelled before completion' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'This job is waiting to run' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'This dataset is currently uploading' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.SETTING_METADATA ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'Metadata is being auto-detected' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'This job is currently running' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.PAUSED ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume' ), '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.ERROR ] = BASE_MVC.wrapTemplate([ + '<% if( !dataset.purged ){ %>', + '<div><%- dataset.misc_blurb %></div>', + '<% } %>', + '<span class="help-text">', _l( 'An error occurred with this dataset' ), ':</span>', + '<div class="job-error-text"><%- dataset.misc_info %></div>' + ], 'dataset' ); + summaryTemplates[ STATES.EMPTY ] = BASE_MVC.wrapTemplate([ + '<div>', _l( 'No data' ), ': <i><%- dataset.misc_blurb %></i></div>' + ], 'dataset' ); + summaryTemplates.unknown = BASE_MVC.wrapTemplate([ + '<div>Error: unknown dataset state: "<%- dataset.state %>"</div>' + ], 'dataset' ); + + // this is applied to both old and new style display apps + var displayApplicationsTemplate = BASE_MVC.wrapTemplate([ + '<% _.each( apps, function( app ){ %>', + '<div class="display-application">', + '<span class="display-application-location"><%- app.label %></span> ', + '<span class="display-application-links">', + '<% _.each( app.links, function( link ){ %>', + '<a target="<%= link.target %>" href="<%= link.href %>">', + '<% print( _l( link.text ) ); %>', + '</a> ', + '<% }); %>', + '</span>', + '</div>', + '<% }); %>' + ], 'apps' ); + + return _.extend( {}, _super.prototype.templates, { + warnings : warnings, + details : detailsTemplate, + summaries : summaryTemplates, + displayApplications : displayApplicationsTemplate + }); +}()); + + +// ============================================================================ + return { + DatasetListItemView : DatasetListItemView + }; +}); This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in BjoernGruening/galaxy-central-4 (pull request #454)
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f300953ad98/ Changeset: 2f300953ad98 User: jmchilton Date: 2014-08-12 15:04:01 Summary: Merged in BjoernGruening/galaxy-central-4 (pull request #454) Fixes for recent Tool Shed code cleanups Affected #: 2 files diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -239,8 +239,7 @@ tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True ) self.__ensure_can_install_repos( trans ) install_repository_manager = InstallRepositoryManager( trans.app ) - installed_tool_shed_repositories = install_repository_manager.install( trans.app, - tool_shed_url, + installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url, name, owner, changeset_revision, diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -694,7 +694,8 @@ name, owner, changeset_revision ) - installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict, + installed_tool_shed_repositories = self.__install_repositories( tool_shed_url, + repository_revision_dict, repo_info_dicts, install_options ) return installed_tool_shed_repositories @@ -788,7 +789,7 @@ # at this point because repository dependencies may have added additional repositories for installation # along with the single specified repository. encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ - initiate_repository_installation( self.app, installation_dict ) + self.initiate_repository_installation( installation_dict ) # Some repositories may have repository dependencies that are required to be installed before the # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in # the required order. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/382b019fcdc1/ Changeset: 382b019fcdc1 User: BjoernGruening Date: 2014-08-12 10:33:27 Summary: install_repository_manager do not need trans.app anymore. Affected #: 1 file diff -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f -r 382b019fcdc10b72fc77a9284d7adcfeb3170cd8 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -239,8 +239,7 @@ tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True ) self.__ensure_can_install_repos( trans ) install_repository_manager = InstallRepositoryManager( trans.app ) - installed_tool_shed_repositories = install_repository_manager.install( trans.app, - tool_shed_url, + installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url, name, owner, changeset_revision, https://bitbucket.org/galaxy/galaxy-central/commits/0df3fe8e9945/ Changeset: 0df3fe8e9945 User: BjoernGruening Date: 2014-08-12 10:38:24 Summary: First argument to __install_repositories is the Tool Shed URL (tool_shed_url) Affected #: 1 file diff -r 382b019fcdc10b72fc77a9284d7adcfeb3170cd8 -r 0df3fe8e99457c75cefeab162dac3e90f948d764 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -694,7 +694,8 @@ name, owner, changeset_revision ) - installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict, + installed_tool_shed_repositories = self.__install_repositories( tool_shed_url, + repository_revision_dict, repo_info_dicts, install_options ) return installed_tool_shed_repositories https://bitbucket.org/galaxy/galaxy-central/commits/f3c84cf5296f/ Changeset: f3c84cf5296f User: BjoernGruening Date: 2014-08-12 10:41:45 Summary: initiate_repository_installation was not updated in the recent code restructuring efforts Affected #: 1 file diff -r 0df3fe8e99457c75cefeab162dac3e90f948d764 -r f3c84cf5296f6b9bed917f71693ff32dd92188f4 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -789,7 +789,7 @@ # at this point because repository dependencies may have added additional repositories for installation # along with the single specified repository. encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ - initiate_repository_installation( self.app, installation_dict ) + self.initiate_repository_installation( installation_dict ) # Some repositories may have repository dependencies that are required to be installed before the # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in # the required order. https://bitbucket.org/galaxy/galaxy-central/commits/2f300953ad98/ Changeset: 2f300953ad98 User: jmchilton Date: 2014-08-12 15:04:01 Summary: Merged in BjoernGruening/galaxy-central-4 (pull request #454) Fixes for recent Tool Shed code cleanups Affected #: 2 files diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -239,8 +239,7 @@ tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True ) self.__ensure_can_install_repos( trans ) install_repository_manager = InstallRepositoryManager( trans.app ) - installed_tool_shed_repositories = install_repository_manager.install( trans.app, - tool_shed_url, + installed_tool_shed_repositories = install_repository_manager.install( tool_shed_url, name, owner, changeset_revision, diff -r 19309418c86450b7f39691460eb430e100883cb4 -r 2f300953ad98992a620b1f0678eb72505f8cdfc2 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -694,7 +694,8 @@ name, owner, changeset_revision ) - installed_tool_shed_repositories = self.__install_repositories( repository_revision_dict, + installed_tool_shed_repositories = self.__install_repositories( tool_shed_url, + repository_revision_dict, repo_info_dicts, install_options ) return installed_tool_shed_repositories @@ -788,7 +789,7 @@ # at this point because repository dependencies may have added additional repositories for installation # along with the single specified repository. encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ - initiate_repository_installation( self.app, installation_dict ) + self.initiate_repository_installation( installation_dict ) # Some repositories may have repository dependencies that are required to be installed before the # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in # the required order. 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: jmchilton: Fix multi-page tool help parsing.
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/19309418c864/ Changeset: 19309418c864 User: jmchilton Date: 2014-08-12 14:19:04 Summary: Fix multi-page tool help parsing. Patch thanks to Hans-Philipp Brachvogel. Affected #: 2 files diff -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f -r 19309418c86450b7f39691460eb430e100883cb4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1482,10 +1482,10 @@ help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, + self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer ), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], - encoding_errors='replace' ) ) + encoding_errors='replace' ) for x in self.help_by_page ] except: log.exception( "error in multi-page help for tool %s" % self.name ) diff -r 700560884da71e8bd3bdad6ddbe4edfde9566f7f -r 19309418c86450b7f39691460eb430e100883cb4 test/functional/tools/multi_page.xml --- a/test/functional/tools/multi_page.xml +++ b/test/functional/tools/multi_page.xml @@ -14,6 +14,10 @@ <outputs><data format="txt" name="output" /></outputs> + <help> + <page>Page 1 Help.</page> + <page>Page 2 Help.</page> + </help><tests><test><param name="p1" value="3" /> 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: natefoo: Added tag latest_2014.08.11 for changeset 52b5cc75a175
by commits-noreply＠bitbucket.org 11 Aug '14

11 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b6d2c77d8bce/ Changeset: b6d2c77d8bce Branch: stable User: natefoo Date: 2014-08-11 23:22:49 Summary: Added tag latest_2014.08.11 for changeset 52b5cc75a175 Affected #: 1 file diff -r 52b5cc75a1757eddfb94ee373193c9d8fa2ec442 -r b6d2c77d8bce44cdaba188ce949ed69f94be6bc4 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,3 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 +52b5cc75a1757eddfb94ee373193c9d8fa2ec442 latest_2014.08.11 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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