From f70df2206097ec99683e0433c597ad2b2ac2decf Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 22 Mar 2016 08:55:29 -0400 Subject: [PATCH] Upgrade content selector, add test cases --- .../scripts/mvc/form/form-parameters.js | 4 +- .../scripts/mvc/form/form-select-content.js | 347 ------------------ .../scripts/mvc/ui/ui-select-content.js | 239 ++++++++++++ .../scripts/mvc/ui/ui-select-default.js | 2 +- client/galaxy/scripts/utils/utils.js | 13 +- client/galaxy/style/less/ui.less | 8 +- static/maps/mvc/form/form-parameters.js.map | 2 +- .../maps/mvc/form/form-select-content.js.map | 2 +- static/maps/mvc/ui/ui-select-default.js.map | 2 +- static/maps/utils/utils.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 22 +- .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 10 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/bundled/login.bundled.js | 2 +- static/scripts/bundled/login.bundled.js.map | 2 +- static/scripts/mvc/form/form-parameters.js | 2 +- .../scripts/mvc/form/form-select-content.js | 2 +- static/scripts/mvc/ui/ui-select-default.js | 2 +- static/scripts/utils/utils.js | 2 +- static/style/blue/base.css | 2 +- test/qunit/test-app.js | 4 + test/qunit/tests/ui_tests.js | 77 +++- 23 files changed, 361 insertions(+), 391 deletions(-) delete mode 100644 client/galaxy/scripts/mvc/form/form-select-content.js create mode 100644 client/galaxy/scripts/mvc/ui/ui-select-content.js diff --git a/client/galaxy/scripts/mvc/form/form-parameters.js b/client/galaxy/scripts/mvc/form/form-parameters.js index 567adce09a1..02904fc3479 100644 --- a/client/galaxy/scripts/mvc/form/form-parameters.js +++ b/client/galaxy/scripts/mvc/form/form-parameters.js @@ -3,7 +3,7 @@ */ define(['utils/utils', 'mvc/ui/ui-misc', - 'mvc/form/form-select-content', + 'mvc/ui/ui-select-content', 'mvc/ui/ui-select-library', 'mvc/ui/ui-select-ftp', 'mvc/ui/ui-color-picker'], @@ -54,7 +54,7 @@ define(['utils/utils', */ _fieldData: function( input_def ) { var self = this; - return new SelectContent.View( this.app, { + return new SelectContent.View({ id : 'field-' + input_def.id, extensions : input_def.extensions, optional : input_def.optional, diff --git a/client/galaxy/scripts/mvc/form/form-select-content.js b/client/galaxy/scripts/mvc/form/form-select-content.js deleted file mode 100644 index 6f95889f6b1..00000000000 --- a/client/galaxy/scripts/mvc/form/form-select-content.js +++ /dev/null @@ -1,347 +0,0 @@ -// dependencies -define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'], function(Utils, Ui, Tabs) { -// hda/hdca content selector ui element -var View = Backbone.View.extend({ - // initialize - initialize : function(app, options) { - // link app and options - this.app = app; - this.options = options; - - // track current history elements - this.history = {}; - - - // link this - var self = this; - - // add element - this.setElement('
'); - - // list of select fieldsFormSection - this.list = {}; - - // radio button options - var radio_buttons = []; - - // identify selector type - if (options.type == 'data_collection') { - this.mode = 'collection'; - } else { - if (options.multiple) { - this.mode = 'multiple'; - } else { - this.mode = 'single'; - } - } - - // set initial state - this.current = this.mode; - this.list = {}; - - // error messages - var extensions = Utils.textify(options.extensions); - var hda_error = 'No dataset available.'; - if (extensions) { - hda_error = 'No ' + extensions + ' dataset available.'; - } - var hdca_error = 'No dataset list available.'; - if (extensions) { - hdca_error = 'No ' + extensions + ' dataset collection available.'; - } - - // add single dataset selector - if (this.mode == 'single') { - radio_buttons.push({ - icon : 'fa-file-o', - value : 'single', - tooltip : 'Single dataset' - }); - this.select_single = new Ui.Select.View({ - optional : options.optional, - error_text : hda_error, - onchange : function() { - self.trigger('change'); - } - }); - this.list['single'] = { - field: this.select_single, - type : 'hda' - }; - } - - // add multiple dataset selector - if (this.mode == 'single' || this.mode == 'multiple') { - radio_buttons.push({ - icon : 'fa-files-o', - value : 'multiple', - tooltip : 'Multiple datasets' - }); - this.select_multiple = new Ui.Select.View({ - multiple : true, - searchable : false, - optional : options.optional, - error_text : hda_error, - onchange : function() { - self.trigger('change'); - } - }); - this.list['multiple'] = { - field: this.select_multiple, - type : 'hda' - }; - } - - // add collection selector - if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') { - radio_buttons.push({ - icon : 'fa-folder-o', - value : 'collection', - tooltip : 'Dataset collection' - }); - var multiple = this.mode == 'multiple'; - this.select_collection = new Ui.Select.View({ - error_text : hdca_error, - multiple : multiple, - searchable : false, - optional : options.optional, - onchange : function() { - self.trigger('change'); - } - }); - this.list['collection'] = { - field: this.select_collection, - type : 'hdca' - }; - } - - // create button - this.button_type = new Ui.RadioButton.View({ - value : this.current, - data : radio_buttons, - onchange: function(value) { - self.current = value; - self.refresh(); - self.trigger('change'); - } - }); - - // add batch mode information - this.$batch = $(this.template_batch()); - - // number of radio buttons - var n_buttons = _.size(this.list); - - // add button to dom - var button_width = 0; - if (n_buttons > 1) { - this.$el.append(this.button_type.$el); - button_width = Math.max(0, _.size(this.list) * 35) + 'px'; - } - - // append field elements - for (var i in this.list) { - this.$el.append(this.list[i].field.$el.css({ - 'margin-left': button_width - })); - } - - // append batch message - this.$el.append(this.$batch.css({ - 'margin-left': button_width - })); - - // update options - this.update(options.data); - - // set initial value - if (this.options.value !== undefined) { - this.value(this.options.value); - } - - // refresh view - this.refresh(); - - // add change event. fires on trigger - this.on('change', function() { - if (options.onchange) { - options.onchange(self.value()); - } - }); - }, - - /** Indicate that select fields are being updated */ - wait: function() { - for (var i in this.list) { - this.list[i].field.wait(); - } - }, - - /** Indicate that the options update has been completed */ - unwait: function() { - for (var i in this.list) { - this.list[i].field.unwait(); - } - }, - - /** Update content selector */ - update: function(options) { - // update a particular select field - var self = this; - function _update(field, options) { - if (field) { - // identify available options - var select_options = []; - for (var i in options) { - var item = options[i]; - select_options.push({ - hid : item.hid, - label: item.hid + ': ' + item.name, - value: item.id - }); - // backup to local history - self.history[item.id + '_' + item.src] = item; - } - // update field - field.add( select_options, function( a, b ) { return b.hid - a.hid } ); - } - } - - // update available options - _update(this.select_single, options.hda); - _update(this.select_multiple, options.hda); - _update(this.select_collection, options.hdca); - }, - - /** Return the currently selected dataset values */ - value : function (new_value) { - // update current value - if (new_value !== undefined) { - if (new_value && new_value.values) { - try { - // create list with values - var list = []; - for (var i in new_value.values) { - list.push(new_value.values[i].id); - } - - // identify suitable select field - if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hdca') { - this.current = 'collection'; - this.select_collection.value(list); - } else { - if (this.mode == 'multiple') { - this.current = 'multiple'; - this.select_multiple.value(list); - } else { - this.current = 'single'; - this.select_single.value(list[0]); - } - } - } catch (err) { - Galaxy.emit.debug('tools-select-content::value()', 'Skipped.'); - } - } else { - for (var i in this.list) { - this.list[i].field.value(null); - } - } - } - - // refresh view - this.refresh(); - - // validate value - var id_list = this._select().value(); - if (id_list === null) { - return null; - } - - // transform into an array - if (!(id_list instanceof Array)) { - id_list = [id_list]; - } - - // check if value exists - if (id_list.length === 0) { - return null; - } - - // prepare result dict - var result = { - batch : this._batch(), - values : [] - } - - // append to dataset ids - for (var i in id_list) { - var details = this.history[id_list[i] + '_' + this.list[this.current].type]; - if (details) { - result.values.push(details); - } else { - return null; - } - } - - // sort by history ids - result.values.sort(function(a, b){ - return a.hid - b.hid; - }); - - // return - return result; - }, - - /** Refreshes data selection view */ - refresh: function() { - this.button_type.value(this.current); - for (var i in this.list) { - var $el = this.list[i].field.$el; - if (this.current == i) { - $el.show(); - } else { - $el.hide(); - } - } - if (this._batch()) { - this.$batch.show(); - } else { - this.$batch.hide(); - } - }, - - /** Assists in selecting the current field */ - _select: function() { - return this.list[this.current].field; - }, - - /** Assists in identifying the batch mode */ - _batch: function() { - if (this.current == 'collection') { - var hdca = this.history[this._select().value() + '_hdca']; - if (hdca && hdca.map_over_type) { - return true; - } - } - if (this.current != 'single') { - if (this.mode == 'single') { - return true; - } - } - return false; - }, - - /** Batch message template */ - template_batch: function() { - return '
' + - '' + - 'This is a batch mode input field. A separate job will be triggered for each dataset.' + - '
'; - } -}); - -return { - View: View -} - -}); diff --git a/client/galaxy/scripts/mvc/ui/ui-select-content.js b/client/galaxy/scripts/mvc/ui/ui-select-content.js new file mode 100644 index 00000000000..8ff685eb927 --- /dev/null +++ b/client/galaxy/scripts/mvc/ui/ui-select-content.js @@ -0,0 +1,239 @@ +define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-select-default' ], function( Utils, Ui, Select ) { + +/** List of available content selectors options */ +var Configurations = { + 'data': [ + { name: 'single', src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', batchmode: false, multiple: false }, + { name: 'multiple', src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', batchmode: true, multiple: true }, + { name: 'collection', src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', batchmode: true, multiple: false } ], + 'data_collection': [ + { name: 'collection', src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', batchmode: false, multiple: false } ], + 'data_multiple': [ + { name: 'multiple', src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', batchmode: false, multiple: true }, + { name: 'collection', src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', batchmode: false, multiple: false } ] +}; + +/** View for hda and hdca content selector ui elements */ +var View = Backbone.View.extend({ + initialize : function( options ) { + var self = this; + this.model = options && options.model || new Backbone.Model( options ); + this.setElement( $( '
' ).addClass( 'ui-select-content' ) ); + this.$batch = $( '
' ).addClass( 'ui-form-info' ) + .append( $( '' ).addClass( 'fa fa-sitemap' ) ) + .append( $( '' ).html( 'This is a batch mode input field. A separate job will be triggered for each dataset.' ) ); + + // track current history elements + this.history = {}; + + // add listeners + this.listenTo( this.model, 'change', this.render, this ); + this.listenTo( this.model, 'change:type change:multiple', this._changeType, this ); + this.listenTo( this.model, 'change:value', this._changeValue, this ); + this.listenTo( this.model, 'change:data', this._changeData, this ); + this.listenTo( this.model, 'change:wait', this._changeWait, this ); + this.render(); + + // update selectable data and initial value + this.model.get( 'value' ) !== undefined && this.model.trigger( 'change:value' ); + this.model.trigger( 'change:type' ); + this.model.trigger( 'change:value' ); + + // add change event. fires on trigger + this.on( 'change', function() { options.onchange && options.onchange( self.value() ) } ); + }, + + render: function() { + var self = this; + _.each( this.fields, function( field, i ) { + if ( self.model.get( 'current' ) == i ) { + field.$el.show(); + self.$batch[ self.config[ i ].batchmode && 'show' || 'hide' ](); + self.button_type.value( i ); + } else { + field.$el.hide(); + } + }); + }, + + /** Indicate that select fields are being updated */ + wait: function() { + this.model.set( 'wait', true ); + }, + + /** Indicate that the options update has been completed */ + unwait: function() { + this.model.set( 'wait', false ); + }, + + /** Update data representing selectable options */ + update: function( options ) { + this.model.set( 'data', options ); + }, + + /** Return the currently selected dataset values */ + value: function ( new_value ) { + new_value !== undefined && this.model.set( 'value', new_value ); + var current = this.model.get( 'current' ); + if ( this.config[ current ] ) { + var id_list = this.fields[ current ].value(); + if (id_list !== null) { + id_list = $.isArray( id_list ) ? id_list : [ id_list ]; + if ( id_list.length > 0 ) { + var result = { batch: this._batch(), values: [] }; + for ( var i in id_list ) { + var details = this.history[ id_list[ i ] + '_' + this.config[ current ].src ]; + if ( details ) { + result.values.push( details ); + } else { + Galaxy.emit.debug( 'tools-select-content::_changeValue()', 'Requested details not found for \'' + id_list[ i ] + '\'.' ); + return null; + } + } + result.values.sort( function( a, b ) { return a.hid - b.hid } ); + return result; + } + } + } else { + Galaxy.emit.debug( 'tools-select-content::_changeValue()', 'Invalid value/source \'' + new_value + '\'.' ); + } + return null; + }, + + /** Change of type */ + _changeType: function() { + var self = this; + this.model.set( 'current', 0 ); + + // identify selector type + var config_id = String( this.model.get( 'type' ) ) + ( this.model.get( 'multiple' ) ? '_multiple' : '' ); + if ( Configurations[ config_id ] ) { + this.config = Configurations[ config_id ]; + } else { + this.config = Configurations[ 'data' ]; + Galaxy.emit.debug( 'tools-select-content::_changeType()', 'Invalid configuration/type id \'' + config_id + '\'.' ); + } + + // prepare error messages + var extensions = Utils.textify( this.model.get( 'extensions' ) ); + var hda_error = extensions ? 'No ' + extensions + ' dataset available.' : 'No dataset available.'; + var hdca_error = extensions ? 'No ' + extensions + ' dataset collection available.' : 'No dataset collection available.'; + + // build views + this.fields = []; + this.button_data = []; + _.each( this.config, function( c, i ) { + self.button_data.push({ + value : i, + icon : c.icon, + tooltip : c.label + }); + self.fields.push( + new Select.View({ + optional : self.model.get( 'optional' ), + multiple : c.multiple, + searchable : !c.multiple, + error_text : c.type === 'hda' ? hda_error : hdca_error, + onchange : function() { + self.trigger( 'change' ); + } + }) + ); + }); + this.button_type = new Ui.RadioButton.View({ + value : this.model.get( 'current' ), + data : this.button_data, + onchange: function( value ) { + self.model.set( 'current', value ); + self.trigger('change'); + } + }); + + // append views + this.$el.empty(); + var button_width = 0; + if ( this.fields.length > 1 ) { + this.$el.append( this.button_type.$el ); + button_width = Math.max( 0, this.fields.length * 35 ) + 'px'; + } + _.each( this.fields, function( field ) { + self.$el.append( field.$el.css( { 'margin-left': button_width } ) ); + }); + this.$el.append( this.$batch.css( { 'margin-left': button_width } ) ); + this.model.trigger( 'change:data' ); + }, + + /** Change of wait flag */ + _changeWait: function() { + var self = this; + _.each( this.fields, function( field ) { field[ self.model.get( 'wait' ) ? 'wait' : 'unwait' ]() } ); + }, + + /** Change of available options */ + _changeData: function() { + var options = this.model.get( 'data' ); + var self = this; + var select_options = {}; + _.each( options, function( items, src ) { + select_options[ src ] = []; + _.each( items, function( item ) { + select_options[ src ].push({ + hid : item.hid, + label: item.hid + ': ' + item.name, + value: item.id + }); + self.history[ item.id + '_' + src ] = item; + }); + }); + _.each( this.config, function( c, i ) { + self.fields[ i ].add( select_options[ c.src ], function( a, b ) { return b.hid - a.hid } ); + }); + }, + + /** Change of incoming value */ + _changeValue: function () { + var new_value = this.model.get( 'value' ); + if ( new_value && new_value.values && new_value.values.length > 0 ) { + // create list with content ids + var list = []; + _.each( new_value.values, function( value ) { + list.push( value.id ); + }); + // sniff first suitable field type from config list + var src = new_value.values[ 0 ].src; + var multiple = new_value.values.length > 1; + var current = -1; + for( var i = 0; i < this.config.length; i++ ) { + var field = this.fields[ i ]; + var c = this.config[ i ]; + if ( current === -1 && c.src == src && [ multiple, true ].indexOf( c.multiple ) !== -1 ) { + this.model.set( 'current', current = i ); + field.value( list ); + } + } + } else { + _.each( this.fields, function( field ) { + field.value( null ); + }); + } + }, + + /** Assists in identifying the batch mode */ + _batch: function() { + var current = this.model.get( 'current' ); + var config = this.config[ current ]; + if ( config.src == 'hdca' && !config.multiple ) { + var hdca = this.history[ this.fields[ current ].value() + '_hdca' ]; + if ( hdca && hdca.map_over_type ) { + return true; + } + } + return config.batchmode; + } +}); + +return { + View: View +} + +}); diff --git a/client/galaxy/scripts/mvc/ui/ui-select-default.js b/client/galaxy/scripts/mvc/ui/ui-select-default.js index 6651d328e16..3f27ef0fda8 100644 --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -191,7 +191,7 @@ var View = Backbone.View.extend({ _.each( this.model.get( 'options' ), function( v ) { !_.findWhere( options, v ) && options.push( v ); }); - sorter && options.sort( sorter ); + sorter && options && options.sort( sorter ); this.update( options ); }, update: function(options) { diff --git a/client/galaxy/scripts/utils/utils.js b/client/galaxy/scripts/utils/utils.js index cc5e05aa19b..b59ff070680 100644 --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -64,13 +64,12 @@ function validate ( value ) { * Convert list to pretty string * @param{String} lst - List of strings to be converted in human readable list sentence */ -function textify(lst) { - var lst = lst.toString(); - if (lst) { - lst = lst.replace(/,/g, ', '); - var pos = lst.lastIndexOf(', '); - if (pos != -1) { - lst = lst.substr(0, pos) + ' or ' + lst.substr(pos+1); +function textify( lst ) { + if ( $.isArray( lst ) ) { + var lst = lst.toString().replace( /,/g, ', ' ); + var pos = lst.lastIndexOf( ', ' ); + if ( pos != -1 ) { + lst = lst.substr( 0, pos ) + ' or ' + lst.substr( pos + 1 ); } return lst; } diff --git a/client/galaxy/style/less/ui.less b/client/galaxy/style/less/ui.less index 98cc707b9ff..2b16dcd6425 100644 --- a/client/galaxy/style/less/ui.less +++ b/client/galaxy/style/less/ui.less @@ -286,8 +286,12 @@ } .ui-form-info { - &:extend(.toolParamHelp); - clear: both !important; + &:extend(.toolParamHelp); + clear: both !important; + i { + font-size: 1.2em; + padding: 2px 5px; + } } .ui-form-footer-info { diff --git a/static/maps/mvc/form/form-parameters.js.map b/static/maps/mvc/form/form-parameters.js.map index 2f621eea3f7..0d1cfc987a2 100644 --- a/static/maps/mvc/form/form-parameters.js.map +++ b/static/maps/mvc/form/form-parameters.js.map @@ -1 +1 @@ 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';return i+=t.title?' '+t.title+"":'',i+="
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    '},_templateRow:function(t){return'
    '+t.name+"
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    '),this.$message=a("
    "),this.$options=a(this._template(i)),this.$menu=a('
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n,s;(function(o){n=[i(6),i(18),i(5)],s=function(t,e,i){var n=o.View.extend({tagName:"div",className:"citations",render:function(){return this.$el.append("

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t=this.get("element_identifier");return["DatasetDCE(",t,")"].join("")}})),h=c.extend({model:d,initialize:function(t,e){this.debug(this+"(DatasetDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),u=a.Model.extend(e.LoggableMixin).extend(e.SearchableModelMixin).extend({_logNamespace:n,defaults:{collection_type:null,deleted:!1},collectionClass:c,initialize:function(t,e){this.debug(this+"(DatasetCollection).initialize:",t,e,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var t=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(t),this.elements},toJSON:function(){var t=a.Model.prototype.toJSON.call(this);return this.elements&&(t.elements=this.elements.toJSON()),t},inReadyState:function(){var t=this.get("populated");return this.isDeletedOrPurged()||t},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(t){return this.elements},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var t=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+t.join(",")+")"}}),p=u.extend({collectionClass:h,initialize:function(t,e){this.debug(this+"(ListDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),g=p.extend({initialize:function(t,e){this.debug(this+"(PairDatasetCollection).initialize:",t,e),p.prototype.initialize.call(this,t,e)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),f=u.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",t,")"].join("")}})),m=c.extend({model:f,initialize:function(t,e){this.debug(this+"(NestedDCDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),v=g.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedPairDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",t,")"].join("")}})),_=m.extend({model:v,initialize:function(t,e){this.debug(this+"(NestedPairDCDCECollection).initialize:",t,e),m.prototype.initialize.call(this,t,e)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),y=u.extend({collectionClass:_,initialize:function(t,e){this.debug(this+"(ListPairedDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:p,PairDatasetCollection:g,ListPairedDatasetCollection:y}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(41),i(10),i(6),i(8),i(86),i(5),i(83)],s=function(t,e,i,n,s,c){"use strict";function d(t){var e=t.toJSON(),i=f(e,{creationFn:function(e,i){return 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.discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(t){t.stopPropagation(),this.select(t)},_clickName:function(t){t.stopPropagation(),t.preventDefault();var e=([c("Enter a new name for the element"),":\n(",c("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(c("Enter a new name for the element")+":",this.element.name));e&&(this.element.name=e,this.render())},_clickDiscard:function(t){t.stopPropagation(),this.discard()},_dragstart:function(t){t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(t){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"DatasetCollectionElementView()"}}),p=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,elementViewClass:u,collectionClass:t.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for 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i=t._isElementInvalid(e);return i&&t.invalidElements.push({element:e,text:i}),!i}),this.workingElements},_isElementInvalid:function(t){return"dataset"!==t.history_content_type?c("is not a dataset"):t.state!==e.OK?c(a.contains(e.NOT_READY_STATES,t.state)?"hasn't finished running yet":"has errored, is paused, or is not accessible"):t.deleted||t.purged?c("has been deleted or purged"):null},_mangleDuplicateNames:function(){var t=900,e=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+e+")",e+=1,e>=t)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(t){},render:function(t,e){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(t,e){var i=this,n=l("
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    "}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(39),i(53),i(52),i(49)],s=function(t,e,i,n,s,l){return o.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(t,e){this.app=t},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(this.app.incompatible=!0,i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){var e=this;return new i.View(this.app,{id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,data:t.options,onchange:function(){e.app.trigger("change")}})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];a.each(t.options,function(t){i.push({label:t[0],value:t[1]})});var n=e.Select;switch(t.display){case"checkboxes":n=e.Checkbox;break;case"radio":n=e.Radio}var s=this;return new n.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){s.app.trigger("change")}})},_fieldDrilldown:function(t){if(t.is_workflow)return this._fieldText(t);var i=this;return new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,onchange:function(){i.app.trigger("change")}})},_fieldText:function(i){if(i.options)if(i.area=i.multiple,t.validate(i.value)){if(r.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}}else i.value=null;var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(t){i.onchange?i.onchange(t):o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:function(){i.app.trigger("change")}})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){var i=this;return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){i.app.trigger("change")}})},_fieldColor:function(t){var e=this;return new l({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldLibrary:function(t){var e=this;return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})},_fieldFtp:function(t){var e=this;return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(14),i(9),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("
    "),this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title_new,tooltip:"Add new "+this.options.title_new+" block",floating:"clear",onclick:function(){i.onnew&&i.onnew()}}),this.table=new e.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append(a("
    ").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(14),i(7),i(9),i(37),i(35),i(36)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d(t,i),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.options.onchange=function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")};for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$el.addClass("ui-table-section"),this.table.add(o.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,a=new h(i.app,{inputs:e});o.add({id:s,$el:a.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=r.size(t.cache),l=0;ll?t.cache[l]:t.inputs);this.app.options.sustain_repeats&&o.hideOptions();var d=new c(this.app,{label:t.title||t.name,help:t.help,field:o});this.table.add(d.$el),this.table.append(t.id)},_addSection:function(t){var e=this,s=new h(e.app,{inputs:t.inputs}),o=new i.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),a=new n.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:o}});a.append(s.$el),a.append(l("
    ").addClass("ui-form-info").html(t.help)),a.setOperation("button_visible",function(){a.collapsed?a.expand():a.collapse()}),a.on("expanded",function(){o.setIcon("fa-eye")}),a.on("collapsed",function(){o.setIcon("fa-eye-slash")}),this.app.on("expand",function(t){a.$("#"+t).length>0&&a.expand()}),t.expanded&&a.expand(),this.table.add(a.$el),this.table.append(t.id)},_addRow:function(t){var e=t.id,i=this.parameters.create(t);this.app.field_list[e]=i;var n=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,text_value:t.text_value||t.value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(27)],s=function(t,e,i){var n=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement('
    '),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),"single"!=this.mode&&"multiple"!=this.mode||(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var g in this.list)this.$el.append(this.list[g].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({hid:o.hid,label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.add(n,function(t,e){return e.hid-t.hid})}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode},template_batch:function(){return'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(9),i(7),i(38),i(34)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("
    "),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(31),i(42),i(5)],s=function(t,e,i){"use strict";function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(10),i(6),i(5)],s=function(t,e,i){"use strict";var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){ -n=[i(42),i(74),i(41),i(10),i(6),i(5)],s=function(t,e,i,n,s,l){"use strict";var c="history",d=o.Collection.extend(s.LoggableMixin).extend({_logNamespace:c,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){function t(t){return!t.inReadyState()}return new d(this.filter(t))},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new d(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new d(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new d(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new d(this.filter(t))},visibleAndUndeleted:function(){function t(t){return t.get("visible")&&!t.get("deleted")}return new d(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetch:function(t){return t=t||{},t.data=a.defaults(t.data||{},{v:"dev"}),o.Collection.prototype.fetch.call(this,t)},fetchUpdated:function(t,e){return e=e||{},e.traditional=!0,e.data=[{name:"v",value:"dev"}],t&&(e.data=e.data.concat(this._filtersFromMap({"update_time-ge":t.toISOString()}))),e.merge=!0,e.remove=!1,this.fetch(e)},_filtersFromMap:function(t){var e=[];return a.each(t,function(t,i){e.push({name:"q",value:i}),e.push({name:"qv",value:t})}),e},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){"use strict";var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a('
    '),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=t.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=t.wrapTemplate(['
    ']),o=t.wrapTemplate(['
    ']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.listenTo(t.foldout,"close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['
    ',"
    "],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(57),i(7),i(40),i(20),i(18),i(29)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){return t=t.tool_model||t,t.display?(a._buildForm(t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),void e.resolve()):void(window.location=Galaxy.root)},error:function(t,n){var s=t&&t.err_msg||"Uncaught error.";401==n.status?window.location=Galaxy.root+"user/login?"+o.param({redirect:Galaxy.root+"?tool_id="+a.options.id}):a.$el.is(":empty")?a.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("
    ").append(s.help(t));if(t.citations){var i=o("
    "),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(17),i(12),i(19)],s=function(t,e,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),l=o.Collection.extend({model:r}),c=r.extend({}),d=r.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(t){this.set("value",parseFloat(t))}}),u=r.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});r.subModelTypes={integer:d,"float":h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new l(t.map(e.inputs,function(t){var e=r.subModelTypes[t.type]||r;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new p(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(p.prototype,s);var g=(o.View.extend({}),o.Collection.extend({model:p})),f=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof f?(i=t,i.hide()):t instanceof p&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length");if(t.append(S.tool_link(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}return this.$el.append(t),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof p){var i=new w({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof f){var n=new b({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new C({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof m){var i=new x({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof p){var n=new w({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof f){var s=new b({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:t.template(['',' ',''].join("")),panel_section:t.template(['
    ','<%- name %>',"
    ",'