diff --git a/client/GruntFile.js b/client/GruntFile.js index 31f632d4de1..3065871ef90 100644 --- a/client/GruntFile.js +++ b/client/GruntFile.js @@ -11,7 +11,7 @@ module.exports = function(grunt) { uglify: { target : { - files: [{ + files: [{ expand : true, cwd : SRC_SYMLINK, src : '**/*.js', @@ -45,7 +45,7 @@ module.exports = function(grunt) { if_return : true, join_vars : true, cascade : true, - drop_console : true + // drop_console : true } } }, diff --git a/client/galaxy/scripts/mvc/collection/collection-li.js b/client/galaxy/scripts/mvc/collection/collection-li.js index 59d683f6d7c..ef236323b26 100644 --- a/client/galaxy/scripts/mvc/collection/collection-li.js +++ b/client/galaxy/scripts/mvc/collection/collection-li.js @@ -24,8 +24,9 @@ var DCListItemView = FoldoutListItemView.extend( /** override to add linkTarget */ initialize : function( attributes ){ - FoldoutListItemView.prototype.initialize.call( this, attributes ); this.linkTarget = attributes.linkTarget || '_blank'; + this.hasUser = attributes.hasUser; + FoldoutListItemView.prototype.initialize.call( this, attributes ); }, // ......................................................................... rendering @@ -51,7 +52,8 @@ var DCListItemView = FoldoutListItemView.extend( _getFoldoutPanelOptions : function(){ var options = FoldoutListItemView.prototype._getFoldoutPanelOptions.call( this ); return _.extend( options, { - linkTarget : this.linkTarget + linkTarget : this.linkTarget, + hasUser : this.hasUser }); }, diff --git a/client/galaxy/scripts/mvc/collection/collection-panel.js b/client/galaxy/scripts/mvc/collection/collection-panel.js index f96df68a4ac..e20662b7944 100644 --- a/client/galaxy/scripts/mvc/collection/collection-panel.js +++ b/client/galaxy/scripts/mvc/collection/collection-panel.js @@ -37,7 +37,6 @@ var CollectionPanel = _super.extend( this.linkTarget = attributes.linkTarget || '_blank'; this.hasUser = attributes.hasUser; - /** */ this.panelStack = []; /** */ diff --git a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js index eededbd7e83..81be7ad8367 100644 --- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js @@ -270,7 +270,8 @@ var CurrentHistoryPanel = _super.extend( this.annotationEditor.on( 'hiddenUntilActivated:shown hiddenUntilActivated:hidden', function( annotationEditor ){ panel.preferences.set( 'annotationEditorShown', annotationEditor.hidden ); - }); + } + ); }, /** Override to scroll to cached position (in prefs) after swapping */ @@ -303,7 +304,6 @@ var CurrentHistoryPanel = _super.extend( /** Override to remove any drill down panels */ addItemView : function( model, collection, options ){ -console.debug( 'addItemView:', model, collection ); var view = _super.prototype.addItemView.call( this, model, collection, options ); if( !view ){ return view; } if( this.panelStack.length ){ return this._collapseDrilldownPanel(); } diff --git a/client/galaxy/scripts/mvc/history/history-panel.js b/client/galaxy/scripts/mvc/history/history-panel.js index f10d0bb4228..2222a0924f2 100644 --- a/client/galaxy/scripts/mvc/history/history-panel.js +++ b/client/galaxy/scripts/mvc/history/history-panel.js @@ -404,7 +404,7 @@ var HistoryPanel = _super.extend( return this.showDeleted; }, - /** Handle the user toggling the deleted visibility by: + /** Handle the user toggling the hidden visibility by: * (1) storing the new value in the persistent storage * (2) re-rendering the history * @returns {Boolean} new show_hidden setting diff --git a/client/galaxy/scripts/mvc/list/list-item.js b/client/galaxy/scripts/mvc/list/list-item.js index df7f8b92926..81f55e9b03b 100644 --- a/client/galaxy/scripts/mvc/list/list-item.js +++ b/client/galaxy/scripts/mvc/list/list-item.js @@ -380,7 +380,7 @@ ListItemView.prototype.templates = (function(){ * _renderDetails does the work of creating this.details: a sub-view that shows the nested list */ var FoldoutListItemView = ListItemView.extend({ - + /** If 'foldout': show the sub-panel inside the expanded item * If 'drilldown': only fire events and handle by pub-sub * (allow the panel containing this item to attach it, hide itself, etc.) diff --git a/client/galaxy/scripts/mvc/list/list-panel.js b/client/galaxy/scripts/mvc/list/list-panel.js index a24c2356a22..343a30bc2ff 100644 --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -364,11 +364,11 @@ var ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( if( panel.views.length ){ panel._attachItems( $whereTo ); panel.$emptyMessage( $whereTo ).hide(); - + } else { panel._renderEmptyMessage( $whereTo ).show(); } - + return panel.views; }, @@ -543,7 +543,7 @@ var ListPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( /** get views based on model.id */ viewFromModelId : function( id ){ 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\ No newline at end of file diff --git a/static/maps/libs/raven.js.map b/static/maps/libs/raven.js.map index b7333038a9d..55f81382e09 100644 --- a/static/maps/libs/raven.js.map +++ b/static/maps/libs/raven.js.map @@ -1 +1 @@ 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"+b.join("")+""+e+"").text(a),e=this.model.get_metadata("column_types");return void 0!==c?d.attr("colspan",c).addClass("stringalign"):e&&b"),d=this.model.get_metadata("columns");return this.row_count%2!==0&&c.addClass("dark_row"),b.length===d?_.each(b,function(a,b){c.append(this._renderCell(a,b))},this):b.length>d?(_.each(b.slice(0,d-1),function(a,b){c.append(this._renderCell(a,b))},this),c.append(this._renderCell(b.slice(d-1).join(" "),d-1))):d>5&&b.length===d-1?(_.each(b,function(a,b){c.append(this._renderCell(a,b))},this),c.append($(""))):c.append(this._renderCell(a,0,d)),this.row_count++,c},_renderChunk:function(a){var b=this.$el.find("table");_.each(a.ck_data.split("\n"),function(a){""!==a&&b.append(this._renderRow(a))},this)}}),i=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),scroll_elt=_.find(this.$el.parents(),function(a){return"auto"===$(a).css("overflow")}),scroll_elt||(scroll_elt=window),this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),j=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:a.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),k=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(a){function b(a,b){for(var c=0;c").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var a=$("").attr({id:"content_table",cellpadding:0});this.$el.append(a);var b=this.model.get_metadata("column_names"),c=$("").appendTo(a),d=$("").appendTo(c);if(b)d.append("");else for(var e=1;e<=this.model.get_metadata("columns");e++)d.append("");var f=this,g=this.model.get("first_data_chunk");g?this._renderChunk(g):$.when(f.model.get_next_chunk()).then(function(a){f._renderChunk(a)}),this.scroll_elt.scroll(function(){f.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(a,b,c){var d=$("
"+b.join("")+""+e+"").text(a),e=this.model.get_metadata("column_types");return void 0!==c?d.attr("colspan",c).addClass("stringalign"):e&&b"),d=this.model.get_metadata("columns");return this.row_count%2!==0&&c.addClass("dark_row"),b.length===d?_.each(b,function(a,b){c.append(this._renderCell(a,b))},this):b.length>d?(_.each(b.slice(0,d-1),function(a,b){c.append(this._renderCell(a,b))},this),c.append(this._renderCell(b.slice(d-1).join(" "),d-1))):d>5&&b.length===d-1?(_.each(b,function(a,b){c.append(this._renderCell(a,b))},this),c.append($(""))):c.append(this._renderCell(a,0,d)),this.row_count++,c},_renderChunk:function(a){var b=this.$el.find("table");_.each(a.ck_data.split("\n"),function(a){""!==a&&b.append(this._renderRow(a))},this)}}),i=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),scroll_elt=_.find(this.$el.parents(),function(a){return"auto"===$(a).css("overflow")}),scroll_elt||(scroll_elt=window),this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),j=h.extend({initialize:function(a){h.prototype.initialize.call(this,a),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:a.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),k=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(a){function b(a,b){for(var c=0;c");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("
").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(a.id&&!this.list[a.id]){this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()}},del:function(a){if(this.list[a]){this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()}},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}}); +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-portlet","mvc/ui/ui-misc"],function(a,b,c,d){var e=Backbone.View.extend({optionsDefault:{title:"Section",max:null,min:null},initialize:function(c){this.options=a.merge(c,this.optionsDefault),this.setElement("
");this.button_new=new d.ButtonIcon({icon:"fa-plus",title:"Insert "+c.title_new,tooltip:"Add new "+c.title_new+" block",floating:"clear",onclick:function(){c.onnew&&c.onnew()}}),this.table=new b.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append($("
").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(a){if(!a.id||this.list[a.id])return void console.debug("form-repeat::add - Duplicate repeat block id.");this.n++;var b=new d.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){a.ondel&&a.ondel()}}),e=new c.View({id:a.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:b}});e.append(a.$el),e.$el.addClass("section-row"),this.list[a.id]=e,this.table.add(e.$el),this.table.append("row_"+a.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(a){if(!this.list[a])return void console.debug("form-repeat::del - Invalid repeat block id.");this.n--;var b=this.table.get("row_"+a);b.remove(),delete this.list[a],this.button_new.enable(),this._refresh()},_refresh:function(){var a=0;for(var b in this.list){var c=this.list[b];c.title(++a+": "+this.options.title),this.n>this.options.min?c.showOperation("button_delete"):c.hideOperation("button_delete")}}});return{View:e}}); //# sourceMappingURL=../../../maps/mvc/form/form-repeat.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-select-content.js b/static/scripts/mvc/form/form-select-content.js index c0d476aa1bb..d695833fc70 100644 --- a/static/scripts/mvc/form/form-select-content.js +++ b/static/scripts/mvc/form/form-select-content.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){history={};var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d;var e=this;this.setElement('
'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var c=[];for(var d in b){var e=b[d];c.push({label:e.hid+": "+e.name,value:e.id}),history[e.id+"_"+e.src]=e}a.update(c)}}b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
This is a batch mode input field. A separate job will be triggered for each dataset.
'}});return{View:c}}); +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(a,b){history={};var c=Backbone.View.extend({initialize:function(c,d){this.app=c,this.options=d;var e=this;this.setElement('
'),this.list={};var f=[];this.mode="data_collection"==d.type?"collection":d.multiple?"multiple":"single",this.current=this.mode,this.list={};var g=a.textify(d.extensions),h="No dataset available.";g&&(h="No "+g+" dataset available.");var i="No dataset list available.";g&&(i="No "+g+" dataset collection available."),"single"==this.mode&&(f.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new b.Select.View({optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(f.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new b.Select.View({multiple:!0,searchable:!1,optional:d.optional,error_text:h,onchange:function(){e.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),("single"==this.mode||"multiple"==this.mode||"collection"==this.mode)&&(f.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"}),this.select_collection=new b.Select.View({error_text:i,optional:d.optional,onchange:function(){e.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}),this.button_type=new b.RadioButton.View({value:this.current,data:f,onchange:function(a){e.current=a,e.refresh(),e.trigger("change")}}),this.$batch=$(this.template_batch());var j=_.size(this.list),k=0;j>1&&(this.$el.append(this.button_type.$el),k=Math.max(0,35*_.size(this.list))+"px");for(var l in this.list)this.$el.append(this.list[l].field.$el.css({"margin-left":k}));this.$el.append(this.$batch.css({"margin-left":k})),this.update(d.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){d.onchange&&d.onchange(e.value())})},wait:function(){for(var a in this.list)this.list[a].field.wait()},unwait:function(){for(var a in this.list)this.list[a].field.unwait()},update:function(a){function b(a,b){if(a){var c=[];for(var d in b){var e=b[d];c.push({label:e.hid+": "+e.name,value:e.id}),history[e.id+"_"+e.src]=e}a.update(c)}}b(this.select_single,a.hda),b(this.select_multiple,a.hda),b(this.select_collection,a.hdca)},value:function(a){if(void 0!==a)if(a&&a.values)try{var b=[];for(var c in a.values)b.push(a.values[c].id);a&&a.values.length>0&&"hdca"==a.values[0].src?(this.current="collection",this.select_collection.value(b[0])):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(b)):(this.current="single",this.select_single.value(b[0]))}catch(d){console.debug("tools-select-content::value() - Skipped.")}else for(var c in this.list)this.list[c].field.value(null);this.refresh();var e=this._select().value();if(null===e)return null;if(e instanceof Array||(e=[e]),0===e.length)return null;var f={batch:this._batch(),values:[]};for(var c in e){var g=history[e[c]+"_"+this.list[this.current].type];if(!g)return null;f.values.push(g)}return f.values.sort(function(a,b){return a.hid-b.hid}),f},refresh:function(){this.button_type.value(this.current);for(var a in this.list){var b=this.list[a].field.$el;this.current==a?b.show():b.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var a=history[this._select().value()+"_hdca"];if(a&&a.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
This is a batch mode input field. A separate job will be triggered for each dataset.
'}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/form/form-select-content.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-view.js b/static/scripts/mvc/form/form-view.js index 7d9d871b040..44340dd8e60 100644 --- a/static/scripts/mvc/form/form-view.js +++ b/static/scripts/mvc/form/form-view.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("
"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change")}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message})}})}); +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("
"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),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}),console.debug("tools-form-base::initialize() - Completed.")}})}); //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map \ No newline at end of file diff --git a/static/scripts/mvc/history/history-panel-edit.js b/static/scripts/mvc/history/history-panel-edit.js index 0dae7fc3624..6d3bb259252 100644 --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -1,2 +1,2 @@ -define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(a,b,c,d,e,f,g,h,i,j,k){var l=a.HistoryPanel,m=l.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:f.HDCAListItemEdit,initialize:function(a){a=a||{},l.prototype.initialize.call(this,a),this.tagsEditor=null,this.annotationEditor=null,this.purgeAllowed=a.purgeAllowed||!1,this.annotationEditorShown=a.annotationEditorShown||!1,this.tagsEditorShown=a.tagsEditorShown||!1},_setUpListeners:function(){var a=this;l.prototype._setUpListeners.call(a),a.on("drop",function(b,c){a.dataDropped(c),a.dropTargetOff()}),a.on("view:attached view:removed",function(){a._renderCounts()},a)},_setUpCollectionListeners:function(){return l.prototype._setUpCollectionListeners.call(this),this.collection.on("change:deleted",this._handleHdaDeletionChange,this),this.collection.on("change:visible",this._handleHdaVisibleChange,this),this.collection.on("change:purged",function(){this.model.fetch()},this),this},_setUpModelListeners:function(){return l.prototype._setUpModelListeners.call(this),this.model.on("change:nice_size",this.updateHistoryDiskSize,this),this},_buildNewRender:function(){var a=l.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")&&(this._renderTags(a),this._renderAnnotation(a)),a):a},renderItems:function(a){var b=l.prototype.renderItems.call(this,a);return this._renderCounts(a),b},_renderCounts:function(a){function b(a,b){return['',b,""].join("")}a=a||this.$el;var c=this.collection.where({deleted:!0}),d=this.collection.where({visible:!1}),e=[];return this.views.length&&e.push([this.views.length,k("shown")].join(" ")),c.length&&e.push(this.showDeleted?b("toggle-deleted-link",k("hide deleted")):[c.length,b("toggle-deleted-link",k("deleted"))].join(" ")),d.length&&e.push(this.showHidden?b("toggle-hidden-link",k("hide hidden")):[d.length,b("toggle-hidden-link",k("hidden"))].join(" ")),a.find("> .controls .subtitle").html(e.join(", "))},_renderTags:function(a){var b=this;this.tagsEditor=new g.TagsEditor({model:this.model,el:a.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDATagEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDATagEditors(!1,b.fxSpeed)},$activator:i({title:k("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".controls .actions"))})},_renderAnnotation:function(a){var b=this;this.annotationEditor=new h.AnnotationEditor({model:this.model,el:a.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDAAnnotationEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDAAnnotationEditors(!1,b.fxSpeed)},$activator:i({title:k("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".controls .actions"))})},_setUpBehaviors:function(a){if(a=a||this.$el,l.prototype._setUpBehaviors.call(this,a),this.model&&Galaxy.currUser&&!Galaxy.currUser.isAnonymous()&&Galaxy.currUser.id===this.model.get("user_id")){var b=this,c=".controls .name";a.find(c).attr("title",k("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(a){var d=b.model.get("name");a&&a!==d?(b.$el.find(c).text(a),b.model.save({name:a}).fail(function(){b.$el.find(c).text(b.model.previous("name"))})):b.$el.find(c).text(d)}})}},multiselectActions:function(){var a=this,b=[{html:k("Hide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.hide;a.getSelectedModels().ajaxQueue(b)}},{html:k("Unhide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.unhide;a.getSelectedModels().ajaxQueue(b)}},{html:k("Delete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.delete;a.getSelectedModels().ajaxQueue(b)}},{html:k("Undelete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.undelete;a.getSelectedModels().ajaxQueue(b)}}];return a.purgeAllowed&&b.push({html:k("Permanently delete datasets"),func:function(){if(confirm(k("This will permanently remove the data in your datasets. Are you sure?"))){var b=d.HistoryDatasetAssociation.prototype.purge;a.getSelectedModels().ajaxQueue(b)}}}),b.push({html:k("Build Dataset List"),func:function(){a.getSelectedModels().promoteToHistoryDatasetCollection(a.model,"list")}}),b.push({html:k("Build Dataset Pair"),func:function(){a.getSelectedModels().promoteToHistoryDatasetCollection(a.model,"paired")}}),b.push({html:k("Build List of Dataset Pairs"),func:_.bind(a._showPairedCollectionModal,a)}),b},_showPairedCollectionModal:function(){var a=this,b=a.getSelectedModels().toJSON().filter(function(a){return"dataset"===a.history_content_type&&a.state===c.OK});b.length?require(["mvc/collection/paired-collection-creator"],function(c){window.creator=c.pairedCollectionCreatorModal(b,{historyId:a.model.id})}):Galaxy.modal.show({title:k("No valid datasets were selected"),body:k(["Use the checkboxes at the left of the dataset names to select them.","Selected datasets should be error-free and should have completed running."].join(" ")),buttons:{Ok:function(){Galaxy.modal.hide()}},closing_events:!0})},_attachItems:function(a){return this.$list(a).append(this.views.reverse().map(function(a){return a.$el})),this},_attachView:function(a){var b=this;b.views.unshift(a),b.$list().prepend(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},_getItemViewOptions:function(a){var b=l.prototype._getItemViewOptions.call(this,a);return _.extend(b,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),b},_handleHdaDeletionChange:function(a){a.get("deleted")&&!this.showDeleted&&this.removeItemView(a),this._renderCounts()},_handleHdaVisibleChange:function(a){a.hidden()&&!this.storage.showHidden&&this.removeItemView(a),this._renderCounts()},toggleHDATagEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.tagsEditor&&b.tagsEditor.toggle.apply(b.tagsEditor,a)})},toggleHDAAnnotationEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.annotationEditor&&b.annotationEditor.toggle.apply(b.annotationEditor,a)})},events:_.extend(_.clone(l.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(){this.toggleShowDeleted()},"click .toggle-hidden-link":function(){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var a={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)},b=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),b]);for(var c in a)a.hasOwnProperty(c)&&b.on(c,a[c]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),$("
").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),$("
").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(k("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var a=this.$(".history-drop-target").get(0);for(var b in this._dropHandlers)this._dropHandlers.hasOwnProperty(b)&&a.off(b,this._dropHandlers[b]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(a){a.preventDefault(),a.stopPropagation()},dragleave:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(a){a.preventDefault(),a.dataTransfer.dropEffect="move";var b=this,c=a.dataTransfer.getData("text");try{c=JSON.parse(c)}catch(d){this.warn("error parsing JSON from drop:",c)}return this.trigger("droptarget:drop",a,c,b),!1},dataDropped:function(a){var b=this;return _.isObject(a)&&"HistoryDatasetAssociation"===a.model_class&&a.id?b.model.contents.copy(a.id):jQuery.when()},toString:function(){return"HistoryPanelEdit("+(this.model?this.model.get("name"):"")+")"}});return{HistoryPanelEdit:m}}); +define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","ui/fa-icon-button","mvc/ui/popup-menu","utils/localization"],function(a,b,c,d,e,f,g,h,i,j,k){var l=a.HistoryPanel,m=l.extend({HDAViewClass:e.HDAListItemEdit,HDCAViewClass:f.HDCAListItemEdit,initialize:function(a){a=a||{},l.prototype.initialize.call(this,a),this.tagsEditor=null,this.annotationEditor=null,this.purgeAllowed=a.purgeAllowed||!1,this.annotationEditorShown=a.annotationEditorShown||!1,this.tagsEditorShown=a.tagsEditorShown||!1},_setUpListeners:function(){var a=this;l.prototype._setUpListeners.call(a),a.on("drop",function(b,c){a.dataDropped(c),a.dropTargetOff()}),a.on("view:attached view:removed",function(){a._renderCounts()},a)},_setUpCollectionListeners:function(){return l.prototype._setUpCollectionListeners.call(this),this.collection.on("change:deleted",this._handleHdaDeletionChange,this),this.collection.on("change:visible",this._handleHdaVisibleChange,this),this.collection.on("change:purged",function(){this.model.fetch()},this),this},_setUpModelListeners:function(){return l.prototype._setUpModelListeners.call(this),this.model.on("change:nice_size",this.updateHistoryDiskSize,this),this},_buildNewRender:function(){var a=l.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")&&(this._renderTags(a),this._renderAnnotation(a)),a):a},renderItems:function(a){var b=l.prototype.renderItems.call(this,a);return this._renderCounts(a),b},_renderCounts:function(a){function b(a,b){return['',b,""].join("")}a=a||this.$el;var c=this.collection.where({deleted:!0}),d=this.collection.where({visible:!1}),e=[];return this.views.length&&e.push([this.views.length,k("shown")].join(" ")),c.length&&e.push(this.showDeleted?b("toggle-deleted-link",k("hide deleted")):[c.length,b("toggle-deleted-link",k("deleted"))].join(" ")),d.length&&e.push(this.showHidden?b("toggle-hidden-link",k("hide hidden")):[d.length,b("toggle-hidden-link",k("hidden"))].join(" ")),a.find("> .controls .subtitle").html(e.join(", "))},_renderTags:function(a){var b=this;this.tagsEditor=new g.TagsEditor({model:this.model,el:a.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDATagEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDATagEditors(!1,b.fxSpeed)},$activator:i({title:k("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(a.find(".controls .actions"))})},_renderAnnotation:function(a){var b=this;this.annotationEditor=new h.AnnotationEditor({model:this.model,el:a.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){b.toggleHDAAnnotationEditors(!0,b.fxSpeed)},onhide:function(){b.toggleHDAAnnotationEditors(!1,b.fxSpeed)},$activator:i({title:k("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(a.find(".controls .actions"))})},_setUpBehaviors:function(a){if(a=a||this.$el,l.prototype._setUpBehaviors.call(this,a),this.model&&Galaxy.currUser&&!Galaxy.currUser.isAnonymous()&&Galaxy.currUser.id===this.model.get("user_id")){var b=this,c=".controls .name";a.find(c).attr("title",k("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(a){var d=b.model.get("name");a&&a!==d?(b.$el.find(c).text(a),b.model.save({name:a}).fail(function(){b.$el.find(c).text(b.model.previous("name"))})):b.$el.find(c).text(d)}})}},multiselectActions:function(){var a=this,b=[{html:k("Hide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.hide;a.getSelectedModels().ajaxQueue(b)}},{html:k("Unhide datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.unhide;a.getSelectedModels().ajaxQueue(b)}},{html:k("Delete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.delete;a.getSelectedModels().ajaxQueue(b)}},{html:k("Undelete datasets"),func:function(){var b=d.HistoryDatasetAssociation.prototype.undelete;a.getSelectedModels().ajaxQueue(b)}}];return a.purgeAllowed&&b.push({html:k("Permanently delete datasets"),func:function(){if(confirm(k("This will permanently remove the data in your datasets. Are you sure?"))){var b=d.HistoryDatasetAssociation.prototype.purge;a.getSelectedModels().ajaxQueue(b)}}}),b.push({html:k("Build Dataset List"),func:function(){a.getSelectedModels().promoteToHistoryDatasetCollection(a.model,"list")}}),b.push({html:k("Build Dataset Pair"),func:function(){a.getSelectedModels().promoteToHistoryDatasetCollection(a.model,"paired")}}),b.push({html:k("Build List of Dataset Pairs"),func:_.bind(a._showPairedCollectionModal,a)}),b},_showPairedCollectionModal:function(){var a=this,b=a.getSelectedModels().toJSON().filter(function(a){return"dataset"===a.history_content_type&&a.state===c.OK});b.length?require(["mvc/collection/paired-collection-creator"],function(c){window.creator=c.pairedCollectionCreatorModal(b,{historyId:a.model.id})}):Galaxy.modal.show({title:k("No valid datasets were selected"),body:k(["Use the checkboxes at the left of the dataset names to select them.","Selected datasets should be error-free and should have completed running."].join(" ")),buttons:{Ok:function(){Galaxy.modal.hide()}},closing_events:!0})},_attachItems:function(a){return this.$list(a).append(this.views.reverse().map(function(a){return a.$el})),this},_attachView:function(a){var b=this;b.views.unshift(a),b.$list().prepend(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},_getItemViewOptions:function(a){var b=l.prototype._getItemViewOptions.call(this,a);return _.extend(b,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),b},_handleHdaDeletionChange:function(a){a.get("deleted")&&!this.showDeleted&&this.removeItemView(a),this._renderCounts()},_handleHdaVisibleChange:function(a){a.hidden()&&!this.storage.showHidden&&this.removeItemView(a),this._renderCounts()},toggleHDATagEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.tagsEditor&&b.tagsEditor.toggle.apply(b.tagsEditor,a)})},toggleHDAAnnotationEditors:function(){var a=Array.prototype.slice.call(arguments,1);_.each(this.views,function(b){b.annotationEditor&&b.annotationEditor.toggle.apply(b.annotationEditor,a)})},events:_.extend(_.clone(l.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(){this.toggleShowDeleted()},"click .toggle-hidden-link":function(){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var a={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)},b=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),b]);for(var c in a)a.hasOwnProperty(c)&&b.on(c,a[c]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),$("
").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),$("
").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(k("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var a=this.$(".history-drop-target").get(0);for(var b in this._dropHandlers)this._dropHandlers.hasOwnProperty(b)&&(console.debug(b,this._dropHandlers[b]),a.off(b,this._dropHandlers[b]));return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(a){a.preventDefault(),a.stopPropagation()},dragleave:function(a){a.preventDefault(),a.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(a){a.preventDefault(),a.dataTransfer.dropEffect="move";var b=this,c=a.dataTransfer.getData("text");try{c=JSON.parse(c)}catch(d){this.warn("error parsing JSON from drop:",c)}return this.trigger("droptarget:drop",a,c,b),!1},dataDropped:function(a){var b=this;return _.isObject(a)&&"HistoryDatasetAssociation"===a.model_class&&a.id?b.model.contents.copy(a.id):jQuery.when()},toString:function(){return"HistoryPanelEdit("+(this.model?this.model.get("name"):"")+")"}});return{HistoryPanelEdit:m}}); //# sourceMappingURL=../../../maps/mvc/history/history-panel-edit.js.map \ No newline at end of file diff --git a/static/scripts/mvc/job/job-model.js b/static/scripts/mvc/job/job-model.js index fb4e6186f95..0d227e1a694 100644 --- a/static/scripts/mvc/job/job-model.js +++ b/static/scripts/mvc/job/job-model.js @@ -1,2 +1,2 @@ -define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}}); +define(["mvc/history/history-contents","mvc/dataset/states","utils/ajax-queue","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=d.SearchableModelMixin,f=Backbone.Model.extend(d.LoggableMixin).extend(d.mixin(e,{defaults:{model_class:"Job",tool_id:null,exit_code:null,inputs:{},outputs:{},params:{},create_time:null,update_time:null,state:b.NEW},parse:function(a){return a.params=this.parseParams(a.params),a},parseParams:function(a){var b={};return _.each(a,function(a,c){b[c]=JSON.parse(a)}),b},initialize:function(b,c){this.debug(this+"(Job).initialize",b,c),this.set("params",this.parseParams(this.get("params")),{silent:!0}),this.outputCollection=b.outputCollection||new a.HistoryContents([]),this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(a,b){this.log(this+" has changed state:",a,b),this.inReadyState()&&this.trigger("state:ready",a,b,this.previous("state"))})},inReadyState:function(){return _.contains(b.READY_STATES,this.get("state"))},hasDetails:function(){return!_.isEmpty(this.get("outputs"))},urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",toString:function(){return["Job(",this.get("id"),":",this.get("tool_id"),")"].join("")}})),g=Backbone.Collection.extend(d.LoggableMixin).extend({model:f,urlRoot:(window.galaxy_config&&galaxy_config.root?galaxy_config.root:"/")+"api/jobs",url:function(){return this.urlRoot},intialize:function(a,b){console.debug(a,b)},ids:function(){return this.map(function(a){return a.get("id")})},notReady:function(){return this.filter(function(a){return!a.inReadyState()})},haveDetails:function(){return this.all(function(a){return a.hasDetails()})},queueDetailFetching:function(){var a=this,b=new c.AjaxQueue(this.map(function(a){return function(){return a.fetch({silent:!0})}}));return b.done(function(){a.trigger("details-loaded")}),b},matches:function(a){return this.filter(function(b){return b.matches(a)})},toString:function(){return["JobCollection(",this.length,")"].join("")}},{fromHistory:function(a){console.debug(this);var b=this,c=new b([]);return c.fetch({data:{history_id:a}}).done(function(){window.queue=c.queueDetailFetching()}),c}});return{Job:f,JobCollection:g}}); //# sourceMappingURL=../../../maps/mvc/job/job-model.js.map \ No newline at end of file diff --git a/static/scripts/mvc/library/library-foldertoolbar-view.js b/static/scripts/mvc/library/library-foldertoolbar-view.js index d95e8b51571..4bb4b5bf76e 100644 --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -1,3 +1,3 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+"/"+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&c.push(this.parentElement.parentElement.id)});for(var e=[],f=c.length-1;f>=0;f--){var g=c[f],h=new d.HistoryItem;h.url=h.urlRoot+a+"/contents",h.content=g,h.source="library",e.push(h)}this.initChainCallControl({length:e.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(e,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&c.push(this.parentElement.parentElement.id)});var d="/api/libraries/datasets/download/"+b,e={ld_ids:c};this.processDownload(d,e,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+=''}),$('
'+e+"
").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.idb.id?1:a.id=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}))}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url="/api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;g--){var h=new d.Item({id:e[g]});f.push(h)}this.options.chain_call_control.total_number=e.length,this.chainCallDeletingHdas(f)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('
'),tmpl_array.push('
'),tmpl_array.push(" DATA LIBRARIES"),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push(' "),tmpl_array.push("<% } else { %>"),tmpl_array.push(' '),tmpl_array.push("<% } %>"),tmpl_array.push(' '),tmpl_array.push(' "),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(" "),tmpl_array.push("
"),tmpl_array.push('
'),tmpl_array.push("
"),tmpl_array.push("
"),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('
'),tmpl_array.push("

Library name:

"),tmpl_array.push('

<%- library.get("name") %>

'),tmpl_array.push("

Library description:

"),tmpl_array.push('

<%- library.get("description") %>

'),tmpl_array.push("

Library synopsis:

"),tmpl_array.push('

<%- library.get("synopsis") %>

'),tmpl_array.push("
"),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('
'),tmpl_array.push("
"),tmpl_array.push(''),tmpl_array.push(''),tmpl_array.push("
"),tmpl_array.push("
"),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push(''),a.push("Select history: "),a.push('"),a.push(""),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('
'),a.push("Importing selected datasets to history <%= _.escape(history_name) %>"),a.push("
"),a.push('
'),a.push('
'),a.push(' 0% Complete'),a.push("
"),a.push("
"),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('
'),a.push("Adding selected datasets to library folder <%= _.escape(folder_name) %>"),a.push("
"),a.push('
'),a.push('
'),a.push(' 0% Complete'),a.push("
"),a.push("
"),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('
'),a.push("
"),a.push('
'),a.push('
'),a.push(' 0% Complete'),a.push("
"),a.push("
"),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('
'),a.push('
All files you select will be imported into the current folder.
'),a.push(''),a.push('
'),a.push('"),a.push('"),a.push("
"),a.push('
'),a.push('"),a.push('"),a.push("
"),a.push('
'),a.push("
"),a.push("
"),a.push("

You can set extension type and genome for all imported datasets at once:

"),a.push("
"),a.push('Type: '),a.push(' Genome: '),a.push("
"),a.push("
"),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('
'),a.push('
All files within the given folders and their subfolders will be imported into the current folder.
'),a.push('
'),a.push('"),a.push('"),a.push("
"),a.push(''),a.push("
"),a.push("

You can set extension type and genome for all imported datasets at once:

"),a.push("
"),a.push('Type: '),a.push(' Genome: '),a.push("
"),a.push("
"),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('
'),a.push('
'),a.push("Select history: "),a.push('"),a.push("
"),a.push("
"),a.push('
'),a.push("
"),a.push("
"),_.template(a.join(""))},templateHistoryContents:function(){var a=[];return a.push("Choose the datasets to import:"),a.push("
    "),a.push(" <% _.each(history_contents, function(history_item) { %>"),a.push('
  • ">'),a.push(' <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'),a.push("
    • "),a.push(" <% }); %>"),a.push("
"),_.template(a.join(""))},templatePaginator:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>"),tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>"),tmpl_array.push('
    • '),tmpl_array.push('
  • <% print( show_page - 1 ) %>
    • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
    • '),tmpl_array.push('
  • <% print( show_page - 1 ) %>
    • '),tmpl_array.push(" <% } %>"),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
    • '), -tmpl_array.push('
  • <% print( show_page - 1 ) %>
    • '),tmpl_array.push(" <% } %>"),tmpl_array.push('
  • '),tmpl_array.push(' <% print( show_page ) %>'),tmpl_array.push("
    • "),tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>"),tmpl_array.push('
  • <% print( show_page + 1 ) %>
    • '),tmpl_array.push('
    • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
  • <% print( show_page + 1 ) %>
    • '),tmpl_array.push('
    • '),tmpl_array.push(" <% } %>"),tmpl_array.push("
"),tmpl_array.push(" "),tmpl_array.push(' showing <%- items_shown %> of <%- total_items_count %> items'),tmpl_array.push(" "),_.template(tmpl_array.join(""))}});return{FolderToolbarView:f}}); +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(a,b,c,d,e){var f=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:!1,contains_file:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.defaults(a||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(a){this.options=_.extend(this.options,a);var b=this.templateToolBar(),c={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.currUser&&(c.is_admin=Galaxy.currUser.isAdmin(),c.is_anonym=Galaxy.currUser.isAnonymous(),(null!==Galaxy.config.user_library_import_dir||Galaxy.config.allow_library_path_paste!==!1||null!==Galaxy.config.library_import_dir)&&(c.mutiple_add_dataset_options=!0)),this.$el.html(b(c))},renderPaginator:function(a){this.options=_.extend(this.options,a);var b=this.templatePaginator();this.$el.find("#folder_paginator").html(b({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(a){this.options=_.extend(this.options,a),this.options.can_add_library_item===!0?$(".add-library-items").show():$(".add-library-items").hide(),this.options.contains_file===!0&&Galaxy.currUser?Galaxy.currUser.isAnonymous()?($(".dataset-manipulation").show(),$(".logged-dataset-manipulation").hide()):($(".logged-dataset-manipulation").show(),$(".dataset-manipulation").show()):($(".logged-dataset-manipulation").hide(),$(".dataset-manipulation").hide()),this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(a){a.preventDefault(),a.stopPropagation();var b=this,c=this.templateNewFolderInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Create New Folder",body:c(),buttons:{Create:function(){b.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var a=this.serialize_new_folder();if(this.validate_new_folder(a)){var b=new d.FolderAsModel;url_items=Backbone.history.fragment.split("/"),current_folder_id=url_items[url_items.length-1],b.url=b.urlRoot+"/"+current_folder_id,b.save(a,{success:function(a){Galaxy.modal.hide(),c.success("Folder created."),a.set({type:"folder"}),Galaxy.libraries.folderListView.collection.add(a)},error:function(a,b){Galaxy.modal.hide(),c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}else c.error("Folder's name is missing.");return!1},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(a){return""!==a.name},modalBulkImport:function(){var a=$("#folder_table").find(":checked");0===a.length?c.info("You must select some datasets first."):this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(a){var b=this;this.histories=new d.GalaxyHistories,this.histories.fetch({success:function(){a(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var a=$("select[name=dataset_import_bulk] option:selected").val(),b=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=a;var c=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&c.push(this.parentElement.parentElement.id)});for(var e=[],f=c.length-1;f>=0;f--){var g=c[f],h=new d.HistoryItem;h.url=h.urlRoot+a+"/contents",h.content=g,h.source="library",e.push(h)}this.initChainCallControl({length:e.length,action:"to_history",history_name:b}),jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+a),this.chainCallImportingIntoHistory(e,b)},updateProgress:function(){this.progress+=this.progressStep,$(".progress-bar-import").width(Math.round(this.progress)+"%"),txt_representation=Math.round(this.progress)+"% Complete",$(".completion_span").text(txt_representation)},download:function(a,b){var c=[];$("#folder_table").find(":checked").each(function(){""!==this.parentElement.parentElement.id&&c.push(this.parentElement.parentElement.id)});var d="/api/libraries/datasets/download/"+b,e={ld_ids:c};this.processDownload(d,e,"get")},processDownload:function(a,b,d){if(a&&b){b="string"==typeof b?b:$.param(b);var e="";$.each(b.split("&"),function(){var a=this.split("=");e+=''}),$('
'+e+"
").appendTo("body").submit().remove(),c.info("Your download will begin soon.")}else c.error("An error occurred.")},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(a){a.modal=Galaxy.modal;var b=a.templateAddFilesFromHistory(),d=a.options.full_path[a.options.full_path.length-1][1];a.modal.show({closing_events:!0,title:"Adding datasets from your history to folder "+d,body:b({histories:a.histories.models}),buttons:{Add:function(){a.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}}),a.histories.models.length>0?(a.fetchAndDisplayHistoryContents(a.histories.models[0].id),$("#dataset_add_bulk").change(function(b){a.fetchAndDisplayHistoryContents(b.target.value)})):c.error("An error ocurred.")})},importFilesFromPathModal:function(){var a=this;this.modal=Galaxy.modal;var b=this.templateImportPathModal();this.modal.show({closing_events:!0,title:"Please enter paths to import",body:b({}),buttons:{Import:function(){a.importFromPathsClicked(a)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+a.id,{trigger:!0})}}),this.renderSelectBoxes()},fetchExtAndGenomes:function(){var a=this;b.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.idb.id?1:a.id=0;h--)trimmed=f[h].trim(),0!==trimmed.length&&g.push(trimmed);this.initChainCallControl({length:g.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:g,preserve_dirs:a,link_data:b,source:"admin_path",file_type:d,dbkey:e})}else c.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(a){var b;switch(a.action){case"adding_datasets":b=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b({folder_name:this.options.folder_name}));break;case"deleting_datasets":b=this.templateDeletingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(b());break;case"to_history":b=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(b({history_name:a.history_name}));break;default:console.error("Wrong action specified.")}this.progress=0,this.progressStep=100/a.length,this.options.chain_call_control.total_number=a.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(a,b){var d=$("#jstree_browser").jstree().get_selected(!0),e=this.modal.$el.find(".preserve-checkbox").is(":checked"),f=this.modal.$el.find(".link-checkbox").is(":checked"),g=this.select_extension.value(),h=this.select_genome.value(),i=d[0].type,j=[];if(d.length<1)c.info("Please select some items first.");else{this.modal.disableButton("Import");for(var k=d.length-1;k>=0;k--)void 0!==d[k].li_attr.full_path&&j.push(d[k].li_attr.full_path);if(this.initChainCallControl({length:j.length,action:"adding_datasets"}),"folder"===i){var l=b.source+"_folder";this.chainCallImportingFolders({paths:j,preserve_dirs:e,link_data:f,source:l,file_type:g,dbkey:h})}else if("file"===i){var l=b.source+"_file";this.chainCallImportingUserdirFiles({paths:j,file_type:g,dbkey:h,source:l})}}},fetchAndDisplayHistoryContents:function(a){var b=new d.HistoryContents({id:a}),e=this;b.fetch({success:function(b){var c=e.templateHistoryContents();e.histories.get(a).set({contents:b}),e.modal.$el.find("#selected_history_content").html(c({history_contents:b.models.reverse()}))},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},addAllDatasetsFromHistory:function(){var a=this.modal.$el.find("#selected_history_content").find(":checked"),b=[],e=[];if(a.length<1)c.info("You must select some datasets first.");else{this.modal.disableButton("Add"),a.each(function(){var a=$(this.parentElement).data("id");a&&b.push(a)});for(var f=b.length-1;f>=0;f--){history_dataset_id=b[f];var g=new d.Item;g.url="/api/folders/"+this.options.id+"/contents",g.set({from_hda_id:history_dataset_id}),e.push(g)}this.initChainCallControl({length:e.length,action:"adding_datasets"}),this.chainCallAddingHdas(e)}},chainCallImportingIntoHistory:function(a,b){var d=this,e=a.pop();if("undefined"==typeof e)return 0===this.options.chain_call_control.failed_number?c.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?c.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;g--){var h=new d.Item({id:e[g]});f.push(h)}this.options.chain_call_control.total_number=e.length,this.chainCallDeletingHdas(f)}},showLibInfo:function(){var a=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id,b=null,e=this;null!==Galaxy.libraries.libraryListView?(b=Galaxy.libraries.libraryListView.collection.get(a),this.showLibInfoModal(b)):(b=new d.Library({id:a}),b.fetch({success:function(){e.showLibInfoModal(b)},error:function(a,b){c.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}}))},showLibInfoModal:function(a){var b=this.templateLibInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:"Library Information",body:b({library:a}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(a){switch(a.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),c.error("Invalid import source.")}},showPageSizePrompt:function(){var a=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=a&&a==parseInt(a)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(a)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},templateToolBar:function(){return tmpl_array=[],tmpl_array.push('
'),tmpl_array.push('
'),tmpl_array.push(" DATA LIBRARIES"),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push("<% if(mutiple_add_dataset_options) { %>"),tmpl_array.push(' "),tmpl_array.push("<% } else { %>"),tmpl_array.push(' '),tmpl_array.push("<% } %>"),tmpl_array.push(' '),tmpl_array.push(' "),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(' '),tmpl_array.push(" "),tmpl_array.push("
"),tmpl_array.push('
'),tmpl_array.push("
"),tmpl_array.push("
"),_.template(tmpl_array.join(""))},templateLibInfoInModal:function(){return tmpl_array=[],tmpl_array.push('
'),tmpl_array.push("

Library name:

"),tmpl_array.push('

<%- library.get("name") %>

'),tmpl_array.push("

Library description:

"),tmpl_array.push('

<%- library.get("description") %>

'),tmpl_array.push("

Library synopsis:

"),tmpl_array.push('

<%- library.get("synopsis") %>

'),tmpl_array.push("
"),_.template(tmpl_array.join(""))},templateNewFolderInModal:function(){return tmpl_array=[],tmpl_array.push('
'),tmpl_array.push("
"),tmpl_array.push(''),tmpl_array.push(''),tmpl_array.push("
"),tmpl_array.push("
"),_.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var a=[];return a.push(''),a.push("Select history: "),a.push('"),a.push(""),_.template(a.join(""))},templateImportIntoHistoryProgressBar:function(){var a=[];return a.push('
'),a.push("Importing selected datasets to history <%= _.escape(history_name) %>"),a.push("
"),a.push('
'),a.push('
'),a.push(' 0% Complete'),a.push("
"),a.push("
"),a.push(""),_.template(a.join(""))},templateAddingDatasetsProgressBar:function(){var a=[];return a.push('
'),a.push("Adding selected datasets to library folder <%= _.escape(folder_name) %>"),a.push("
"),a.push('
'),a.push('
'),a.push(' 0% Complete'),a.push("
"),a.push("
"),a.push(""),_.template(a.join(""))},templateDeletingDatasetsProgressBar:function(){var a=[];return a.push('
'),a.push("
"),a.push('
'),a.push('
'),a.push(' 0% Complete'),a.push("
"),a.push("
"),a.push(""),_.template(a.join(""))},templateBrowserModal:function(){var a=[];return a.push('
'),a.push('
All files you select will be imported into the current folder.
'),a.push(''),a.push('
'),a.push('"),a.push('"),a.push("
"),a.push('
'),a.push('"),a.push('"),a.push("
"),a.push('
'),a.push("
"),a.push("
"),a.push("

You can set extension type and genome for all imported datasets at once:

"),a.push("
"),a.push('Type: '),a.push(' Genome: '),a.push("
"),a.push("
"),_.template(a.join(""))},templateImportPathModal:function(){var a=[];return a.push('
'),a.push('
All files within the given folders and their subfolders will be imported into the current folder.
'),a.push('
'),a.push('"),a.push('"),a.push("
"),a.push(''),a.push("
"),a.push("

You can set extension type and genome for all imported datasets at once:

"),a.push("
"),a.push('Type: '),a.push(' Genome: '),a.push("
"),a.push("
"),_.template(a.join(""))},templateAddFilesFromHistory:function(){var a=[];return a.push('
'),a.push('
'),a.push("Select history: "),a.push('"),a.push("
"),a.push("
"),a.push('
'),a.push("
"),a.push("
"),_.template(a.join(""))},templateHistoryContents:function(){var a=[];return a.push("Choose the datasets to import:"),a.push("
    "),a.push(" <% _.each(history_contents, function(history_item) { %>"),a.push('
  • ">'),a.push(' <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'),a.push("
    • "),a.push(" <% }); %>"),a.push("
"),_.template(a.join(""))},templatePaginator:function(){return tmpl_array=[],tmpl_array.push('
    '),tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>"),tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>"),tmpl_array.push('
    • '),tmpl_array.push('
  • <% print( show_page - 1 ) %>
    • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
    • '),tmpl_array.push('
  • <% print( show_page - 1 ) %>
    • '),tmpl_array.push(" <% } %>"),tmpl_array.push(" <% } else { %>"), +tmpl_array.push('
    • '),tmpl_array.push('
  • <% print( show_page - 1 ) %>
    • '),tmpl_array.push(" <% } %>"),tmpl_array.push('
  • '),tmpl_array.push(' <% print( show_page ) %>'),tmpl_array.push("
    • "),tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>"),tmpl_array.push('
  • <% print( show_page + 1 ) %>
    • '),tmpl_array.push('
    • '),tmpl_array.push(" <% } else { %>"),tmpl_array.push('
  • <% print( show_page + 1 ) %>
    • '),tmpl_array.push('
    • '),tmpl_array.push(" <% } %>"),tmpl_array.push("
"),tmpl_array.push(" "),tmpl_array.push(' showing <%- items_shown %> of <%- total_items_count %> items'),tmpl_array.push(" "),_.template(tmpl_array.join(""))}});return{FolderToolbarView:f}}); //# sourceMappingURL=../../../maps/mvc/library/library-foldertoolbar-view.js.map \ No newline at end of file diff --git a/static/scripts/mvc/list/list-panel.js b/static/scripts/mvc/list/list-panel.js index 261121bd771..722dc54482a 100644 --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -1,2 +1,2 @@ -define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d){var e=Backbone.View.extend(c.LoggableMixin).extend({viewClass:a.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:d("This list is empty"),noneFoundMsg:d("No matching items found"),searchPlaceholder:d("search"),initialize:function(a){a=a||{},a.logger&&(this.logger=a.logger),this.log(this+".initialize:",a),this.fxSpeed=_.has(a,"fxSpeed")?a.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=a.searchFor||"",this.indicator=new b(this.$el),this.selecting=void 0!==a.selecting?a.selecting:!0,this.selected=a.selected||[],this.lastSelected=null,this.dragItems=a.dragItems||!1,this.viewClass=a.viewClass||this.viewClass,this.views=[],this.collection=a.collection||new this.collectionClass([]),this.filters=a.filters||[],this.$scrollContainer=a.$scrollContainer||this.$scrollContainer,this.title=a.title||"",this.subtitle=a.subtitle||"",this._setUpListeners()},freeViews:function(){return _.each(this.views,function(a){a.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on("error",function(a,b,c,d,e){},this),this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this),this.on("loading-done",function(){this._hideLoadingIndicator(40)},this),this.once("rendered",function(){this.trigger("rendered:initial",this)},this),this.logger&&this.on("all",function(){this.log(this+"",arguments)},this),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.collection.on("error",function(a,b,c,d,e){this.trigger("error",a,b,c,d,e)},this),this.collection.on("reset",function(){this.renderItems()},this),this.collection.on("add",this.addItemView,this),this.collection.on("remove",this.removeItemView,this),this.logger&&this.collection.on("all",function(){this.info(this+"(collection)",arguments)},this),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on("view:selected",function(a,b){if(b&&b.shiftKey&&this.lastSelected){var c=this.viewFromModelId(this.lastSelected);c&&this.selectRange(a,c)}else b&&b.altKey&&!this.selecting&&this.showSelectors();this.selected.push(a.model.id),this.lastSelected=a.model.id},this),this.on("view:de-selected",function(a){this.selected=_.without(this.selected,a.model.id)},this)},render:function(a){this.log(this+".render",a);var b=this._buildNewRender();return this._setUpBehaviors(b),this._queueNewRender(b,a),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var a=$(this.templates.el({},this));return this._renderControls(a),this._renderTitle(a),this._renderSubtitle(a),this._renderSearch(a),this.renderItems(a),a},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=$(this.templates.controls({},this));return a.find(".controls").replaceWith(b),b},_renderTitle:function(){},_renderSubtitle:function(){},_queueNewRender:function(a,b){b=void 0===b?this.fxSpeed:b;var c=this;c.log("_queueNewRender:",a,b),$(c).queue("fx",[function(a){this.$el.fadeOut(b,a)},function(b){c._swapNewRender(a),b()},function(a){this.$el.fadeIn(b,a)},function(a){c.trigger("rendered",c),a()}])},_swapNewRender:function(a){return this.$el.empty().attr("class",this.className).append(a.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(a){return a=a||this.$el,a.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(a),this},_renderMultiselectActionMenu:function(a){a=a||this.$el;var b=a.find(".list-action-menu"),c=this.multiselectActions();if(!c.length)return b.empty();var e=$(['
','",'","
"].join("")),f=c.map(function(a){var b=['
  • ',a.html,"
    • "].join("");return $(b).click(a.func)});return e.find("ul").append(f),b.replaceWith(e),e},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(a){return(a||this.$el).find("> .list-items")},$messages:function(a){return(a||this.$el).find("> .controls .messages")},$emptyMessage:function(a){return(a||this.$el).find("> .empty-message")},renderItems:function(a){a=a||this.$el;var b=this;b.log(this+".renderItems",a);var c=b.$list(a);return b.views=b._filterCollection().map(function(a){return b._createItemView(a).render(0)}),c.empty(),b.views.length?(b._attachItems(a),b.$emptyMessage(a).hide()):b._renderEmptyMessage(a).show(),b.views},_filterCollection:function(){var a=this;return a.collection.filter(_.bind(a._filterItem,a))},_filterItem:function(a){var b=this;return _.every(b.filters.map(function(b){return b.call(a)}))&&(!b.searchFor||a.matchesAll(b.searchFor))},_createItemView:function(a){var b=this._getItemViewClass(a),c=_.extend(this._getItemViewOptions(a),{model:a}),d=new b(c);return this._setUpItemViewListeners(d),d},_getItemViewClass:function(){return this.viewClass},_getItemViewOptions:function(a){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:_.contains(this.selected,a.id),draggable:this.dragItems}},_setUpItemViewListeners:function(a){var b=this;return a.on("all",function(){var a=Array.prototype.slice.call(arguments,0);a[0]="view:"+a[0],b.trigger.apply(b,a)}),a.on("draggable:dragstart",function(a,b){var c={},d=this.getSelectedModels();c=d.length?d.toJSON():[b.model.toJSON()],a.dataTransfer.setData("text",JSON.stringify(c))},this),b},_attachItems:function(a){return this.$list(a).append(this.views.map(function(a){return a.$el})),this},_renderEmptyMessage:function(a){this.debug("_renderEmptyMessage",a,this.searchFor);var b=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(a).text(b)},expandAll:function(){_.each(this.views,function(a){a.expand()})},collapseAll:function(){_.each(this.views,function(a){a.collapse()})},addItemView:function(a){this.log(this+".addItemView:",a);var b=this;if(!b._filterItem(a))return void 0;var c=b._createItemView(a);return $(c).queue("fx",[function(a){b.$emptyMessage().fadeOut(b.fxSpeed,a)},function(a){b._attachView(c),a()}]),c},_attachView:function(a){var b=this;b.views.push(a),b.$list().append(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},removeItemView:function(a){this.log(this+".removeItemView:",a);var b=this,c=b.viewFromModel(a);return c?(b.views=_.without(b.views,c),b.trigger("view:removed",c),$({}).queue("fx",[function(a){c.$el.fadeOut(b.fxSpeed,a)},function(a){c.remove(),b.trigger("view:removed:rendered"),b.views.length?a():b._renderEmptyMessage().fadeIn(b.fxSpeed,a)}]),c):void 0},viewFromModelId:function(a){for(var b=0;bc?this.views.slice(c,d+1):this.views.slice(d,c+1)},_renderSearch:function(a){return a.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)}),a},_firstSearch:function(a){return this.log("onFirstSearch",a),this.searchItems(a)},searchItems:function(a){return this.searchFor=a,this.trigger("search:searching",a,this),this.renderItems(),this.$("> .controls .search-query").val(a),this},clearSearch:function(){return this.searchFor="",this.trigger("search:clear",this),this.renderItems(),this.$("> .controls .search-query").val(""),this},showSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(a),_.each(this.views,function(b){b.showSelector(a)})},hideSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(a),_.each(this.views,function(b){b.hideSelector(a)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(a){_.each(this.views,function(b){b.select(a)})},deselectAll:function(a){this.lastSelected=null,_.each(this.views,function(b){b.deselect(a)})},selectRange:function(a,b){var c=this.viewRange(a,b);return _.each(c,function(a){a.select()}),c},getSelectedViews:function(){return _.filter(this.views,function(a){return a.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(a){return a.model}))},_showLoadingIndicator:function(a,c,d){this.debug("_showLoadingIndicator",this.indicator,a,c,d),c=void 0!==c?c:this.fxSpeed,this.indicator||(this.indicator=new b(this.$el,this.$el.parent()),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(c),this.indicator.show(a,c,d)):this.indicator.show(0,d)},_hideLoadingIndicator:function(a,b){this.debug("_hideLoadingIndicator",this.indicator,a,b),a=void 0!==a?a:this.fxSpeed,this.indicator&&this.indicator.hide(a,b)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(a,b){return b=b||0,this.$scrollContainer().animate({scrollTop:a},b),this},scrollToTop:function(a){return this.scrollTo(0,a)},scrollToItem:function(a,b){if(!a)return this;var c=a.$el.position().top;return this.scrollTo(c,b)},scrollToId:function(a,b){return this.scrollToItem(this.viewFromModelId(a),b)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=function(){var a=c.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),b=c.wrapTemplate(['
    ','
    ','
    <%= view.title %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return{el:a,controls:b}}();var f=e.extend({modelCollectionKey:"contents",initialize:function(a){e.prototype.initialize.call(this,a),this.selecting=void 0!==a.selecting?a.selecting:!1,this.setModel(this.model,a)},setModel:function(a,b){if(b=b||{},this.debug(this+".setModel:",a,b),this.freeModel(),this.freeViews(),a){var c=this.model?this.model.get("id"):null;this.model=a,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:b.collection||new this.collectionClass([]),this._setUpCollectionListeners(),c&&a.get("id")!==c&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.model.on("error",function(){var a=Array.prototype.slice.call(arguments,0);a.unshift("error"),this.trigger.apply(this,a)},this),this},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=this.model?this.model.toJSON():{},c=$(this.templates.controls(b,this));return a.find(".controls").replaceWith(c),c},toString:function(){return"ModelListPanel("+this.model+")"}});return f.prototype.templates=function(){var a=c.wrapTemplate(['
    ','
    ','
    <%= model.name %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return _.extend(_.clone(e.prototype.templates),{controls:a})}(),{ListPanel:e,ModelListPanel:f}}); +define(["mvc/list/list-item","ui/loading-indicator","mvc/base-mvc","utils/localization","ui/search-input"],function(a,b,c,d){var e=Backbone.View.extend(c.LoggableMixin).extend({viewClass:a.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:d("This list is empty"),noneFoundMsg:d("No matching items found"),searchPlaceholder:d("search"),initialize:function(a){a=a||{},a.logger&&(this.logger=a.logger),this.log(this+".initialize:",a),this.fxSpeed=_.has(a,"fxSpeed")?a.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=a.searchFor||"",this.indicator=new b(this.$el),this.selecting=void 0!==a.selecting?a.selecting:!0,this.selected=a.selected||[],this.lastSelected=null,this.dragItems=a.dragItems||!1,this.viewClass=a.viewClass||this.viewClass,this.views=[],this.collection=a.collection||new this.collectionClass([]),this.filters=a.filters||[],this.$scrollContainer=a.$scrollContainer||this.$scrollContainer,this.title=a.title||"",this.subtitle=a.subtitle||"",this._setUpListeners()},freeViews:function(){return _.each(this.views,function(a){a.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on("error",function(a,b,c,d,e){console.error(a,b,c,d,e)},this),this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this),this.on("loading-done",function(){this._hideLoadingIndicator(40)},this),this.once("rendered",function(){this.trigger("rendered:initial",this)},this),this.logger&&this.on("all",function(){this.log(this+"",arguments)},this),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.collection.on("error",function(a,b,c,d,e){this.trigger("error",a,b,c,d,e)},this),this.collection.on("reset",function(){this.renderItems()},this),this.collection.on("add",this.addItemView,this),this.collection.on("remove",this.removeItemView,this),this.logger&&this.collection.on("all",function(){this.info(this+"(collection)",arguments)},this),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on("view:selected",function(a,b){if(b&&b.shiftKey&&this.lastSelected){var c=this.viewFromModelId(this.lastSelected);c&&this.selectRange(a,c)}else b&&b.altKey&&!this.selecting&&this.showSelectors();this.selected.push(a.model.id),this.lastSelected=a.model.id},this),this.on("view:de-selected",function(a){this.selected=_.without(this.selected,a.model.id)},this)},render:function(a){this.log(this+".render",a);var b=this._buildNewRender();return this._setUpBehaviors(b),this._queueNewRender(b,a),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var a=$(this.templates.el({},this));return this._renderControls(a),this._renderTitle(a),this._renderSubtitle(a),this._renderSearch(a),this.renderItems(a),a},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=$(this.templates.controls({},this));return a.find(".controls").replaceWith(b),b},_renderTitle:function(){},_renderSubtitle:function(){},_queueNewRender:function(a,b){b=void 0===b?this.fxSpeed:b;var c=this;c.log("_queueNewRender:",a,b),$(c).queue("fx",[function(a){this.$el.fadeOut(b,a)},function(b){c._swapNewRender(a),b()},function(a){this.$el.fadeIn(b,a)},function(a){c.trigger("rendered",c),a()}])},_swapNewRender:function(a){return this.$el.empty().attr("class",this.className).append(a.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(a){return a=a||this.$el,a.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(a),this},_renderMultiselectActionMenu:function(a){a=a||this.$el;var b=a.find(".list-action-menu"),c=this.multiselectActions();if(!c.length)return b.empty();var e=$(['
    ','",'","
    "].join("")),f=c.map(function(a){var b=['
  • ',a.html,"
    • "].join("");return $(b).click(a.func)});return e.find("ul").append(f),b.replaceWith(e),e},multiselectActions:function(){return[]},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(a){return(a||this.$el).find("> .list-items")},$messages:function(a){return(a||this.$el).find("> .controls .messages")},$emptyMessage:function(a){return(a||this.$el).find("> .empty-message")},renderItems:function(a){a=a||this.$el;var b=this;b.log(this+".renderItems",a);var c=b.$list(a);return b.views=b._filterCollection().map(function(a){return b._createItemView(a).render(0)}),c.empty(),b.views.length?(b._attachItems(a),b.$emptyMessage(a).hide()):b._renderEmptyMessage(a).show(),b.views},_filterCollection:function(){var a=this;return a.collection.filter(_.bind(a._filterItem,a))},_filterItem:function(a){var b=this;return _.every(b.filters.map(function(b){return b.call(a)}))&&(!b.searchFor||a.matchesAll(b.searchFor))},_createItemView:function(a){var b=this._getItemViewClass(a),c=_.extend(this._getItemViewOptions(a),{model:a}),d=new b(c);return this._setUpItemViewListeners(d),d},_getItemViewClass:function(){return this.viewClass},_getItemViewOptions:function(a){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:_.contains(this.selected,a.id),draggable:this.dragItems}},_setUpItemViewListeners:function(a){var b=this;return a.on("all",function(){var a=Array.prototype.slice.call(arguments,0);a[0]="view:"+a[0],b.trigger.apply(b,a)}),a.on("draggable:dragstart",function(a,b){var c={},d=this.getSelectedModels();c=d.length?d.toJSON():[b.model.toJSON()],a.dataTransfer.setData("text",JSON.stringify(c))},this),b},_attachItems:function(a){return this.$list(a).append(this.views.map(function(a){return a.$el})),this},_renderEmptyMessage:function(a){this.debug("_renderEmptyMessage",a,this.searchFor);var b=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(a).text(b)},expandAll:function(){_.each(this.views,function(a){a.expand()})},collapseAll:function(){_.each(this.views,function(a){a.collapse()})},addItemView:function(a){this.log(this+".addItemView:",a);var b=this;if(!b._filterItem(a))return void 0;var c=b._createItemView(a);return $(c).queue("fx",[function(a){b.$emptyMessage().fadeOut(b.fxSpeed,a)},function(a){b._attachView(c),a()}]),c},_attachView:function(a){var b=this;b.views.push(a),b.$list().append(a.render(0).$el.hide()),b.trigger("view:attached",a),a.$el.slideDown(b.fxSpeed,function(){b.trigger("view:attached:rendered")})},removeItemView:function(a){console.log(this+".removeItemView:",a),this.log(this+".removeItemView:",a);var b=this,c=b.viewFromModel(a);return c?(b.views=_.without(b.views,c),b.trigger("view:removed",c),$({}).queue("fx",[function(a){c.$el.fadeOut(b.fxSpeed,a)},function(a){c.remove(),b.trigger("view:removed:rendered"),b.views.length?a():b._renderEmptyMessage().fadeIn(b.fxSpeed,a)}]),c):void 0},viewFromModelId:function(a){for(var b=0;bc?this.views.slice(c,d+1):this.views.slice(d,c+1)},_renderSearch:function(a){return a.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)}),a},_firstSearch:function(a){return this.log("onFirstSearch",a),this.searchItems(a)},searchItems:function(a){return this.searchFor=a,this.trigger("search:searching",a,this),this.renderItems(),this.$("> .controls .search-query").val(a),this},clearSearch:function(){return this.searchFor="",this.trigger("search:clear",this),this.renderItems(),this.$("> .controls .search-query").val(""),this},showSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(a),_.each(this.views,function(b){b.showSelector(a)})},hideSelectors:function(a){a=void 0!==a?a:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(a),_.each(this.views,function(b){b.hideSelector(a)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(a){_.each(this.views,function(b){b.select(a)})},deselectAll:function(a){this.lastSelected=null,_.each(this.views,function(b){b.deselect(a)})},selectRange:function(a,b){var c=this.viewRange(a,b);return _.each(c,function(a){a.select()}),c},getSelectedViews:function(){return _.filter(this.views,function(a){return a.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(a){return a.model}))},_showLoadingIndicator:function(a,c,d){this.debug("_showLoadingIndicator",this.indicator,a,c,d),c=void 0!==c?c:this.fxSpeed,this.indicator||(this.indicator=new b(this.$el,this.$el.parent()),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(c),this.indicator.show(a,c,d)):this.indicator.show(0,d)},_hideLoadingIndicator:function(a,b){this.debug("_hideLoadingIndicator",this.indicator,a,b),a=void 0!==a?a:this.fxSpeed,this.indicator&&this.indicator.hide(a,b)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(a,b){return b=b||0,this.$scrollContainer().animate({scrollTop:a},b),this},scrollToTop:function(a){return this.scrollTo(0,a)},scrollToItem:function(a,b){if(!a)return this;var c=a.$el.position().top;return this.scrollTo(c,b)},scrollToId:function(a,b){return this.scrollToItem(this.viewFromModelId(a),b)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=function(){var a=c.wrapTemplate(["
    ",'
    ','
    ','
    ',"
    "]),b=c.wrapTemplate(['
    ','
    ','
    <%= view.title %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return{el:a,controls:b}}();var f=e.extend({modelCollectionKey:"contents",initialize:function(a){e.prototype.initialize.call(this,a),this.selecting=void 0!==a.selecting?a.selecting:!1,this.setModel(this.model,a)},setModel:function(a,b){if(b=b||{},this.debug(this+".setModel:",a,b),this.freeModel(),this.freeViews(),a){var c=this.model?this.model.get("id"):null;this.model=a,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:b.collection||new this.collectionClass([]),this._setUpCollectionListeners(),c&&a.get("id")!==c&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.model.on("error",function(){var a=Array.prototype.slice.call(arguments,0);a.unshift("error"),this.trigger.apply(this,a)},this),this},_renderControls:function(a){this.debug(this+"(ListPanel)._renderControls");var b=this.model?this.model.toJSON():{},c=$(this.templates.controls(b,this));return a.find(".controls").replaceWith(c),c},toString:function(){return"ModelListPanel("+this.model+")"}});return f.prototype.templates=function(){var a=c.wrapTemplate(['
    ','
    ','
    <%= model.name %>
    ',"
    ",'
    <%= view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return _.extend(_.clone(e.prototype.templates),{controls:a})}(),{ListPanel:e,ModelListPanel:f}}); //# sourceMappingURL=../../../maps/mvc/list/list-panel.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-base.js b/static/scripts/mvc/tools/tools-form-base.js index 24a1e490c58..0c5bf916463 100644 --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -1,2 +1,2 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("
    "),this.container=a.container||"body",$(this.container).append(this.$el),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this,d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g)},error:function(a){c.deferred.done(g);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url,c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),c.deferred.done(f)},error:function(a){c.deferred.done(f)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tools/tools-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(a){var c=parent.Galaxy;this.is_admin=c&&c.currUser?c.currUser.get("is_admin"):!1,this.deferred=new b,this.setElement("
    "),this.container=a.container||"body",$(this.container).append(this.$el),this._buildForm(a)},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:"fa-wrench",title:""+b.name+" "+b.description+" (Galaxy Tool Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(){c._updateModel()})}},this.options),this.form=new d(this.options),this._footer(),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b){var c=this,d=galaxy_config.root+"api/tools/"+b.id+"/build?";if(b.job_id)d+="job_id="+b.job_id;else if(b.dataset_id)d+="dataset_id="+b.dataset_id;else{d+="tool_version="+b.version+"&";var e=top.location.href,f=e.indexOf("?");-1!=e.indexOf("tool_id=")&&-1!==f&&(d+=e.slice(f+1))}var g=this.deferred.register();a.request({type:"GET",url:d,success:function(a){c._buildForm(a.tool_model||a),c.form.message.update({status:"success",message:"Now you are using '"+c.options.name+"' version "+c.options.version+".",persistent:!1}),c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model ready."),console.debug(a)},error:function(a){c.deferred.done(g),console.debug("tools-form::initialize() - Initial tool model request failed."),console.debug(a);var b=a.error||"Uncaught error.";c.form.modal.show({title:"Tool cannot be executed",body:b,buttons:{Close:function(){c.form.modal.hide()}}})}})},_updateModel:function(){var b=this.options.update_url,c=this,d=this.form,e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};d.wait(!0);var f=this.deferred.register();console.debug("tools-form-base::_updateModel() - Sending current state (see below)."),console.debug(e),a.request({type:"POST",url:b,data:e,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),d.wait(!1),console.debug("tools-form-base::_updateModel() - Received new model (see below)."),console.debug(a),c.deferred.done(f)},error:function(a){c.deferred.done(f),console.debug("tools-form-base::_updateModel() - Refresh request failed."),console.debug(a)}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(){a._buildModel({id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+b.id)}}),this.is_admin&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options;if(""!=a.help&&this.form.$el.append(e.help(a)),a.citations){var b=$("
    "),c=new f.ToolCitationCollection;c.tool_id=a.id;var d=new g.CitationListView({el:b,collection:c});d.render(),c.fetch(),this.form.$el.append(b)}}})}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-base.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-workflow.js b/static/scripts/mvc/tools/tools-form-workflow.js index 7269523ab50..f5b433e1b1d 100644 --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,this.node){this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_dynamic:!1,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&(a.optional=-1==["data","data_hidden","hidden","repeat","conditional"].indexOf(a.type))}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})}},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); +define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_dynamic:!1,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&(a.optional=-1==["data","data_hidden","hidden","repeat","conditional"].indexOf(a.type))}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-jobs.js b/static/scripts/mvc/tools/tools-jobs.js index f6926c6c383..d4b1708c3a3 100644 --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}}):void(e&&e())},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}}); +define(["utils/utils","mvc/tools/tools-template"],function(a,b){return{submit:function(c,d,e){var f=this,g={tool_id:d.id,tool_version:d.version,inputs:c.data.create()};return c.trigger("reset"),this._validation(c,g)?(console.debug(g),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:g,success:function(a){e&&e(),c.reciept(b.success(a)),f._refreshHdas()},error:function(a){if(e&&e(),a&&a.message&&a.message.data){var d=c.data.matchResponse(a.message.data);for(var f in d){c.highlight(f,d[f]);break}}else console.debug(a),a&&c.modal.show({title:"Job submission failed",body:b.error(g),buttons:{Close:function(){c.modal.hide()}}})}})):(console.debug("tools-jobs::submit - Submission canceled. Validation failed."),void(e&&e()))},_validation:function(a,b){var c=b.inputs,d=-1,e=null;for(var f in c){var g=c[f],h=a.data.match(f),i=a.field_list[h],j=a.input_list[h];if(h&&j&&i){if(!j.optional&&null==g)return a.highlight(h),!1;if(g&&g.batch){var k=g.values.length,l=null;if(k>0&&(l=g.values[0]&&g.values[0].src),l)if(null===e)e=l;else if(e!==l)return a.highlight(h,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===d)d=k;else if(d!==k)return a.highlight(h,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+k+" selection(s) while a previous field contains "+d+"."),!1}}else console.debug("tools-jobs::_validation - Retrieving input objects failed.")}return!0},_refreshHdas:function(){parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()}}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-jobs.js.map \ No newline at end of file diff --git a/static/scripts/mvc/ui/ui-frames.js b/static/scripts/mvc/ui/ui-frames.js index aea84c96ad5..b9e78655ec1 100644 --- a/static/scripts/mvc/ui/ui-frames.js +++ b/static/scripts/mvc/ui/ui-frames.js @@ -1,2 +1,2 @@ -define([],function(){var a=Backbone.View.extend({options:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0,onchange:null},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:null,initialize:function(a){var b=this;a&&(this.options=_.defaults(a,this.options)),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(this._template()),$(this.el).append(this._templateBackground()),$(this.el).append(this._templateMenu()),$(this.el_main).append($(this.el));var c="#frame-shadow";$(this.el).append(this._templateShadow(c.substring(1))),this.frame_shadow={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1},this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list[c]=this.frame_shadow,this._panelRefresh(),this.visible?this.show():this.hide();var b=this;$(window).resize(function(){b.visible&&b._panelRefresh()})},add:function(a){var b={title:"",content:null,target:"",type:null};if(a=a?_.defaults(a,b):b,a.content){if(this.frame_counter>=this.options.frame_max)return void alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");var c="#frame-"+this.frame_counter_id++;if(0!==$(c).length)return void alert("This frame already exists. This page might contain multiple frame managers.");this.top=this.options.top_min;var d=null;if("url"===a.type)d=$(this._templateFrameUrl(c.substring(1),a.title,a.content));else if("other"===a.type){d=$(this._templateFrame(c.substring(1),a.title));var e=d.find(".f-content");_.isFunction(a.content)?a.content(e):e.append(a.content)}$(this.el).append(d);var f={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1};a.width=this._toPixelCoord("width",this.options.frame.cols),a.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt($(f.id).css("z-index")),this.frame_list[c]=f,this.frame_counter++,this._frameResize(f,{width:a.width,height:a.height}),this._frameInsert(f,{top:0,left:0},!0),this.visible||this.show()}},show:function(){this.visible=!0,this.$el.find(".frame").fadeIn("fast"),this.$el.find(this.frame_shadow.id).hide(),this.$el.find(".frame-background").show(),this._panelRefresh(),this._menuRefresh()},hide:function(){null===this.event.type&&(this.visible=!1,this.$el.find(".frame").fadeOut("fast"),this.$el.find(".frame-background").hide(),this.$el.find(".frame-menu").hide(),this._menuRefresh())},length:function(){return this.frame_counter},setOnChange:function(a){this.options.onchange=a},event:{type:null,target:null,xy:null},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose","mousedown .f-pin":"_eventFrameLock"},_eventFrameMouseDown:function(a){if(null===this.event.type&&(($(a.target).hasClass("f-header")||$(a.target).hasClass("f-title"))&&(this.event.type="drag"),$(a.target).hasClass("f-resize")&&(this.event.type="resize"),null!==this.event.type)){if(a.preventDefault(),this.event.target=this._frameIdentify(a.target),this.event.target.grid_lock)return void(this.event.type=null);this.event.xy={x:a.originalEvent.pageX,y:a.originalEvent.pageY},this._frameDragStart(this.event.target)}},_eventFrameMouseMove:function(a){if("drag"==this.event.type||"resize"==this.event.type){var b={x:a.originalEvent.pageX,y:a.originalEvent.pageY},c={x:b.x-this.event.xy.x,y:b.y-this.event.xy.y};this.event.xy=b;var d=this._frameScreen(this.event.target);if("resize"==this.event.type){d.width+=c.x,d.height+=c.y;var e=this.options.cell-this.options.margin-1;d.width=Math.max(d.width,e),d.height=Math.max(d.height,e),this._frameResize(this.event.target,d),d.width=this._toGridCoord("width",d.width)+1,d.height=this._toGridCoord("height",d.height)+1,d.width=this._toPixelCoord("width",d.width),d.height=this._toPixelCoord("height",d.height),this._frameResize(this.frame_shadow,d),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)})}if("drag"==this.event.type){d.left+=c.x,d.top+=c.y,this._frameOffset(this.event.target,d);var f={top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)};0!==f.left&&f.left++,this._frameInsert(this.frame_shadow,f)}}},_eventFrameMouseUp:function(){("drag"==this.event.type||"resize"==this.event.type)&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target),c=this;$(b.id).fadeOut("fast",function(){$(b.id).remove(),delete c.frame_list[b.id],c.frame_counter--,c._panelRefresh(!0),c._panelAnimationComplete(),c.visible&&0==c.frame_counter&&c.hide()})}},_eventFrameLock:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target);b.grid_lock?(b.grid_lock=!1,$(b.id).find(".f-pin").removeClass("toggle"),$(b.id).find(".f-header").removeClass("f-not-allowed"),$(b.id).find(".f-title").removeClass("f-not-allowed"),$(b.id).find(".f-resize").show(),$(b.id).find(".f-close").show()):(b.grid_lock=!0,$(b.id).find(".f-pin").addClass("toggle"),$(b.id).find(".f-header").addClass("f-not-allowed"),$(b.id).find(".f-title").addClass("f-not-allowed"),$(b.id).find(".f-resize").hide(),$(b.id).find(".f-close").hide())}},_eventHide:function(){null===this.event.type&&this.hide()},_eventPanelScroll:function(a){if(null===this.event.type&&this.visible){var b=$(a.srcElement).parents(".frame");if(0!==b.length)return void a.stopPropagation();a.preventDefault();var c=a.originalEvent.detail?a.originalEvent.detail:a.originalEvent.wheelDelta/-3;this._panelScroll(c)}},_eventPanelScroll_up:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(a){return this.frame_list["#"+$(a).closest(".frame").attr("id")]},_frameDragStart:function(a){this._frameFocus(a,!0);var b=this._frameScreen(a);this._frameResize(this.frame_shadow,b),this._frameGrid(this.frame_shadow,a.grid_location),a.grid_location=null,$(this.frame_shadow.id).show(),$(".f-cover").show()},_frameDragStop:function(a){this._frameFocus(a,!1);var b=this._frameScreen(this.frame_shadow);this._frameResize(a,b),this._frameGrid(a,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,$(this.frame_shadow.id).hide(),$(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(a,b){var c="width"==a||"height"==a?1:-1;return"top"==a&&(b-=this.top),parseInt((b+c*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(a,b){var c="width"==a||"height"==a?1:-1,d=b*this.options.cell-c*this.options.margin;return"top"==a&&(d+=this.top),d},_toGrid:function(a){return{top:this._toGridCoord("top",a.top),left:this._toGridCoord("left",a.left),width:this._toGridCoord("width",a.width),height:this._toGridCoord("height",a.height)}},_toPixel:function(a){return{top:this._toPixelCoord("top",a.top),left:this._toPixelCoord("left",a.left),width:this._toPixelCoord("width",a.width),height:this._toPixelCoord("height",a.height)}},_isCollision:function(a){function b(a,b){return!(a.left>b.left+b.width-1||a.left+a.width-1b.top+b.height-1||a.top+a.height-1c?-1:c>d?1:0}),e=0;e
    '},_templateFrame:function(a,b){return b||(b=""),'
    '+b+'
    '},_templateFrameUrl:function(a,b,c){c+=-1==c.indexOf("?")?"?":"&",c+="widget=True";var d=$(this._templateFrame(a,b));return d.find(".f-content").append(''),d},_templateShadow:function(a){return'
    '},_templateBackground:function(){return'
    '},_templateMenu:function(){return'
    '}});return{View:a}}); +define([],function(){var a=Backbone.View.extend({options:{frame:{cols:6,rows:3},rows:1e3,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:!0,onchange:null},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:null,initialize:function(a){var b=this;a&&(this.options=_.defaults(a,this.options)),this.visible=this.options.visible,this.top=this.top_max=this.options.top_min,this.setElement(this._template()),$(this.el).append(this._templateBackground()),$(this.el).append(this._templateMenu()),$(this.el_main).append($(this.el));var c="#frame-shadow";$(this.el).append(this._templateShadow(c.substring(1))),this.frame_shadow={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1},this._frameResize(this.frame_shadow,{width:0,height:0}),this.frame_list[c]=this.frame_shadow,this._panelRefresh(),this.visible?this.show():this.hide();var b=this;$(window).resize(function(){b.visible&&b._panelRefresh()})},add:function(a){var b={title:"",content:null,target:"",type:null};if(a=a?_.defaults(a,b):b,a.content){if(this.frame_counter>=this.options.frame_max)return void alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");var c="#frame-"+this.frame_counter_id++;if(0!==$(c).length)return void alert("This frame already exists. This page might contain multiple frame managers.");this.top=this.options.top_min;var d=null;if("url"===a.type)d=$(this._templateFrameUrl(c.substring(1),a.title,a.content));else if("other"===a.type){d=$(this._templateFrame(c.substring(1),a.title));var e=d.find(".f-content");_.isFunction(a.content)?a.content(e):e.append(a.content)}$(this.el).append(d);var f={id:c,screen_location:{},grid_location:{},grid_rank:null,grid_lock:!1};a.width=this._toPixelCoord("width",this.options.frame.cols),a.height=this._toPixelCoord("height",this.options.frame.rows),this.frame_z=parseInt($(f.id).css("z-index")),this.frame_list[c]=f,this.frame_counter++,this._frameResize(f,{width:a.width,height:a.height}),this._frameInsert(f,{top:0,left:0},!0),this.visible||this.show()}},show:function(){this.visible=!0,this.$el.find(".frame").fadeIn("fast"),this.$el.find(this.frame_shadow.id).hide(),this.$el.find(".frame-background").show(),this._panelRefresh(),this._menuRefresh()},hide:function(){null===this.event.type&&(this.visible=!1,this.$el.find(".frame").fadeOut("fast"),this.$el.find(".frame-background").hide(),this.$el.find(".frame-menu").hide(),this._menuRefresh())},length:function(){return this.frame_counter},setOnChange:function(a){this.options.onchange=a},event:{type:null,target:null,xy:null},events:{mousemove:"_eventFrameMouseMove",mouseup:"_eventFrameMouseUp",mouseleave:"_eventFrameMouseUp",mousewheel:"_eventPanelScroll",DOMMouseScroll:"_eventPanelScroll","mousedown .frame":"_eventFrameMouseDown","mousedown .frame-background":"_eventHide","mousedown .frame-scroll-up":"_eventPanelScroll_up","mousedown .frame-scroll-down":"_eventPanelScroll_down","mousedown .f-close":"_eventFrameClose","mousedown .f-pin":"_eventFrameLock"},_eventFrameMouseDown:function(a){if(null===this.event.type&&(($(a.target).hasClass("f-header")||$(a.target).hasClass("f-title"))&&(this.event.type="drag"),$(a.target).hasClass("f-resize")&&(this.event.type="resize"),null!==this.event.type)){if(a.preventDefault(),this.event.target=this._frameIdentify(a.target),this.event.target.grid_lock)return void(this.event.type=null);this.event.xy={x:a.originalEvent.pageX,y:a.originalEvent.pageY},this._frameDragStart(this.event.target)}},_eventFrameMouseMove:function(a){if("drag"==this.event.type||"resize"==this.event.type){var b={x:a.originalEvent.pageX,y:a.originalEvent.pageY},c={x:b.x-this.event.xy.x,y:b.y-this.event.xy.y};this.event.xy=b;var d=this._frameScreen(this.event.target);if("resize"==this.event.type){d.width+=c.x,d.height+=c.y;var e=this.options.cell-this.options.margin-1;d.width=Math.max(d.width,e),d.height=Math.max(d.height,e),this._frameResize(this.event.target,d),d.width=this._toGridCoord("width",d.width)+1,d.height=this._toGridCoord("height",d.height)+1,d.width=this._toPixelCoord("width",d.width),d.height=this._toPixelCoord("height",d.height),this._frameResize(this.frame_shadow,d),this._frameInsert(this.frame_shadow,{top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)})}if("drag"==this.event.type){d.left+=c.x,d.top+=c.y,this._frameOffset(this.event.target,d);var f={top:this._toGridCoord("top",d.top),left:this._toGridCoord("left",d.left)};0!==f.left&&f.left++,this._frameInsert(this.frame_shadow,f)}}},_eventFrameMouseUp:function(){("drag"==this.event.type||"resize"==this.event.type)&&(this._frameDragStop(this.event.target),this.event.type=null)},_eventFrameClose:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target),c=this;$(b.id).fadeOut("fast",function(){$(b.id).remove(),delete c.frame_list[b.id],c.frame_counter--,c._panelRefresh(!0),c._panelAnimationComplete(),c.visible&&0==c.frame_counter&&c.hide()})}},_eventFrameLock:function(a){if(null===this.event.type){a.preventDefault();var b=this._frameIdentify(a.target);b.grid_lock?(b.grid_lock=!1,$(b.id).find(".f-pin").removeClass("toggle"),$(b.id).find(".f-header").removeClass("f-not-allowed"),$(b.id).find(".f-title").removeClass("f-not-allowed"),$(b.id).find(".f-resize").show(),$(b.id).find(".f-close").show()):(b.grid_lock=!0,$(b.id).find(".f-pin").addClass("toggle"),$(b.id).find(".f-header").addClass("f-not-allowed"),$(b.id).find(".f-title").addClass("f-not-allowed"),$(b.id).find(".f-resize").hide(),$(b.id).find(".f-close").hide())}},_eventHide:function(){null===this.event.type&&this.hide()},_eventPanelScroll:function(a){if(null===this.event.type&&this.visible){var b=$(a.srcElement).parents(".frame");if(0!==b.length)return void a.stopPropagation();a.preventDefault();var c=a.originalEvent.detail?a.originalEvent.detail:a.originalEvent.wheelDelta/-3;this._panelScroll(c)}},_eventPanelScroll_up:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(-this.options.scroll))},_eventPanelScroll_down:function(a){null===this.event.type&&(a.preventDefault(),this._panelScroll(this.options.scroll))},_frameIdentify:function(a){return this.frame_list["#"+$(a).closest(".frame").attr("id")]},_frameDragStart:function(a){this._frameFocus(a,!0);var b=this._frameScreen(a);this._frameResize(this.frame_shadow,b),this._frameGrid(this.frame_shadow,a.grid_location),a.grid_location=null,$(this.frame_shadow.id).show(),$(".f-cover").show()},_frameDragStop:function(a){this._frameFocus(a,!1);var b=this._frameScreen(this.frame_shadow);this._frameResize(a,b),this._frameGrid(a,this.frame_shadow.grid_location,!0),this.frame_shadow.grid_location=null,$(this.frame_shadow.id).hide(),$(".f-cover").hide(),this._panelAnimationComplete()},_toGridCoord:function(a,b){var c="width"==a||"height"==a?1:-1;return"top"==a&&(b-=this.top),parseInt((b+c*this.options.margin)/this.options.cell,10)},_toPixelCoord:function(a,b){var c="width"==a||"height"==a?1:-1,d=b*this.options.cell-c*this.options.margin;return"top"==a&&(d+=this.top),d},_toGrid:function(a){return{top:this._toGridCoord("top",a.top),left:this._toGridCoord("left",a.left),width:this._toGridCoord("width",a.width),height:this._toGridCoord("height",a.height)}},_toPixel:function(a){return{top:this._toPixelCoord("top",a.top),left:this._toPixelCoord("left",a.left),width:this._toPixelCoord("width",a.width),height:this._toPixelCoord("height",a.height)}},_isCollision:function(a){function b(a,b){return!(a.left>b.left+b.width-1||a.left+a.width-1b.top+b.height-1||a.top+a.height-1c?-1:c>d?1:0}),e=0;e
    '},_templateFrame:function(a,b){return b||(b=""),'
    '+b+'
    '},_templateFrameUrl:function(a,b,c){c+=-1==c.indexOf("?")?"?":"&",c+="widget=True";var d=$(this._templateFrame(a,b));return d.find(".f-content").append(''),d},_templateShadow:function(a){return'
    '},_templateBackground:function(){return'
    '},_templateMenu:function(){return'
    '}});return{View:a}}); //# sourceMappingURL=../../../maps/mvc/ui/ui-frames.js.map \ No newline at end of file diff --git a/static/scripts/mvc/ui/ui-select.js b/static/scripts/mvc/ui/ui-select.js index 2cba7b6fa99..f7ec2b55fd9 100644 --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -1,2 +1,2 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),this.options.container&&(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple)){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return''}});return{View:b}}); +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(b){if(this.options=a.merge(b,this.optionsDefault),this.setElement(this._template(this.options)),!this.options.container)return void console.log("ui-select::initialize() : container not specified.");if(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple){this.options.value&&this._setValue(this.options.value);var c=this;this.options.onchange&&this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(a){var b=this._getValue();void 0!==a&&this._setValue(a);var c=this._getValue();return c!=b&&this.options.onchange&&this.options.onchange(c),c},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(a){this.select_data.push({id:a.id,text:a.text}),this._refresh()},del:function(a){var b=this._getIndex(a);-1!=b&&(this.select_data.splice(b,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(a){this.select_data=[];for(var b in a.data)this.select_data.push(a.data[b]);this._refresh()},_refresh:function(){if(this.options.multiple){var a={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(a)}else{var b=this._getValue(),a={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(a),this._setValue(b)}},_getIndex:function(a){for(var b in this.select_data)if(this.select_data[b].id==a)return b;return-1},_getValue:function(){return this.$el.select2("val")},_setValue:function(a){var b=this._getIndex(a);-1==b&&this.select_data.length>0&&(a=this.select_data[0].id),this.$el.select2("val",a)},_template:function(){return''}});return{View:b}}); //# sourceMappingURL=../../../maps/mvc/ui/ui-select.js.map \ No newline at end of file diff --git a/static/scripts/utils/deferred.js b/static/scripts/utils/deferred.js index e4249d15900..8d93e813da1 100644 --- a/static/scripts/utils/deferred.js +++ b/static/scripts/utils/deferred.js @@ -1,2 +1,2 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})}); +define(["utils/utils"],function(a){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var a=this.queue[0];this.queue.splice(0,1),a&&a()}})},execute:function(a){this.queue.push(a),this.trigger("refresh")},register:function(){var b=a.uid();return this.process[b]=!0,this.counter++,console.debug("Deferred:register() - Register "+b),b},done:function(a){this.process[a]&&(delete this.process[a],this.counter--,console.debug("Deferred:done() - Unregister "+a),this.trigger("refresh"))},reset:function(){this.queue=[]},ready:function(){return 0==this.counter}})}); //# sourceMappingURL=../../maps/utils/deferred.js.map \ No newline at end of file diff --git a/static/scripts/utils/graph.js b/static/scripts/utils/graph.js index 4224fea67e8..5d5a8839b45 100644 --- a/static/scripts/utils/graph.js +++ b/static/scripts/utils/graph.js @@ -1,2 +1,2 @@ -define([],function(){function a(a,b){for(var c in b)if(b.hasOwnProperty(c)&&(!a.hasOwnProperty(c)||a[c]!==b[c]))return!1;return!0}function b(b,c){var d="function"==typeof c?c:void 0,e="object"==typeof c?c:void 0,f=[],g=0;for(var h in b)if(b.hasOwnProperty(h)){var i=b[h];d?f.push(d.call(i,i,h,g)):e?"object"==typeof i&&a(i,e)&&f.push(i):f.push(i),g+=1}return f}function c(a,b,c){var d=this;return d.source=void 0!==a?a:null,d.target=void 0!==b?b:null,d.data=c||null,d}function d(a,b){var c=this;return c.name=void 0!==a?a:"(unnamed)",c.data=b||null,c.edges={},c.degree=0,c}function e(a,b,c){return this.directed=a||!1,this.init(c).read(b)}function f(a,b,c){function d(a){return Math.floor(Math.random()*a)}for(var f={nodes:[],links:[]},g=0;b>g;g++)f.nodes.push({name:g});for(g=0;c>g;g++)f.links.push({source:d(b),target:d(b)});return new e(a,f)}c.prototype.toString=function(){return this.source+"->"+this.target},c.prototype.toJSON=function(){var a={source:this.source,target:this.target};return this.data&&(a.data=this.data),a},d.prototype.toString=function(){return"Vertex("+this.name+")"},d.prototype.eachEdge=function(a){return b(this.edges,a)},d.prototype.toJSON=function(){return{name:this.name,data:this.data}};var g=function(a,b){var c=this;return c.graph=a,c.processFns=b||{vertexEarly:function(){},edge:function(){},vertexLate:function(){}},c._cache={},c};g.prototype.search=function(a){var b=this;return a in b._cache?b._cache[a]:(a instanceof d||(a=b.graph.vertices[a]),b._cache[a.name]=b._search(a))},g.prototype._search=function(a,b){return b=b||{discovered:{},edges:[]}},g.prototype.searchTree=function(a){return this._searchTree(this.search(a))},g.prototype._searchTree=function(a){var b=this;return new e(!0,{edges:a.edges,vertices:Object.keys(a.discovered).map(function(a){return b.graph.vertices[a].toJSON()})})};var h=function(a,b){var c=this;return g.call(this,a,b),c};h.prototype=new g,h.prototype.constructor=h,h.prototype._search=function(a,b){function c(a,c){var f=this;d.processFns.edge&&d.processFns.edge.call(d,f,c,b),b.discovered[a.name]||(b.discovered[a.name]=!0,b.edges.push({source:f.name,target:a.name}),e.push(a))}b=b||{discovered:{},edges:[]};var d=this,e=[];for(b.discovered[a.name]=!0,e.push(a);e.length;){var f=e.shift();d.processFns.vertexEarly&&d.processFns.vertexEarly.call(d,f,b),d.graph.eachAdjacent(f,c),d.processFns.vertexLate&&d.processFns.vertexLate.call(d,f,b)}return b};var i=function(a,b){var c=this;return g.call(this,a,b),c};return i.prototype=new g,i.prototype.constructor=i,i.prototype._search=function(a,b){function c(a,c){var f=this;e.processFns.edge&&e.processFns.edge.call(e,f,c,b),b.discovered[a.name]||(b.edges.push({source:f.name,target:a.name}),d(a))}function d(a){b.discovered[a.name]=!0,e.processFns.vertexEarly&&e.processFns.vertexEarly.call(e,a,b),b.entryTimes[a.name]=f++,e.graph.eachAdjacent(a,c),e.processFns.vertexLate&&e.processFns.vertexLate.call(e,a,b),b.exitTimes[a.name]=f++}b=b||{discovered:{},edges:[],entryTimes:{},exitTimes:{}};var e=this,f=0;return d(a),b},window.Graph=e,e.prototype.init=function(a){a=a||{};var b=this;return b.allowReflexiveEdges=a.allowReflexiveEdges||!1,b.vertices={},b.numEdges=0,b},e.prototype.read=function(a){if(!a)return this;var b=this;return a.hasOwnProperty("nodes")?b.readNodesAndLinks(a):a.hasOwnProperty("vertices")?b.readVerticesAndEdges(a):b},e.prototype.readNodesAndLinks=function(a){if(!a||!a.hasOwnProperty("nodes"))return this;var b=this;return a.nodes.forEach(function(a){b.createVertex(a.name,a.data)}),(a.links||[]).forEach(function(c){var d=a.nodes[c.source].name,e=a.nodes[c.target].name;b.createEdge(d,e,b.directed)}),b},e.prototype.readVerticesAndEdges=function(a){if(!a||!a.hasOwnProperty("vertices"))return this;var b=this;return a.vertices.forEach(function(a){b.createVertex(a.name,a.data)}),(a.edges||[]).forEach(function(a){b.createEdge(a.source,a.target,b.directed)}),b},e.prototype.createVertex=function(a,b){return this.vertices[a]?this.vertices[a]:this.vertices[a]=new d(a,b)},e.prototype.createEdge=function(a,b,d,e){var f=a===b;if(!this.allowReflexiveEdges&&f)return null;if(sourceVertex=this.vertices[a],targetVertex=this.vertices[b],!sourceVertex||!targetVertex)return null;var g=this,h=new c(a,b,e);return sourceVertex.edges[b]=h,sourceVertex.degree+=1,g.numEdges+=1,f||d||g.createEdge(b,a,!0),h},e.prototype.edges=function(a){return Array.prototype.concat.apply([],this.eachVertex(function(b){return b.eachEdge(a)}))},e.prototype.eachVertex=function(a){return b(this.vertices,a)},e.prototype.adjacent=function(a){var c=this;return b(a.edges,function(a){return c.vertices[a.target]})},e.prototype.eachAdjacent=function(a,c){var d=this;return b(a.edges,function(b){var e=d.vertices[b.target];return c.call(a,e,b)})},e.prototype.print=function(){var a=this;return a.eachVertex(function(a){a.eachEdge(function(a){})}),a},e.prototype.toDOT=function(){var a=this,b=[];return b.push("graph bler {"),a.edges(function(a){b.push(" "+a.from+" -- "+a.to+";")}),b.push("}"),b.join("\n")},e.prototype.toNodesAndLinks=function(){var a=this,b={};return{nodes:a.eachVertex(function(a,c,d){return b[a.name]=d,a.toJSON()}),links:a.edges(function(a){var c=a.toJSON();return c.source=b[a.source],c.target=b[a.target],c})}},e.prototype.toVerticesAndEdges=function(){var a=this;return{vertices:a.eachVertex(function(a){return a.toJSON()}),edges:a.edges(function(a){return a.toJSON()})}},e.prototype.breadthFirstSearch=function(a){return new h(this).search(a)},e.prototype.breadthFirstSearchTree=function(a){return new h(this).searchTree(a)},e.prototype.depthFirstSearch=function(a){return new i(this).search(a)},e.prototype.depthFirstSearchTree=function(a){return new i(this).searchTree(a)},e.prototype.weakComponents=function(){function a(a){var e=new i(d)._search(a);return b=b.filter(function(a){return!(a in e.discovered)}),{vertices:Object.keys(e.discovered).map(function(a){return c.vertices[a].toJSON()}),edges:e.edges.map(function(a){var b=void 0!==c.vertices[a.target].edges[a.source];if(c.directed&&b){var d=a.source;a.source=a.target,a.target=d}return a})}}var b,c=this,d=this,f=[];for(c.directed&&(d=new e(!1,c.toNodesAndLinks())),b=Object.keys(d.vertices);b.length;){var g=d.vertices[b.shift()];f.push(a(g))}return f},e.prototype.weakComponentGraph=function(){var a=this.weakComponents();return new e(this.directed,{vertices:a.reduce(function(a,b){return a.concat(b.vertices)},[]),edges:a.reduce(function(a,b){return a.concat(b.edges)},[])})},e.prototype.weakComponentGraphArray=function(){var a=this;return this.weakComponents().map(function(b){return new e(a.directed,b)})},{Vertex:d,Edge:c,BreadthFirstSearch:h,DepthFirstSearch:i,Graph:e,randGraph:f}}); +define([],function(){function a(a,b){for(var c in b)if(b.hasOwnProperty(c)&&(!a.hasOwnProperty(c)||a[c]!==b[c]))return!1;return!0}function b(b,c){var d="function"==typeof c?c:void 0,e="object"==typeof c?c:void 0,f=[],g=0;for(var h in b)if(b.hasOwnProperty(h)){var i=b[h];d?f.push(d.call(i,i,h,g)):e?"object"==typeof i&&a(i,e)&&f.push(i):f.push(i),g+=1}return f}function c(a,b,c){var d=this;return d.source=void 0!==a?a:null,d.target=void 0!==b?b:null,d.data=c||null,d}function d(a,b){var c=this;return c.name=void 0!==a?a:"(unnamed)",c.data=b||null,c.edges={},c.degree=0,c}function e(a,b,c){return this.directed=a||!1,this.init(c).read(b)}function f(a,b,c){function d(a){return Math.floor(Math.random()*a)}for(var f={nodes:[],links:[]},g=0;b>g;g++)f.nodes.push({name:g});for(g=0;c>g;g++)f.links.push({source:d(b),target:d(b)});return new e(a,f)}c.prototype.toString=function(){return this.source+"->"+this.target},c.prototype.toJSON=function(){var a={source:this.source,target:this.target};return this.data&&(a.data=this.data),a},d.prototype.toString=function(){return"Vertex("+this.name+")"},d.prototype.eachEdge=function(a){return b(this.edges,a)},d.prototype.toJSON=function(){return{name:this.name,data:this.data}};var g=function(a,b){var c=this;return c.graph=a,c.processFns=b||{vertexEarly:function(){},edge:function(){},vertexLate:function(){}},c._cache={},c};g.prototype.search=function(a){var b=this;return a in b._cache?b._cache[a]:(a instanceof d||(a=b.graph.vertices[a]),b._cache[a.name]=b._search(a))},g.prototype._search=function(a,b){return b=b||{discovered:{},edges:[]}},g.prototype.searchTree=function(a){return this._searchTree(this.search(a))},g.prototype._searchTree=function(a){var b=this;return new e(!0,{edges:a.edges,vertices:Object.keys(a.discovered).map(function(a){return b.graph.vertices[a].toJSON()})})};var h=function(a,b){var c=this;return g.call(this,a,b),c};h.prototype=new g,h.prototype.constructor=h,h.prototype._search=function(a,b){function c(a,c){var f=this;d.processFns.edge&&d.processFns.edge.call(d,f,c,b),b.discovered[a.name]||(b.discovered[a.name]=!0,b.edges.push({source:f.name,target:a.name}),e.push(a))}b=b||{discovered:{},edges:[]};var d=this,e=[];for(b.discovered[a.name]=!0,e.push(a);e.length;){var f=e.shift();d.processFns.vertexEarly&&d.processFns.vertexEarly.call(d,f,b),d.graph.eachAdjacent(f,c),d.processFns.vertexLate&&d.processFns.vertexLate.call(d,f,b)}return b};var i=function(a,b){var c=this;return g.call(this,a,b),c};return i.prototype=new g,i.prototype.constructor=i,i.prototype._search=function(a,b){function c(a,c){var f=this;e.processFns.edge&&e.processFns.edge.call(e,f,c,b),b.discovered[a.name]||(b.edges.push({source:f.name,target:a.name}),d(a))}function d(a){b.discovered[a.name]=!0,e.processFns.vertexEarly&&e.processFns.vertexEarly.call(e,a,b),b.entryTimes[a.name]=f++,e.graph.eachAdjacent(a,c),e.processFns.vertexLate&&e.processFns.vertexLate.call(e,a,b),b.exitTimes[a.name]=f++}b=b||{discovered:{},edges:[],entryTimes:{},exitTimes:{}};var e=this,f=0;return d(a),b},window.Graph=e,e.prototype.init=function(a){a=a||{};var b=this;return b.allowReflexiveEdges=a.allowReflexiveEdges||!1,b.vertices={},b.numEdges=0,b},e.prototype.read=function(a){if(!a)return this;var b=this;return a.hasOwnProperty("nodes")?b.readNodesAndLinks(a):a.hasOwnProperty("vertices")?b.readVerticesAndEdges(a):b},e.prototype.readNodesAndLinks=function(a){if(!a||!a.hasOwnProperty("nodes"))return this;var b=this;return a.nodes.forEach(function(a){b.createVertex(a.name,a.data)}),(a.links||[]).forEach(function(c){var d=a.nodes[c.source].name,e=a.nodes[c.target].name;b.createEdge(d,e,b.directed)}),b},e.prototype.readVerticesAndEdges=function(a){if(!a||!a.hasOwnProperty("vertices"))return this;var b=this;return a.vertices.forEach(function(a){b.createVertex(a.name,a.data)}),(a.edges||[]).forEach(function(a){b.createEdge(a.source,a.target,b.directed)}),b},e.prototype.createVertex=function(a,b){return this.vertices[a]?this.vertices[a]:this.vertices[a]=new d(a,b)},e.prototype.createEdge=function(a,b,d,e){var f=a===b;if(!this.allowReflexiveEdges&&f)return null;if(sourceVertex=this.vertices[a],targetVertex=this.vertices[b],!sourceVertex||!targetVertex)return null;var g=this,h=new c(a,b,e);return sourceVertex.edges[b]=h,sourceVertex.degree+=1,g.numEdges+=1,f||d||g.createEdge(b,a,!0),h},e.prototype.edges=function(a){return Array.prototype.concat.apply([],this.eachVertex(function(b){return b.eachEdge(a)}))},e.prototype.eachVertex=function(a){return b(this.vertices,a)},e.prototype.adjacent=function(a){var c=this;return b(a.edges,function(a){return c.vertices[a.target]})},e.prototype.eachAdjacent=function(a,c){var d=this;return b(a.edges,function(b){var e=d.vertices[b.target];return c.call(a,e,b)})},e.prototype.print=function(){var a=this;return console.log("Graph has "+Object.keys(a.vertices).length+" vertices"),a.eachVertex(function(a){console.log(a.toString()),a.eachEdge(function(a){console.log(" "+a)})}),a},e.prototype.toDOT=function(){var a=this,b=[];return b.push("graph bler {"),a.edges(function(a){b.push(" "+a.from+" -- "+a.to+";")}),b.push("}"),b.join("\n")},e.prototype.toNodesAndLinks=function(){var a=this,b={};return{nodes:a.eachVertex(function(a,c,d){return b[a.name]=d,a.toJSON()}),links:a.edges(function(a){var c=a.toJSON();return c.source=b[a.source],c.target=b[a.target],c})}},e.prototype.toVerticesAndEdges=function(){var a=this;return{vertices:a.eachVertex(function(a){return a.toJSON()}),edges:a.edges(function(a){return 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d={level:a,namespace:this.options.clientPrefix+b,args:c};return this.options.addTime&&(d.time=(new Date).toISOString()),d},a.prototype._postCache=function(a){if(a=a||{},this._emitToConsole("info","MetricsLogger",["_postCache",a,this._postSize]),!this.options.postUrl||this._sending)return jQuery.when({});var b=this,c=a.count||b._postSize,d=b.cache.get(c),e=d.length,f="function"==typeof b.options.getPingData?b.options.getPingData():{};return f.metrics=JSON.stringify(d),b._sending=!0,jQuery.post(b.options.postUrl,f).always(function(){b._sending=!1}).fail(function(a){b._postSize=b.options.maxCacheSize,this.emit("error","MetricsLogger",["_postCache error:",a.readyState,a.status,a.responseJSON||a.responseText])}).done(function(a){"function"==typeof b.options.onServerResponse&&b.options.onServerResponse(a),b.cache.remove(e),b._postSize=b.options.postSize})},a.prototype._delayPost=function(){var 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    ").addClass("elt-label").appendTo(e.parent_div),g=($("").addClass("slider-name").text(e.name+" ").appendTo(f),$("").text(this.low+"-"+this.high)),h=$("").addClass("slider-value").appendTo(f).append("[").append(g).append("]");e.values_span=g;var i=$("
    ").addClass("slider").appendTo(e.parent_div);e.control_element=$("
    ").attr("id",e.name+"-filter-control").appendTo(i),e.control_element.slider({range:!0,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(a,b){e.slide(a,b)},change:function(a,b){e.control_element.slider("option","slide").call(e.control_element,a,b)}}),e.slider=e.control_element,e.slider_label=g,b(h,g,e.control_element);var j=$("
    ").addClass("display-controls").appendTo(e.parent_div);this.transparency_icon=d("Use filter for data transparency","layer-transparent",function(){e.manager.alpha_filter!==e?(e.manager.alpha_filter=e,e.manager.parent_div.find(".layer-transparent").removeClass("active").hide(),e.transparency_icon.addClass("active").show()):(e.manager.alpha_filter=null,e.transparency_icon.removeClass("active")),e.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(j).hide(),this.height_icon=d("Use filter for data height","arrow-resize-090",function(){e.manager.height_filter!==e?(e.manager.height_filter=e,e.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide(),e.height_icon.addClass("active").show()):(e.manager.height_filter=null,e.height_icon.removeClass("active")),e.manager.track.request_draw({force:!0,clear_after:!0})}).appendTo(j).hide(),e.parent_div.hover(function(){e.transparency_icon.show(),e.height_icon.show()},function(){e.manager.alpha_filter!==e&&e.transparency_icon.hide(),e.manager.height_filter!==e&&e.height_icon.hide()}),$("
    ").appendTo(e.parent_div)};b(e.prototype,{to_dict:function(){var a=c.prototype.to_dict.call(this);return b(a,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new e({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(a,b){var c=b-a;return 2>=c?.01:1},slide:function(a,b){var c=b.values;this.values_span.text(c[0]+"-"+c[1]),this.low=c[0],this.high=c[1];var d=this;setTimeout(function(){c[0]===d.low&&c[1]===d.high&&d.manager.track.request_draw({force:!0,clear_after:!0})},25)},applies_to:function(a){return a.length>this.index?!0:!1},_keep_val:function(a){return isNaN(a)||a>=this.low&&a<=this.high},keep:function(a){if(!this.applies_to(a))return!0;var b=a[this.index];if(b instanceof Array){for(var c=!0,d=0;dthis.max&&(this.max=Math.ceil(e),b=!0)}return b},update_ui_elt:function(){this.minb)&&(this.slider.slider("option","min",this.min),this.slider.slider("option","max",this.max),this.slider.slider("option","step",this.get_slider_step(this.min,this.max)),this.slider.slider("option","values",[this.min,this.max]))}});var f=function(a,b){if(this.track=a,this.alpha_filter=null,this.height_filter=null,this.filters=[],this.parent_div=$("
    ").addClass("filters").hide(),this.parent_div.bind("drag",function(a){a.stopPropagation()}).click(function(a){a.stopPropagation()}).bind("dblclick",function(a){a.stopPropagation()}).bind("keydown",function(a){a.stopPropagation()}),b&&"filters"in b){for(var c,d=("alpha_filter"in b?b.alpha_filter:null),f=("height_filter"in b?b.height_filter:null),g=b.filters,h=0;h").addClass("param-row").appendTo(this.parent_div),j=$("").attr("value","Run on complete dataset").appendTo(i),k=this;j.click(function(){k.run_on_dataset()})}};return b(f.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){for(var a,b={},c=[],d=0;d= "+a.low),a.max!==a.high&&(b=c(d,a.tool_id,[]),b[b.length]=a.tool_exp_name+" <= "+a.high));var f=[];for(var g in d)f[f.length]=[g,d[g]];!function a(b,c){var d=c[0],e=d[0],f=d[1],g="("+f.join(") and (")+")",h={cond:g,input:b,target_dataset_id:b,tool_id:e};c=c.slice(1),$.getJSON(run_tool_url,h,function(b){b.error?Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+e,buttons:{Close:Galaxy.modal.hide()}}):0===c.length?Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}}):a(b.dataset_id,c)})}(this.track.dataset_id,f)}}),{FiltersManager:f,NumberFilter:e}}); //# sourceMappingURL=../../../maps/viz/trackster/filters.js.map \ No newline at end of file diff --git a/static/scripts/viz/visualization.js b/static/scripts/viz/visualization.js index 9b6c5179a10..6376a8e4bc4 100644 --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,2 +1,2 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(a,b,c,d){var e={toJSON:function(){var b=this,c={};return a.each(b.constructor.to_json_keys,function(a){var d=b.get(a);a in b.constructor.to_json_mappers&&(d=b.constructor.to_json_mappers[a](d,b)),c[a]=d}),c}},f=function(a,b,c,d){$.ajax({url:a,data:c,error:function(){alert("Grid failed")},success:function(a){Galaxy.modal.show({title:"Select datasets for new tracks",body:a,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var a=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var c={data_type:"track_config",hda_ldda:"hda"},d=$(this).val();"id"!==$(this).attr("name")&&(c.hda_ldda="ldda"),a[a.length]=$.ajax({url:b+"/"+d,data:c,dataType:"json"})}),$.when.apply($,a).then(function(){var a=arguments[0]instanceof Array?$.map(arguments,function(a){return a[0]}):[arguments[0]];d(a)}),Galaxy.modal.hide()}}})}})},g=function(a){this.default_font=void 0!==a?a:"9px Monaco, Lucida Console, monospace",this.dummy_canvas=this.new_canvas(),this.dummy_context=this.dummy_canvas.getContext("2d"),this.dummy_context.font=this.default_font,this.char_width_px=this.dummy_context.measureText("A").width,this.patterns={},this.load_pattern("right_strand","/visualization/strand_right.png"),this.load_pattern("left_strand","/visualization/strand_left.png"),this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png"),this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};a.extend(g.prototype,{load_pattern:function(a,b){var c=this.patterns,d=this.dummy_context,e=new Image;e.src=galaxy_config.root+"static/images"+b,e.onload=function(){c[a]=d.createPattern(e,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("")[0];return window.G_vmlCanvasManager&&G_vmlCanvasManager.initElement(a),a.manager=this,a}});var h=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=b.toString(),f=a.indexOf(d,function(a){return a.toString()===e});return-1!==f&&(c[e].stale?(d.splice(f,1),delete c[e]):this.move_key_to_end(b,f)),c[e]},set_elt:function(a,b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=a.toString(),f=this.attributes.num_elements;if(!c[e]){if(d.length>=f){var g=d.shift();delete c[g.toString()]}d.push(a)}return c[e]=b,b},move_key_to_end:function(a,b){this.attributes.key_ary.splice(b,1),this.attributes.key_ary.push(a)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),i=h.extend({defaults:a.extend({},h.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(){return!0},can_subset:function(){return!1}}),initialize:function(){h.prototype.initialize.call(this);var a=this.get("init_data");a&&this.add_data(a)},add_data:function(b){this.get("num_elements")m.get("start")?a.set("end",a.get("start")+this.attributes.min_region_size):a.set("start",a.get("end")-this.attributes.min_region_size),a.set("genome",this.attributes.genome),a.trim()}return this.load_data(a,b,d,e)},set_data:function(a,b){this.set_elt(a,b)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(a,b,c,d,e){var f=this._mark_stale(a);if(f&&this.get("data_mode_compatible")(f,b)){var g=a.get("start");e===this.DEEP_DATA_REQ?$.extend(d,{start_val:f.data.length+1}):e===this.BROAD_DATA_REQ&&(g=(f.max_high?f.max_high:f.data[f.data.length-1][2])+1);var h=a.copy().set("start",g),i=this,j=this.load_data(h,b,c,d),k=$.Deferred();return this.set_data(a,k),$.when(j).then(function(b){b.data&&(b.data=f.data.concat(b.data),b.max_low&&(b.max_low=f.max_low),b.message&&(b.message=b.message.replace(/[0-9]+/,b.data.length))),i.set_data(a,b),k.resolve(b)}),k}},can_get_more_detailed_data:function(a){var b=this.get_elt(a);return"bigwig"===b.dataset_type&&b.data.length<8e3},get_more_detailed_data:function(a,b,c,d,e){var f=this._mark_stale(a);if(f)return e||(e={}),"bigwig"===f.dataset_type&&(e.num_samples=1e3*d),this.load_data(a,b,c,e)},_mark_stale:function(a){var b=this.get_elt(a);return b.stale=!0,b},get_genome_wide_data:function(b){var c=this,d=!0,e=a.map(b.get("chroms_info").chrom_info,function(a){var b=c.get_elt(new l({chrom:a.chrom,start:0,end:a.len}));return b||(d=!1),b});if(d)return e;var f=$.Deferred();return $.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(a){c.add_data(a.data),f.resolve(a.data)}),f},subset_entry:function(b,c){var d={bigwig:function(b,c){return a.filter(b,function(a){return a[0]>=c.get("start")&&a[0]<=c.get("end")})},refseq:function(a,c){var d=c.get("start")-b.region.get("start");return b.data.slice(d,d+c.length())}},e=b.data;return!b.region.same(c)&&b.dataset_type in d&&(e=d[b.dataset_type](b.data,c)),{region:c,data:e,dataset_type:b.dataset_type}}}),j=i.extend({initialize:function(a){var b=new Backbone.Model;b.urlRoot=a.data_url,this.set("dataset",b)},load_data:function(a,b,c,d){return a.length()<=1e5?i.prototype.load_data.call(this,a,b,c,d):{data:null,region:a}}}),k=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(a){this.id=a.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(b){var c=a.find(this.get_chroms_info(),function(a){return a.chrom===b});return new l({chrom:c.chrom,end:c.len})},get_chrom_len:function(b){return a.find(this.get_chroms_info(),function(a){return a.chrom===b}).len}}),l=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(a){return this.attributes.chrom===a.get("chrom")&&this.attributes.start===a.get("start")&&this.attributes.end===a.get("end")},initialize:function(a){if(a.from_str){var b=a.from_str.split(":"),c=b[0],d=b[1].split("-");this.set({chrom:c,start:parseInt(d[0],10),end:parseInt(d[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new l({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(a){var b,c=this.get("chrom"),d=a.get("chrom"),e=this.get("start"),f=a.get("start"),g=this.get("end"),h=a.get("end");return c&&d&&c!==d?l.overlap_results.DIF_CHROMS:b=f>e?f>g?l.overlap_results.BEFORE:h>g?l.overlap_results.OVERLAP_START:l.overlap_results.CONTAINS:e>f?e>h?l.overlap_results.AFTER:h>=g?l.overlap_results.CONTAINED_BY:l.overlap_results.OVERLAP_END:g>=h?l.overlap_results.CONTAINS:l.overlap_results.CONTAINED_BY},trim:function(){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var a=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>a&&(this.attributes.end=a-1)}return this},contains:function(a){return this.compute_overlap(a)===l.overlap_results.CONTAINS},overlaps:function(b){return 0===a.intersection([this.compute_overlap(b)],[l.overlap_results.DIF_CHROMS,l.overlap_results.BEFORE,l.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),m=Backbone.Collection.extend({model:l}),n=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(a){this.set("region",new l(a.region))}}),o=Backbone.Collection.extend({model:n}),p=Backbone.Model.extend(e).extend({defaults:{mode:"Auto"},initialize:function(a){this.set("dataset",new b.Dataset(a.dataset));var c=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(c,a.prefs));var e=this.get("preloaded_data");e=e?e.data:[],this.set("data_manager",new i({dataset:this.get("dataset"),init_data:e}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(b,c){return 0===a.size(b)&&(b={name:c.get("config").get("name").get("value"),color:c.get("config").get("color").get("value")}),b},dataset:function(a){return{id:a.id,hda_ldda:a.get("hda_ldda")}}}}),q=Backbone.Collection.extend({model:p}),r=Backbone.Model.extend({defaults:{title:"",type:""},urlRoot:galaxy_config.root+"api/visualizations",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),s=r.extend(e).extend({defaults:a.extend({},r.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(a){this.set("drawables",new q(a.tracks));var b=[];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(b,a.prefs)),this.unset("tracks"),this.get("drawables").each(function(a){a.unset("preloaded_data")})},add_tracks:function(a){this.get("drawables").add(a)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(a,b){return{obj_type:"View",prefs:{name:b.get("title"),content_visible:!0},drawables:b.get("drawables")}}}}),t=Backbone.Router.extend({initialize:function(a){this.view=a.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var b=this;b.view.on("navigate",function(a){b.navigate(a)})},change_location:function(a){this.view.go_to(a)}});return{BackboneTrack:p,BrowserBookmark:n,BrowserBookmarkCollection:o,Cache:h,CanvasManager:g,Genome:k,GenomeDataManager:i,GenomeRegion:l,GenomeRegionCollection:m,GenomeVisualization:s,GenomeReferenceDataManager:j,TrackBrowserRouter:t,Visualization:r,select_datasets:f}}); +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(a,b,c,d){var e={toJSON:function(){var b=this,c={};return a.each(b.constructor.to_json_keys,function(a){var d=b.get(a);a in b.constructor.to_json_mappers&&(d=b.constructor.to_json_mappers[a](d,b)),c[a]=d}),c}},f=function(a,b,c,d){$.ajax({url:a,data:c,error:function(){alert("Grid failed")},success:function(a){Galaxy.modal.show({title:"Select datasets for new tracks",body:a,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var a=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var c={data_type:"track_config",hda_ldda:"hda"},d=$(this).val();"id"!==$(this).attr("name")&&(c.hda_ldda="ldda"),a[a.length]=$.ajax({url:b+"/"+d,data:c,dataType:"json"})}),$.when.apply($,a).then(function(){var a=arguments[0]instanceof Array?$.map(arguments,function(a){return a[0]}):[arguments[0]];d(a)}),Galaxy.modal.hide()}}})}})},g=function(a){this.default_font=void 0!==a?a:"9px Monaco, Lucida Console, monospace",this.dummy_canvas=this.new_canvas(),this.dummy_context=this.dummy_canvas.getContext("2d"),this.dummy_context.font=this.default_font,this.char_width_px=this.dummy_context.measureText("A").width,this.patterns={},this.load_pattern("right_strand","/visualization/strand_right.png"),this.load_pattern("left_strand","/visualization/strand_left.png"),this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png"),this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};a.extend(g.prototype,{load_pattern:function(a,b){var c=this.patterns,d=this.dummy_context,e=new Image;e.src=galaxy_config.root+"static/images"+b,e.onload=function(){c[a]=d.createPattern(e,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("")[0];return window.G_vmlCanvasManager&&G_vmlCanvasManager.initElement(a),a.manager=this,a}});var h=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=b.toString(),f=a.indexOf(d,function(a){return a.toString()===e});return-1!==f&&(c[e].stale?(d.splice(f,1),delete c[e]):this.move_key_to_end(b,f)),c[e]},set_elt:function(a,b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,e=a.toString(),f=this.attributes.num_elements;if(!c[e]){if(d.length>=f){var g=d.shift();delete c[g.toString()]}d.push(a)}return c[e]=b,b},move_key_to_end:function(a,b){this.attributes.key_ary.splice(b,1),this.attributes.key_ary.push(a)},clear:function(){this.attributes.obj_cache={},this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return 0===this.size()?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}}),i=h.extend({defaults:a.extend({},h.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(){return!0},can_subset:function(){return!1}}),initialize:function(){h.prototype.initialize.call(this);var a=this.get("init_data");a&&this.add_data(a)},add_data:function(b){this.get("num_elements")m.get("start")?a.set("end",a.get("start")+this.attributes.min_region_size):a.set("start",a.get("end")-this.attributes.min_region_size),a.set("genome",this.attributes.genome),a.trim()}return this.load_data(a,b,d,e)},set_data:function(a,b){this.set_elt(a,b)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(a,b,c,d,e){var f=this._mark_stale(a);if(!f||!this.get("data_mode_compatible")(f,b))return void console.log("ERROR: problem with getting more data: current data is not compatible");var g=a.get("start");e===this.DEEP_DATA_REQ?$.extend(d,{start_val:f.data.length+1}):e===this.BROAD_DATA_REQ&&(g=(f.max_high?f.max_high:f.data[f.data.length-1][2])+1);var h=a.copy().set("start",g),i=this,j=this.load_data(h,b,c,d),k=$.Deferred();return this.set_data(a,k),$.when(j).then(function(b){b.data&&(b.data=f.data.concat(b.data),b.max_low&&(b.max_low=f.max_low),b.message&&(b.message=b.message.replace(/[0-9]+/,b.data.length))),i.set_data(a,b),k.resolve(b)}),k},can_get_more_detailed_data:function(a){var b=this.get_elt(a);return"bigwig"===b.dataset_type&&b.data.length<8e3},get_more_detailed_data:function(a,b,c,d,e){var f=this._mark_stale(a);return f?(e||(e={}),"bigwig"===f.dataset_type&&(e.num_samples=1e3*d),this.load_data(a,b,c,e)):void console.log("ERROR getting more detailed data: no current data")},_mark_stale:function(a){var b=this.get_elt(a);return b||console.log("ERROR: no data to mark as stale: ",this.get("dataset"),a.toString()),b.stale=!0,b},get_genome_wide_data:function(b){var c=this,d=!0,e=a.map(b.get("chroms_info").chrom_info,function(a){var b=c.get_elt(new l({chrom:a.chrom,start:0,end:a.len}));return b||(d=!1),b});if(d)return e;var f=$.Deferred();return $.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(a){c.add_data(a.data),f.resolve(a.data)}),f},subset_entry:function(b,c){var d={bigwig:function(b,c){return a.filter(b,function(a){return a[0]>=c.get("start")&&a[0]<=c.get("end")})},refseq:function(a,c){var d=c.get("start")-b.region.get("start");return b.data.slice(d,d+c.length())}},e=b.data;return!b.region.same(c)&&b.dataset_type in d&&(e=d[b.dataset_type](b.data,c)),{region:c,data:e,dataset_type:b.dataset_type}}}),j=i.extend({initialize:function(a){var b=new Backbone.Model;b.urlRoot=a.data_url,this.set("dataset",b)},load_data:function(a,b,c,d){return a.length()<=1e5?i.prototype.load_data.call(this,a,b,c,d):{data:null,region:a}}}),k=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(a){this.id=a.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(b){var c=a.find(this.get_chroms_info(),function(a){return a.chrom===b});return new l({chrom:c.chrom,end:c.len})},get_chrom_len:function(b){return a.find(this.get_chroms_info(),function(a){return a.chrom===b}).len}}),l=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(a){return this.attributes.chrom===a.get("chrom")&&this.attributes.start===a.get("start")&&this.attributes.end===a.get("end")},initialize:function(a){if(a.from_str){var b=a.from_str.split(":"),c=b[0],d=b[1].split("-");this.set({chrom:c,start:parseInt(d[0],10),end:parseInt(d[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end"),this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new l({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(a){var b,c=this.get("chrom"),d=a.get("chrom"),e=this.get("start"),f=a.get("start"),g=this.get("end"),h=a.get("end");return c&&d&&c!==d?l.overlap_results.DIF_CHROMS:b=f>e?f>g?l.overlap_results.BEFORE:h>g?l.overlap_results.OVERLAP_START:l.overlap_results.CONTAINS:e>f?e>h?l.overlap_results.AFTER:h>=g?l.overlap_results.CONTAINED_BY:l.overlap_results.OVERLAP_END:g>=h?l.overlap_results.CONTAINS:l.overlap_results.CONTAINED_BY},trim:function(){if(this.attributes.start<0&&(this.attributes.start=0),this.attributes.genome){var a=this.attributes.genome.get_chrom_len(this.attributes.chrom);this.attributes.end>a&&(this.attributes.end=a-1)}return this},contains:function(a){return this.compute_overlap(a)===l.overlap_results.CONTAINS},overlaps:function(b){return 0===a.intersection([this.compute_overlap(b)],[l.overlap_results.DIF_CHROMS,l.overlap_results.BEFORE,l.overlap_results.AFTER]).length}},{overlap_results:{DIF_CHROMS:1e3,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}}),m=Backbone.Collection.extend({model:l}),n=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(a){this.set("region",new l(a.region))}}),o=Backbone.Collection.extend({model:n}),p=Backbone.Model.extend(e).extend({defaults:{mode:"Auto"},initialize:function(a){this.set("dataset",new b.Dataset(a.dataset));var c=[{key:"name",default_value:this.get("dataset").get("name")},{key:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1}];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(c,a.prefs));var e=this.get("preloaded_data");e=e?e.data:[],this.set("data_manager",new i({dataset:this.get("dataset"),init_data:e}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(b,c){return 0===a.size(b)&&(b={name:c.get("config").get("name").get("value"),color:c.get("config").get("color").get("value")}),b},dataset:function(a){return{id:a.id,hda_ldda:a.get("hda_ldda")}}}}),q=Backbone.Collection.extend({model:p}),r=Backbone.Model.extend({defaults:{title:"",type:""},urlRoot:galaxy_config.root+"api/visualizations",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}}),s=r.extend(e).extend({defaults:a.extend({},r.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(a){this.set("drawables",new q(a.tracks));var b=[];this.set("config",d.ConfigSettingCollection.from_models_and_saved_values(b,a.prefs)),this.unset("tracks"),this.get("drawables").each(function(a){a.unset("preloaded_data")})},add_tracks:function(a){this.get("drawables").add(a)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(a,b){return{obj_type:"View",prefs:{name:b.get("title"),content_visible:!0},drawables:b.get("drawables")}}}}),t=Backbone.Router.extend({initialize:function(a){this.view=a.view,this.route(/([\w]+)$/,"change_location"),this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/,"change_location");var b=this;b.view.on("navigate",function(a){b.navigate(a)})},change_location:function(a){this.view.go_to(a)}});return{BackboneTrack:p,BrowserBookmark:n,BrowserBookmarkCollection:o,Cache:h,CanvasManager:g,Genome:k,GenomeDataManager:i,GenomeRegion:l,GenomeRegionCollection:m,GenomeVisualization:s,GenomeReferenceDataManager:j,TrackBrowserRouter:t,Visualization:r,select_datasets:f}}); //# sourceMappingURL=../../maps/viz/visualization.js.map \ No newline at end of file diff --git a/static/style/blue/base.css b/static/style/blue/base.css index 6bc866344c5..7e31952647d 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -2017,6 +2017,8 @@ div.permissionContainer{padding-left:20px} .list-panel .controls>*:not(:empty){margin-bottom:8px} .list-panel .controls .name{word-wrap:break-word;font-weight:bold} .list-panel .controls .subtitle{color:#777;font-size:90%}.list-panel .controls .subtitle a{color:inherit} +.list-panel .controls .editable-text{border:solid transparent 1px} +.list-panel .controls .editable-text:hover{cursor:pointer;border:1px dotted #999999} .list-panel .controls .actions{display:inline-block;float:right}.list-panel .controls .actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} .list-panel .controls .actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} .list-panel .controls .actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} @@ -2088,31 +2090,27 @@ div.permissionContainer{padding-left:20px} .dataset .details .dataset-peek{margin-bottom:8px;width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset .details .dataset-peek th{color:white;background:#5f6990} .dataset .details .dataset-peek table,.dataset .details .dataset-peek th,.dataset .details .dataset-peek tr,.dataset .details .dataset-peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} .history-content.dataset .title-bar .title .hid:after,.history-content.dataset-collection .title-bar .title .hid:after{content:':'} -.history-panel .controls{margin:10px 10px 0px 10px;padding:0px}.history-panel .controls .messages{margin-bottom:0px}.history-panel .controls .messages>*{cursor:pointer}.history-panel .controls .messages>*:last-child{margin-bottom:8px} -.history-panel .controls .title{margin-bottom:4px}.history-panel .controls .title input{width:100%;margin:-3px 0 -3px -3px;font-weight:bold} -.history-panel .controls .subtitle:not(:empty){margin-top:-4px;margin-bottom:6px} -.history-panel .controls .editable-text{border:solid transparent 1px} -.history-panel .controls .editable-text:hover{cursor:pointer;border:1px dotted #999999} -.history-panel .controls .history-size{display:inline-block;margin-top:4px;color:black} -.history-panel .controls .actions{margin-bottom:0px} -.history-panel .controls .quota-message{display:none;margin:8px 0px 5px 0px} -.history-panel .controls .tags-display,.history-panel .controls .annotation-display{display:none;margin-bottom:8px}.history-panel .controls .tags-display label,.history-panel .controls .annotation-display label{display:block;margin:0px;padding:0px;font-weight:normal;color:#555} -.history-panel .controls .tags-display label:after,.history-panel .controls .annotation-display label:after{content:':'} -.history-panel .controls .tags-display .select2-container{min-width:0px}.history-panel .controls .tags-display .select2-container .select2-choices{border-radius:3px} -.history-panel .controls .tags-display input{border-radius:3px} -.history-panel .controls .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.5);padding:4px;white-space:pre-wrap;overflow:auto} -.history-panel .controls .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} -.history-panel .controls .annotation-display textarea{margin:0px 0px 2px 0px;border-radius:3px;width:100%} +.history-panel>.controls{margin:10px 10px 0px 10px;padding:0px}.history-panel>.controls .messages{margin-bottom:0px}.history-panel>.controls .messages>*{cursor:pointer}.history-panel>.controls .messages>*:last-child{margin-bottom:8px} +.history-panel>.controls .title{margin-bottom:4px}.history-panel>.controls .title input{width:100%;margin:-3px 0 -3px -3px;font-weight:bold} +.history-panel>.controls .subtitle:not(:empty){margin-top:-4px;margin-bottom:6px} +.history-panel>.controls .history-size{display:inline-block;margin-top:4px;color:black} +.history-panel>.controls .actions{margin-bottom:0px} +.history-panel>.controls .quota-message{display:none;margin:8px 0px 5px 0px} +.history-panel>.controls .tags-display,.history-panel>.controls .annotation-display{display:none;margin-bottom:8px}.history-panel>.controls .tags-display label,.history-panel>.controls .annotation-display label{display:block;margin:0px;padding:0px;font-weight:normal;color:#555} +.history-panel>.controls .tags-display label:after,.history-panel>.controls .annotation-display label:after{content:':'} +.history-panel>.controls .tags-display .select2-container{min-width:0px}.history-panel>.controls .tags-display .select2-container .select2-choices{border-radius:3px} +.history-panel>.controls .tags-display input{border-radius:3px} +.history-panel>.controls .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.5);padding:4px;white-space:pre-wrap;overflow:auto} +.history-panel>.controls .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} +.history-panel>.controls .annotation-display textarea{margin:0px 0px 2px 0px;border-radius:3px;width:100%} .history-panel .list-item.history-content{border-width:1px 0px 0px 0px}.history-panel .list-item.history-content:last-child{border-width:1px 0px 1px 0px} .history-panel .empty-message{margin:0px 10px 0px 10px} .history-panel .dataset-collection .subtitle{margin-top:2px} -.history-panel .dataset-collection-panel .controls{padding:0px} -.history-panel .dataset-collection-panel .list-items{margin-top:0px} -.annotated-history-panel .controls{margin:0px}.annotated-history-panel .controls .name{font-size:150%;margin-bottom:4px} -.annotated-history-panel .controls .subtitle{color:black}.annotated-history-panel .controls .subtitle:not(:empty){margin:0px 0px 0px 4px} -.annotated-history-panel .controls .messages:not(:empty){margin-top:16px} -.annotated-history-panel .controls .annotation-display{display:block;border:1px solid lightgrey;border-width:1px 0px 0px 0px;padding:4px 0px 4px 0px;margin:4px 4px 0px 4px;white-space:pre-wrap}.annotated-history-panel .controls .annotation-display:empty{display:none} -.annotated-history-panel .controls .search{padding:16px 0px 0px 0px;margin-bottom:0px} +.annotated-history-panel>.controls{margin:0px}.annotated-history-panel>.controls .name{font-size:150%;margin-bottom:4px} +.annotated-history-panel>.controls .subtitle{color:black}.annotated-history-panel>.controls .subtitle:not(:empty){margin:0px 0px 0px 4px} +.annotated-history-panel>.controls .messages:not(:empty){margin-top:16px} +.annotated-history-panel>.controls .annotation-display{display:block;border:1px solid lightgrey;border-width:1px 0px 0px 0px;padding:4px 0px 4px 0px;margin:4px 4px 0px 4px;white-space:pre-wrap}.annotated-history-panel>.controls .annotation-display:empty{display:none} +.annotated-history-panel>.controls .search{padding:16px 0px 0px 0px;margin-bottom:0px} .annotated-history-panel table.list-items{width:100%;table-layout:fixed}.annotated-history-panel table.list-items .headers{border-bottom:2px solid grey} .annotated-history-panel table.list-items .headers th{padding:8px} .annotated-history-panel table.list-items>tbody>tr{cursor:pointer;border-bottom:1px solid grey}.annotated-history-panel table.list-items>tbody>tr>td{margin:0px;padding:0px;vertical-align:top}.annotated-history-panel table.list-items>tbody>tr>td:nth-child(1){width:50%} @@ -2201,7 +2199,7 @@ pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Cons .dataset-collection-panel{margin:0px;padding:0px}.dataset-collection-panel .vertically-spaced{margin-top:4px} .dataset-collection-panel .controls{padding:8px}.dataset-collection-panel .controls .navigation{margin-top:4px}.dataset-collection-panel .controls .navigation .back .fa-icon{margin-right:4px;font-size:120%;font-weight:bold;text-decoration:none} .dataset-collection-panel .controls .title{margin-top:12px}.dataset-collection-panel .controls .title .name{font-weight:bold} -.dataset-collection-panel .list-items{margin-top:8px}.dataset-collection-panel .list-items .dataset-collection-element{border-width:1px 0px 0px 0px}.dataset-collection-panel .list-items .dataset-collection-element:last-child{border-bottom-width:1px} +.dataset-collection-panel .list-items .dataset-collection-element{border-width:1px 0px 0px 0px}.dataset-collection-panel .list-items .dataset-collection-element:last-child{border-bottom-width:1px} .job.list-item{border:1px solid #bfbfbf}.job.list-item .title-bar .subtitle{color:grey;font-size:80%} .job.list-item>.details{padding:0px}.job.list-item>.details .params{padding:0px 8px 0px 8px}.job.list-item>.details .params .param .prompt,.job.list-item>.details .params .input .prompt{font-size:80%;color:grey} .job.list-item>.details .params .param .value,.job.list-item>.details .params .input .value{display:inline-block;font-weight:bold} diff --git a/static/style/src/less/collections.less b/static/style/src/less/collections.less index 3bf32477206..66b570f60b9 100644 --- a/static/style/src/less/collections.less +++ b/static/style/src/less/collections.less @@ -33,7 +33,7 @@ .controls { padding: 8px; - + .navigation { margin-top: 4px; .back { @@ -54,7 +54,6 @@ } } .list-items { - margin-top: 8px; .dataset-collection-element { border-width: 1px 0px 0px 0px; &:last-child { diff --git a/static/style/src/less/history.less b/static/style/src/less/history.less index d2fdb9e5f31..2e936eb05c2 100644 --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -238,7 +238,7 @@ .visualizations-dropdown { display: inline-block; } - + .left { .icon-btn-group(); float: left; @@ -347,7 +347,7 @@ // ---------------------------------------------------------------------------- history .history-panel { - .controls { + & > .controls { margin: 10px 10px 0px 10px; padding: 0px; @@ -374,14 +374,6 @@ margin-top: -4px; margin-bottom: 6px; } - .editable-text { - border: solid transparent 1px; - } - .editable-text:hover { - cursor: pointer; - border: 1px dotted #999999; - } - .history-size { display: inline-block; margin-top: 4px; @@ -473,20 +465,12 @@ margin-top: 2px; } } - .dataset-collection-panel { - .controls { - padding: 0px; - } - .list-items { - margin-top: 0px; - } - } } // ---------------------------------------------------------------------------- annotated-history-panel .annotated-history-panel { - .controls { + & > .controls { margin: 0px; .name { font-size: 150%; diff --git a/static/style/src/less/list-item.less b/static/style/src/less/list-item.less index a74dde23c38..44a9dfd8fe7 100644 --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -143,6 +143,14 @@ color: inherit; } } + .editable-text { + border: solid transparent 1px; + } + .editable-text:hover { + cursor: pointer; + border: 1px dotted #999999; + } + .actions { .icon-btn-group(); float: right;