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commit/galaxy-central: carlfeberhard: History panel (editable and current): show contents count and links to toggle show deleted/hidden in subtitle; minor style fixes
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/875056dd4063/ Changeset: 875056dd4063 User: carlfeberhard Date: 2014-09-29 18:45:29+00:00 Summary: History panel (editable and current): show contents count and links to toggle show deleted/hidden in subtitle; minor style fixes Affected #: 16 files diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 client/galaxy/scripts/mvc/history/history-panel-edit-current.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js @@ -398,14 +398,17 @@ //TODO: move show_deleted/hidden into panel from opt menu and remove this /** add listeners to an external options menu (templates/webapps/galaxy/root/index.mako) */ connectToOptionsMenu : function( optionsMenu ){ + var panel = this; if( !optionsMenu ){ - return this; + return panel; } // set a visible indication in the popupmenu for show_hidden/deleted based on the currHistoryPanel's settings - this.on( 'new-storage', function( storage, panel ){ - if( optionsMenu && storage ){ - optionsMenu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = storage.get( 'show_deleted' ); - optionsMenu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = storage.get( 'show_hidden' ); + this.on( 'new-storage show-deleted show-hidden', function(){ +//TODO: global + var menu = ( Galaxy && Galaxy.historyOptionsMenu )? Galaxy.historyOptionsMenu : undefined; + if( menu ){ + menu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = panel.showDeleted; + menu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = panel.showHidden; } }); return this; diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 client/galaxy/scripts/mvc/history/history-panel-edit.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js @@ -115,6 +115,42 @@ return $newRender; }, + /** override to render counts when the items are rendered */ + renderItems : function( $whereTo ){ + var views = _super.prototype.renderItems.call( this, $whereTo ); + this._renderCounts( $whereTo ); + return views; + }, + + /** override to show counts, what's deleted/hidden, and links to toggle those */ + _renderCounts : function( $whereTo ){ +//TODO: too complicated + function toggleLink( _class, text ){ + return [ '<a class="', _class, '" href="javascript:void(0);">', text, '</a>' ].join( '' ); + } + $whereTo = $whereTo || this.$el; + var deleted = this.collection.where({ deleted: true }), + hidden = this.collection.where({ visible: false }), + msgs = []; + + if( this.views.length ){ + msgs.push( [ this.views.length, _l( 'shown' ) ].join( ' ' ) ); + } + if( deleted.length ){ + msgs.push( ( !this.showDeleted )? + ([ deleted.length, toggleLink( 'toggle-deleted-link', _l( 'deleted' ) ) ].join( ' ' )) + :( toggleLink( 'toggle-deleted-link', _l( 'hide deleted' ) ) ) + ); + } + if( hidden.length ){ + msgs.push( ( !this.showHidden )? + ([ hidden.length, toggleLink( 'toggle-hidden-link', _l( 'hidden' ) ) ].join( ' ' )) + :( toggleLink( 'toggle-hidden-link', _l( 'hide hidden' ) ) ) + ); + } + return $whereTo.find( '.subtitle' ).html( msgs.join( ', ' ) ); + }, + /** render the tags sub-view controller */ _renderTags : function( $where ){ var panel = this; @@ -318,6 +354,7 @@ * @param {Model} the item model to check */ _handleHdaDeletionChange : function( itemModel ){ + this._renderCounts(); if( itemModel.get( 'deleted' ) && !this.showDeleted ){ this.removeItemView( itemModel ); } @@ -327,6 +364,7 @@ * @param {Model} the item model to check */ _handleHdaVisibleChange : function( itemModel ){ + this._renderCounts(); if( itemModel.hidden() && !this.storage.showHidden ){ this.removeItemView( itemModel ); } @@ -355,7 +393,9 @@ // ------------------------------------------------------------------------ panel events /** event map */ events : _.extend( _.clone( _super.prototype.events ), { - 'click .show-selectors-btn' : 'toggleSelectors' + 'click .show-selectors-btn' : 'toggleSelectors', + 'click .toggle-deleted-link' : function( ev ){ this.toggleShowDeleted(); }, + 'click .toggle-hidden-link' : function( ev ){ this.toggleShowHidden(); } }), /** Update the history size display (curr. upper right of panel). diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 client/galaxy/scripts/mvc/history/history-panel.js --- a/client/galaxy/scripts/mvc/history/history-panel.js +++ b/client/galaxy/scripts/mvc/history/history-panel.js @@ -395,6 +395,7 @@ if( store ){ this.storage.set( 'show_deleted', show ); } + this.trigger( 'show-hidden', show ); //TODO:?? to events on storage('change:show_deleted') this.renderItems(); return this.showDeleted; @@ -412,6 +413,7 @@ if( store ){ this.storage.set( 'show_hidden', show ); } + this.trigger( 'show-hidden', show ); //TODO:?? to events on storage('change:show_deleted') this.renderItems(); return this.showHidden; @@ -606,9 +608,7 @@ '<div class="title">', '<div class="name"><%= history.name %></div>', '</div>', - '<div class="subtitle">', - //'<%= view.collection.length %>', _l( ' items' ), - '</div>', + '<div class="subtitle"></div>', '<div class="history-size"><%= history.nice_size %></div>', '<div class="actions"></div>', diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -484,13 +484,13 @@ var panel = this, view = panel.viewFromModel( model ); if( !view ){ return undefined; } + panel.views = _.without( panel.views, view ); // potentially show the empty message if no views left // use anonymous queue here - since remove can happen multiple times $({}).queue( 'fx', [ function( next ){ view.$el.fadeOut( panel.fxSpeed, next ); }, function( next ){ - panel.views = _.without( panel.views, view ); view.remove(); if( !panel.views.length ){ panel._renderEmptyMessage().fadeIn( panel.fxSpeed, next ); diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -398,14 +398,17 @@ //TODO: move show_deleted/hidden into panel from opt menu and remove this /** add listeners to an external options menu (templates/webapps/galaxy/root/index.mako) */ connectToOptionsMenu : function( optionsMenu ){ + var panel = this; if( !optionsMenu ){ - return this; + return panel; } // set a visible indication in the popupmenu for show_hidden/deleted based on the currHistoryPanel's settings - this.on( 'new-storage', function( storage, panel ){ - if( optionsMenu && storage ){ - optionsMenu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = storage.get( 'show_deleted' ); - optionsMenu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = storage.get( 'show_hidden' ); + this.on( 'new-storage show-deleted show-hidden', function(){ +//TODO: global + var menu = ( Galaxy && Galaxy.historyOptionsMenu )? Galaxy.historyOptionsMenu : undefined; + if( menu ){ + menu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = panel.showDeleted; + menu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = panel.showHidden; } }); return this; diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -115,6 +115,42 @@ return $newRender; }, + /** override to render counts when the items are rendered */ + renderItems : function( $whereTo ){ + var views = _super.prototype.renderItems.call( this, $whereTo ); + this._renderCounts( $whereTo ); + return views; + }, + + /** override to show counts, what's deleted/hidden, and links to toggle those */ + _renderCounts : function( $whereTo ){ +//TODO: too complicated + function toggleLink( _class, text ){ + return [ '<a class="', _class, '" href="javascript:void(0);">', text, '</a>' ].join( '' ); + } + $whereTo = $whereTo || this.$el; + var deleted = this.collection.where({ deleted: true }), + hidden = this.collection.where({ visible: false }), + msgs = []; + + if( this.views.length ){ + msgs.push( [ this.views.length, _l( 'shown' ) ].join( ' ' ) ); + } + if( deleted.length ){ + msgs.push( ( !this.showDeleted )? + ([ deleted.length, toggleLink( 'toggle-deleted-link', _l( 'deleted' ) ) ].join( ' ' )) + :( toggleLink( 'toggle-deleted-link', _l( 'hide deleted' ) ) ) + ); + } + if( hidden.length ){ + msgs.push( ( !this.showHidden )? + ([ hidden.length, toggleLink( 'toggle-hidden-link', _l( 'hidden' ) ) ].join( ' ' )) + :( toggleLink( 'toggle-hidden-link', _l( 'hide hidden' ) ) ) + ); + } + return $whereTo.find( '.subtitle' ).html( msgs.join( ', ' ) ); + }, + /** render the tags sub-view controller */ _renderTags : function( $where ){ var panel = this; @@ -318,6 +354,7 @@ * @param {Model} the item model to check */ _handleHdaDeletionChange : function( itemModel ){ + this._renderCounts(); if( itemModel.get( 'deleted' ) && !this.showDeleted ){ this.removeItemView( itemModel ); } @@ -327,6 +364,7 @@ * @param {Model} the item model to check */ _handleHdaVisibleChange : function( itemModel ){ + this._renderCounts(); if( itemModel.hidden() && !this.storage.showHidden ){ this.removeItemView( itemModel ); } @@ -355,7 +393,9 @@ // ------------------------------------------------------------------------ panel events /** event map */ events : _.extend( _.clone( _super.prototype.events ), { - 'click .show-selectors-btn' : 'toggleSelectors' + 'click .show-selectors-btn' : 'toggleSelectors', + 'click .toggle-deleted-link' : function( ev ){ this.toggleShowDeleted(); }, + 'click .toggle-hidden-link' : function( ev ){ this.toggleShowHidden(); } }), /** Update the history size display (curr. upper right of panel). diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -395,6 +395,7 @@ if( store ){ this.storage.set( 'show_deleted', show ); } + this.trigger( 'show-hidden', show ); //TODO:?? to events on storage('change:show_deleted') this.renderItems(); return this.showDeleted; @@ -412,6 +413,7 @@ if( store ){ this.storage.set( 'show_hidden', show ); } + this.trigger( 'show-hidden', show ); //TODO:?? to events on storage('change:show_deleted') this.renderItems(); return this.showHidden; @@ -606,9 +608,7 @@ '<div class="title">', '<div class="name"><%= history.name %></div>', '</div>', - '<div class="subtitle">', - //'<%= view.collection.length %>', _l( ' items' ), - '</div>', + '<div class="subtitle"></div>', '<div class="history-size"><%= history.nice_size %></div>', '<div class="actions"></div>', diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -484,13 +484,13 @@ var panel = this, view = panel.viewFromModel( model ); if( !view ){ return undefined; } + panel.views = _.without( panel.views, view ); // potentially show the empty message if no views left // use anonymous queue here - since remove can happen multiple times $({}).queue( 'fx', [ function( next ){ view.$el.fadeOut( panel.fxSpeed, next ); }, function( next ){ - panel.views = _.without( panel.views, view ); view.remove(); if( !panel.views.length ){ panel._renderEmptyMessage().fadeIn( panel.fxSpeed, next ); diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/packed/mvc/history/history-panel-edit-current.js --- a/static/scripts/packed/mvc/history/history-panel-edit-current.js +++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){g.prototype._attachItems.call(this,k);var j=this,l;if(j.currentContentId&&(l=j.viewFromModelId(j.currentContentId))){j.setCurrentContent(l)}return this},addItemView:function(l,m,k){var j=g.prototype.addItemView.call(this,l,m,k);if(!j){return j}if(this.panelStack.length){return this._collapseDrilldownPanel()}return j},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){g.prototype._attachItems.call(this,k);var j=this,l;if(j.currentContentId&&(l=j.viewFromModelId(j.currentContentId))){j.setCurrentContent(l)}return this},addItemView:function(l,m,k){var j=g.prototype.addItemView.call(this,l,m,k);if(!j){return j}if(this.panelStack.length){return this._collapseDrilldownPanel()}return j},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){var k=this;if(!j){return k}this.on("new-storage show-deleted show-hidden",function(){var l=(Galaxy&&Galaxy.historyOptionsMenu)?Galaxy.historyOptionsMenu:undefined;if(l){l.findItemByHtml(b("Include Deleted Datasets")).checked=k.showDeleted;l.findItemByHtml(b("Include Hidden Datasets")).checked=k.showHidden}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/packed/mvc/history/history-panel-edit.js --- a/static/scripts/packed/mvc/history/history-panel-edit.js +++ b/static/scripts/packed/mvc/history/history-panel-edit.js @@ -1,1 +1,1 @@ -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","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpListeners:function(){i.prototype._setUpListeners.call(this);this.on("drop",function(l,m){this.dataDropped(m);this.dropTargetOff()})},_setUpCollectionListeners:function(){i.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(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_attachItems:function(l){this.$list(l).append(this.views.reverse().map(function(m){return m.$el}));return this},_attachView:function(m){var l=this;l.views.unshift(m);l.$list().prepend(m.render(0).$el.hide());m.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){if(l.get("deleted")&&!this.showDeleted){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){if(l.hidden()&&!this.storage.showHidden){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var m={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var n=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),n]);for(var l in m){if(m.hasOwnProperty(l)){n.on(l,m[l])}}return this},_renderDropTarget:function(){return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(b("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(l){l.preventDefault();l.stopPropagation()},dragleave:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(n){n.preventDefault();n.dataTransfer.dropEffect="move";var l=this,o=n.dataTransfer.getData("text");try{o=JSON.parse(o)}catch(m){this.warn("error parsing JSON from drop:",o)}this.trigger("droptarget:drop",n,o,l);return false},dataDropped:function(m){var l=this;if(_.isObject(m)&&m.model_class==="HistoryDatasetAssociation"&&m.id){return l.model.contents.copy(m.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file +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","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpListeners:function(){i.prototype._setUpListeners.call(this);this.on("drop",function(l,m){this.dataDropped(m);this.dropTargetOff()})},_setUpCollectionListeners:function(){i.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(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},renderItems:function(m){var l=i.prototype.renderItems.call(this,m);this._renderCounts(m);return l},_renderCounts:function(n){function m(q,r){return['<a class="',q,'" href="javascript:void(0);">',r,"</a>"].join("")}n=n||this.$el;var l=this.collection.where({deleted:true}),p=this.collection.where({visible:false}),o=[];if(this.views.length){o.push([this.views.length,b("shown")].join(" "))}if(l.length){o.push((!this.showDeleted)?([l.length,m("toggle-deleted-link",b("deleted"))].join(" ")):(m("toggle-deleted-link",b("hide deleted"))))}if(p.length){o.push((!this.showHidden)?([p.length,m("toggle-hidden-link",b("hidden"))].join(" ")):(m("toggle-hidden-link",b("hide hidden"))))}return n.find(".subtitle").html(o.join(", "))},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_attachItems:function(l){this.$list(l).append(this.views.reverse().map(function(m){return m.$el}));return this},_attachView:function(m){var l=this;l.views.unshift(m);l.$list().prepend(m.render(0).$el.hide());m.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){this._renderCounts();if(l.get("deleted")&&!this.showDeleted){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){this._renderCounts();if(l.hidden()&&!this.storage.showHidden){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(l){this.toggleShowDeleted()},"click .toggle-hidden-link":function(l){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var m={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var n=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),n]);for(var l in m){if(m.hasOwnProperty(l)){n.on(l,m[l])}}return this},_renderDropTarget:function(){return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(b("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(l){l.preventDefault();l.stopPropagation()},dragleave:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(n){n.preventDefault();n.dataTransfer.dropEffect="move";var l=this,o=n.dataTransfer.getData("text");try{o=JSON.parse(o)}catch(m){this.warn("error parsing JSON from drop:",o)}this.trigger("droptarget:drop",n,o,l);return false},dataDropped:function(m){var l=this;if(_.isObject(m)&&m.model_class==="HistoryDatasetAssociation"&&m.id){return l.model.contents.copy(m.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(d,f,l,b,a,m,g,o,e){var j=o.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(p){var q="expandedIds";this.save(q,_.extend(this.get(q),_.object([p.id],[p.get("id")])))},removeExpanded:function(p){var q="expandedIds";this.save(q,_.omit(this.get(q),p.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});j.storageKeyPrefix="history:";j.historyStorageKey=function h(p){if(!p){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+p)}return(j.storageKeyPrefix+p)};j.get=function c(p){return new j({id:j.historyStorageKey(p)})};j.clearAll=function i(q){for(var p in sessionStorage){if(p.indexOf(j.storageKeyPrefix)===0){sessionStorage.removeItem(p)}}};var n=d.ModelListPanel;var k=n.extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:l.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:n.prototype.className+" history-panel",emptyMsg:e("This history is empty"),noneFoundMsg:e("No matching datasets found"),searchPlaceholder:e("search datasets"),initialize:function(p){n.prototype.initialize.call(this,p);this.linkTarget=p.linkTarget||"_blank"},freeModel:function(){n.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){n.prototype._setUpListeners.call(this);this.on("error",function(q,t,p,s,r){this.errorHandler(q,t,p,s,r)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(s,r,q,t){this.info("loadHistoryWithDetails:",s,r,q,t);var p=function(u){return _.values(j.get(u.id).get("expandedIds"))};return this.loadHistory(s,r,q,t,p)},loadHistory:function(t,s,r,u,p){this.info("loadHistory:",t,s,r,u,p);var q=this;s=s||{};q.trigger("loading",q);var v=f.History.getHistoryData(t,{historyFn:r,contentsFn:u,detailIdsFn:s.initiallyExpanded||p});return q._loadHistoryFromXHR(v,s).fail(function(y,w,x){q.trigger("error",q,y,s,e("An error was encountered while "+w),{historyId:t,history:x||{}})}).always(function(){q.trigger("loading-done",q)})},_loadHistoryFromXHR:function(r,q){var p=this;r.then(function(s,t){p.JSONToModel(s,t,q);p.render()});r.fail(function(t,s){p.render()});return r},refreshContents:function(q,p){if(this.model){return this.model.refresh(q,p)}return $.when()},JSONToModel:function(s,p,q){this.log("JSONToModel:",s,p,q);q=q||{};var r=new f.History(s,p,q);this.setModel(r);return r},setModel:function(q,p){p=p||{};n.prototype.setModel.call(this,q,p);if(this.model){this._setUpWebStorage(p.initiallyExpanded,p.show_deleted,p.show_hidden)}},_setUpWebStorage:function(q,p,r){if(this.storage){this.stopListening(this.storage)}this.storage=new j({id:j.historyStorageKey(this.model.get("id"))});if(_.isObject(q)){this.storage.set("expandedIds",q)}if(_.isBoolean(p)){this.storage.set("show_deleted",p)}if(_.isBoolean(r)){this.storage.set("show_hidden",r)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());this.listenTo(this.storage,{"change:show_deleted":function(s,t){this.showDeleted=t},"change:show_hidden":function(s,t){this.showHidden=t}},this);this.showDeleted=(p!==undefined)?p:this.storage.get("show_deleted");this.showHidden=(r!==undefined)?r:this.storage.get("show_hidden");return this},_buildNewRender:function(){var p=n.prototype._buildNewRender.call(this);if(this.multiselectActions.length){p.find(".controls .actions").prepend(this._renderSelectButton())}return p},_renderSelectButton:function(p){return faIconButton({title:e("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(p){var q=p.get("history_content_type");switch(q){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+q)},_filterItem:function(q){var p=this;return(n.prototype._filterItem.call(p,q)&&(!q.hidden()||p.showHidden)&&(!q.isDeletedOrPurged()||p.showDeleted))},_getItemViewOptions:function(q){var p=n.prototype._getItemViewOptions.call(this,q);return _.extend(p,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[q.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(q){var p=this;n.prototype._setUpItemViewListeners.call(p,q);q.on("expanded",function(r){p.storage.addExpanded(r.model)});q.on("collapsed",function(r){p.storage.removeExpanded(r.model)});return this},getSelectedModels:function(){var p=n.prototype.getSelectedModels.call(this);p.historyId=this.collection.historyId;return p},events:_.extend(_.clone(n.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(p,q){p=(p!==undefined)?(p):(!this.showDeleted);q=(q!==undefined)?(q):(true);this.showDeleted=p;if(q){this.storage.set("show_deleted",p)}this.renderItems();return this.showDeleted},toggleShowHidden:function(p,q){p=(p!==undefined)?(p):(!this.showHidden);q=(q!==undefined)?(q):(true);this.showHidden=p;if(q){this.storage.set("show_hidden",p)}this.renderItems();return this.showHidden},_firstSearch:function(p){var q=this,r=".history-search-input";this.log("onFirstSearch",p);if(q.model.contents.haveDetails()){q.searchItems(p);return}q.$el.find(r).searchInput("toggle-loading");q.model.contents.fetchAllDetails({silent:true}).always(function(){q.$el.find(r).searchInput("toggle-loading")}).done(function(){q.searchItems(p)})},errorHandler:function(r,u,q,t,s){this.error(r,u,q,t,s);if(u&&u.status===0&&u.readyState===0){}else{if(u&&u.status===502){}else{var p=this._parseErrorMessage(r,u,q,t,s);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",p.message,p.details)})}else{this.displayMessage("error",p.message,p.details)}}}},_parseErrorMessage:function(t,w,x,r,p,u){var s=Galaxy.currUser,v={message:this._bePolite(r),details:{message:r,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(w)?(_.omit(x,"xhr")):(x),xhr:w,source:(_.isFunction(t.toJSON))?(t.toJSON()):(t+""),user:(s instanceof g.User)?(s.toJSON()):(s+"")}};_.extend(v.details,p||{});if(w&&_.isFunction(w.getAllResponseHeaders)){var q=w.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(y){return y.split(": ")});v.details.xhr.responseHeaders=_.object(q)}return v},_bePolite:function(p){p=p||e("An error occurred while getting updates from the server");return p+". "+e("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(u,v,t){var r=this;this.scrollToTop();var s=this.$messages(),p=$("<div/>").addClass(u+"message").html(v);if(!_.isEmpty(t)){var q=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(r._messageToModalOptions(u,v,t));return false});p.append(" ",q)}return s.html(p)},_messageToModalOptions:function(s,v,r){var p=this,q={title:"Details"};if(_.isObject(r)){r=_.omit(r,_.functions(r));var u=JSON.stringify(r,null," "),t=$("<pre/>").text(u);q.body=$("<div/>").append(t)}else{q.body=$("<div/>").html(r)}q.buttons={Ok:function(){Galaxy.modal.hide();p.clearMessages()}};return q},clearMessages:function(p){$(p.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(p){return this.scrollToItem(_.first(this.viewsWhereModel({hid:p})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});k.prototype.templates=(function(){var p=o.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle">',"</div>",'<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',e("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',e("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',e("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',e("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(n.prototype.templates),{controls:p})}());return{HistoryPanel:k}}); \ No newline at end of file +define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(d,f,l,b,a,m,g,o,e){var j=o.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(p){var q="expandedIds";this.save(q,_.extend(this.get(q),_.object([p.id],[p.get("id")])))},removeExpanded:function(p){var q="expandedIds";this.save(q,_.omit(this.get(q),p.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});j.storageKeyPrefix="history:";j.historyStorageKey=function h(p){if(!p){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+p)}return(j.storageKeyPrefix+p)};j.get=function c(p){return new j({id:j.historyStorageKey(p)})};j.clearAll=function i(q){for(var p in sessionStorage){if(p.indexOf(j.storageKeyPrefix)===0){sessionStorage.removeItem(p)}}};var n=d.ModelListPanel;var k=n.extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:l.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:n.prototype.className+" history-panel",emptyMsg:e("This history is empty"),noneFoundMsg:e("No matching datasets found"),searchPlaceholder:e("search datasets"),initialize:function(p){n.prototype.initialize.call(this,p);this.linkTarget=p.linkTarget||"_blank"},freeModel:function(){n.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){n.prototype._setUpListeners.call(this);this.on("error",function(q,t,p,s,r){this.errorHandler(q,t,p,s,r)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(s,r,q,t){this.info("loadHistoryWithDetails:",s,r,q,t);var p=function(u){return _.values(j.get(u.id).get("expandedIds"))};return this.loadHistory(s,r,q,t,p)},loadHistory:function(t,s,r,u,p){this.info("loadHistory:",t,s,r,u,p);var q=this;s=s||{};q.trigger("loading",q);var v=f.History.getHistoryData(t,{historyFn:r,contentsFn:u,detailIdsFn:s.initiallyExpanded||p});return q._loadHistoryFromXHR(v,s).fail(function(y,w,x){q.trigger("error",q,y,s,e("An error was encountered while "+w),{historyId:t,history:x||{}})}).always(function(){q.trigger("loading-done",q)})},_loadHistoryFromXHR:function(r,q){var p=this;r.then(function(s,t){p.JSONToModel(s,t,q);p.render()});r.fail(function(t,s){p.render()});return r},refreshContents:function(q,p){if(this.model){return this.model.refresh(q,p)}return $.when()},JSONToModel:function(s,p,q){this.log("JSONToModel:",s,p,q);q=q||{};var r=new f.History(s,p,q);this.setModel(r);return r},setModel:function(q,p){p=p||{};n.prototype.setModel.call(this,q,p);if(this.model){this._setUpWebStorage(p.initiallyExpanded,p.show_deleted,p.show_hidden)}},_setUpWebStorage:function(q,p,r){if(this.storage){this.stopListening(this.storage)}this.storage=new j({id:j.historyStorageKey(this.model.get("id"))});if(_.isObject(q)){this.storage.set("expandedIds",q)}if(_.isBoolean(p)){this.storage.set("show_deleted",p)}if(_.isBoolean(r)){this.storage.set("show_hidden",r)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());this.listenTo(this.storage,{"change:show_deleted":function(s,t){this.showDeleted=t},"change:show_hidden":function(s,t){this.showHidden=t}},this);this.showDeleted=(p!==undefined)?p:this.storage.get("show_deleted");this.showHidden=(r!==undefined)?r:this.storage.get("show_hidden");return this},_buildNewRender:function(){var p=n.prototype._buildNewRender.call(this);if(this.multiselectActions.length){p.find(".controls .actions").prepend(this._renderSelectButton())}return p},_renderSelectButton:function(p){return faIconButton({title:e("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(p){var q=p.get("history_content_type");switch(q){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+q)},_filterItem:function(q){var p=this;return(n.prototype._filterItem.call(p,q)&&(!q.hidden()||p.showHidden)&&(!q.isDeletedOrPurged()||p.showDeleted))},_getItemViewOptions:function(q){var p=n.prototype._getItemViewOptions.call(this,q);return _.extend(p,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[q.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(q){var p=this;n.prototype._setUpItemViewListeners.call(p,q);q.on("expanded",function(r){p.storage.addExpanded(r.model)});q.on("collapsed",function(r){p.storage.removeExpanded(r.model)});return this},getSelectedModels:function(){var p=n.prototype.getSelectedModels.call(this);p.historyId=this.collection.historyId;return p},events:_.extend(_.clone(n.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(p,q){p=(p!==undefined)?(p):(!this.showDeleted);q=(q!==undefined)?(q):(true);this.showDeleted=p;if(q){this.storage.set("show_deleted",p)}this.trigger("show-hidden",p);this.renderItems();return this.showDeleted},toggleShowHidden:function(p,q){p=(p!==undefined)?(p):(!this.showHidden);q=(q!==undefined)?(q):(true);this.showHidden=p;if(q){this.storage.set("show_hidden",p)}this.trigger("show-hidden",p);this.renderItems();return this.showHidden},_firstSearch:function(p){var q=this,r=".history-search-input";this.log("onFirstSearch",p);if(q.model.contents.haveDetails()){q.searchItems(p);return}q.$el.find(r).searchInput("toggle-loading");q.model.contents.fetchAllDetails({silent:true}).always(function(){q.$el.find(r).searchInput("toggle-loading")}).done(function(){q.searchItems(p)})},errorHandler:function(r,u,q,t,s){this.error(r,u,q,t,s);if(u&&u.status===0&&u.readyState===0){}else{if(u&&u.status===502){}else{var p=this._parseErrorMessage(r,u,q,t,s);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",p.message,p.details)})}else{this.displayMessage("error",p.message,p.details)}}}},_parseErrorMessage:function(t,w,x,r,p,u){var s=Galaxy.currUser,v={message:this._bePolite(r),details:{message:r,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(w)?(_.omit(x,"xhr")):(x),xhr:w,source:(_.isFunction(t.toJSON))?(t.toJSON()):(t+""),user:(s instanceof g.User)?(s.toJSON()):(s+"")}};_.extend(v.details,p||{});if(w&&_.isFunction(w.getAllResponseHeaders)){var q=w.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(y){return y.split(": ")});v.details.xhr.responseHeaders=_.object(q)}return v},_bePolite:function(p){p=p||e("An error occurred while getting updates from the server");return p+". "+e("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(u,v,t){var r=this;this.scrollToTop();var s=this.$messages(),p=$("<div/>").addClass(u+"message").html(v);if(!_.isEmpty(t)){var q=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(r._messageToModalOptions(u,v,t));return false});p.append(" ",q)}return s.html(p)},_messageToModalOptions:function(s,v,r){var p=this,q={title:"Details"};if(_.isObject(r)){r=_.omit(r,_.functions(r));var u=JSON.stringify(r,null," "),t=$("<pre/>").text(u);q.body=$("<div/>").append(t)}else{q.body=$("<div/>").html(r)}q.buttons={Ok:function(){Galaxy.modal.hide();p.clearMessages()}};return q},clearMessages:function(p){$(p.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(p){return this.scrollToItem(_.first(this.viewsWhereModel({hid:p})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});k.prototype.templates=(function(){var p=o.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle"></div>','<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',e("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',e("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',e("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',e("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(n.prototype.templates),{controls:p})}());return{HistoryPanel:k}}); \ No newline at end of file diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.dragItems=f.dragItems||false;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},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);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}else{if(g&&g.altKey&&!this.selecting){this.showSelectors()}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragItems}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});g.on("draggable:dragstart",function(k,h){var i={},j=this.getSelectedModels();if(j.length){i=j.toJSON()}else{i=[h.model.toJSON()]}k.dataTransfer.setData("text",JSON.stringify(i))},this);return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g._attachView(f);k()}]);return f},_attachView:function(g){var f=this;f.views.push(g);f.$list().append(g.render(0).$el.hide());g.$el.slideDown(f.fxSpeed)},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.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)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();this.$("> .controls .search-query").val(f);return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.dragItems=f.dragItems||false;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},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);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}else{if(g&&g.altKey&&!this.selecting){this.showSelectors()}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragItems}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});g.on("draggable:dragstart",function(k,h){var i={},j=this.getSelectedModels();if(j.length){i=j.toJSON()}else{i=[h.model.toJSON()]}k.dataTransfer.setData("text",JSON.stringify(i))},this);return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g._attachView(f);k()}]);return f},_attachView:function(g){var f=this;f.views.push(g);f.$list().append(g.render(0).$el.hide());g.$el.slideDown(f.fxSpeed)},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}g.views=_.without(g.views,f);$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.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)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();this.$("> .controls .search-query").val(f);return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1854,6 +1854,7 @@ .list-item .selector{float:left;display:none;width:32px;height:32px;margin:0 0 -6px 0;padding:8px 0 2px 7px;font-size:80%;color:#333;cursor:pointer;vertical-align:middle} .list-item .selector:hover{color:maroon} .list-item .title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px}.list-item .title-bar .title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} +.list-item .title-bar .subtitle{color:#777;font-size:90%}.list-item .title-bar .subtitle a{color:inherit} .list-item .primary-actions{display:inline-block;float:right;margin:6px 10px 0}.list-item .primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} .list-item .primary-actions .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} .list-item .primary-actions .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} @@ -1866,7 +1867,7 @@ .list-panel .vertical-spacing{margin-bottom:8px} .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{color:#777;font-size:90%}.list-panel .controls .subtitle a{color:inherit} .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} @@ -1940,12 +1941,12 @@ .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;padding:0px}.history-panel .controls .messages>*{cursor:pointer} +.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:4px} +.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;color:black} +.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} @@ -1954,11 +1955,11 @@ .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;display:block;border-radius:3px;width:100%} +.history-panel .controls .annotation-display textarea{margin:0px 0px 2px 0px;border-radius:3px;width:100%} .history-panel .controls .list-actions .list-action-popup-btn{float:right} .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;font-size:90%;color:#777} +.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} @@ -2013,7 +2014,7 @@ .dataset-collection-element.state-discarded{background:#eee}.dataset-collection-element.state-discarded .state-icon:before{content:"\f014"} .dataset-collection-element.state-noPermission{background:#eee;filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}.dataset-collection-element.state-noPermission .state-icon{font-size:20px}.dataset-collection-element.state-noPermission .state-icon:before{content:"\f023"} .dataset-collection-element.state-new{background:#eee}.dataset-collection-element.state-new .state-icon:before{content:"\f06a"} -.dataset-collection-element .title-bar .subtitle{margin-top:2px;font-size:90%;color:#777} +.dataset-collection-element .title-bar .subtitle{margin-top:2px} .dataset-collection-element .details{display:none} .history-content.dataset-collection.state-ok,.history-content.dataset-collection.state-failed_metadata{background:#aff1af}.history-content.dataset-collection.state-ok .state-icon,.history-content.dataset-collection.state-failed_metadata .state-icon{display:none} .history-content.dataset-collection.state-error,.history-content.dataset-collection.state-empty{background:#f9c7c5}.history-content.dataset-collection.state-error .state-icon,.history-content.dataset-collection.state-empty .state-icon{background-color:white;border-radius:8px}.history-content.dataset-collection.state-error .state-icon:before,.history-content.dataset-collection.state-empty .state-icon:before{font-size:20px;line-height:16px;color:red;content:"\f057"} @@ -2027,7 +2028,6 @@ .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 .controls .subtitle{color:#777} .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} .collection-creator{height:100%;overflow:hidden;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none}.collection-creator ol,.collection-creator li{list-style:none;padding:0;margin:0} .collection-creator>*:not(.popover){padding:0px 8px 0px 8px} diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/style/src/less/collections.less --- a/static/style/src/less/collections.less +++ b/static/style/src/less/collections.less @@ -4,8 +4,6 @@ .title-bar { .subtitle { margin-top: 2px; - font-size: 90%; - color: #777; } } .details { @@ -54,9 +52,6 @@ font-weight: bold; } } - .subtitle { - color: #777; - } } .list-items { margin-top: 8px; diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -373,11 +373,17 @@ .history-panel { .controls { - margin: 10px; + margin: 10px 10px 0px 10px; padding: 0px; - .messages > * { - cursor: pointer; + .messages { + margin-bottom: 0px; + & > * { + cursor: pointer; + &:last-child { + margin-bottom: 8px; + } + } } .title { @@ -391,7 +397,7 @@ } .subtitle:not(:empty){ margin-top: -4px; - margin-bottom: 4px; + margin-bottom: 6px; } .editable-text { border: solid transparent 1px; @@ -403,6 +409,7 @@ .history-size { display: inline-block; + margin-top: 4px; color: black; } .actions { @@ -442,6 +449,7 @@ } .annotation-display { .annotation { + //display: inline-block; border-radius: 3px; border: 1px solid fadeout( @layout-border-color, 50% ); padding: 4px; @@ -461,7 +469,7 @@ } textarea { margin: 0px 0px 2px 0px; - display: block; + //display: block; border-radius: 3px; width: 100%; } @@ -494,8 +502,6 @@ .dataset-collection { .subtitle { margin-top: 2px; - font-size: 90%; - color: #777; } } .dataset-collection-panel { diff -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 -r 875056dd4063fd1553e3c800d472d336c09636f6 static/style/src/less/list-item.less --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -77,6 +77,13 @@ //&:focus { // color: maroon; //} + .subtitle { + color: #777; + font-size: 90%; + a { + color: inherit; + } + } } .primary-actions { @@ -132,6 +139,9 @@ .subtitle { color: #777; font-size: 90%; + a { + color: inherit; + } } .actions { .icon-btn-group(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Upload: Minor fix, wait for history in show function
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e6c63c296e4/ Changeset: 3e6c63c296e4 User: guerler Date: 2014-09-29 18:24:21+00:00 Summary: Upload: Minor fix, wait for history in show function Affected #: 3 files diff -r b8efe7496a7e591450722765cdca0307ffad957f -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 client/galaxy/scripts/mvc/upload/upload-view.js --- a/client/galaxy/scripts/mvc/upload/upload-view.js +++ b/client/galaxy/scripts/mvc/upload/upload-view.js @@ -83,12 +83,6 @@ this.options = _.defaults(options, this.options); } - // wait for galaxy history panel (workaround due to the use of iframes) - if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) { - window.setTimeout(function() { self.initialize() }, 500) - return; - } - // create model this.ui_button = new UploadButton.Model({ icon : 'fa-upload', @@ -173,6 +167,13 @@ // show/hide upload frame show: function () { + // wait for galaxy history panel + var self = this; + if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) { + window.setTimeout(function() { self.show() }, 500) + return; + } + // create modal if (!this.modal) { // make modal diff -r b8efe7496a7e591450722765cdca0307ffad957f -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -83,12 +83,6 @@ this.options = _.defaults(options, this.options); } - // wait for galaxy history panel (workaround due to the use of iframes) - if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) { - window.setTimeout(function() { self.initialize() }, 500) - return; - } - // create model this.ui_button = new UploadButton.Model({ icon : 'fa-upload', @@ -173,6 +167,13 @@ // show/hide upload frame show: function () { + // wait for galaxy history panel + var self = this; + if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) { + window.setTimeout(function() { self.show() }, 500) + return; + } + // create modal if (!this.modal) { // make modal diff -r b8efe7496a7e591450722765cdca0307ffad957f -r 3e6c63c296e43c0dfbb43c8070365a5b2b2ac3a1 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],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."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.get(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],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."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.get(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.show()},500);return}if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Ui: Open the upload modal if the upload tool is selected from the tool panel, fix code style for masthead and menu views
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8efe7496a7e/ Changeset: b8efe7496a7e User: guerler Date: 2014-09-29 18:10:42+00:00 Summary: Ui: Open the upload modal if the upload tool is selected from the tool panel, fix code style for masthead and menu views Affected #: 12 files diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f client/galaxy/scripts/galaxy.frame.js --- a/client/galaxy/scripts/galaxy.frame.js +++ b/client/galaxy/scripts/galaxy.frame.js @@ -1,9 +1,8 @@ // dependencies define(["galaxy.masthead", "mvc/ui/ui-frames"], function(mod_masthead, Frames) { -// frame manager -var GalaxyFrame = Backbone.View.extend( -{ +/** Frame manager uses the ui-frames to create the scratch book masthead icon and functionality **/ +var GalaxyFrame = Backbone.View.extend({ // base element el_main: 'body', @@ -17,8 +16,7 @@ button_load : null, // initialize - initialize : function(options) - { + initialize : function(options) { // add to masthead menu var self = this; @@ -28,8 +26,7 @@ }); // add activate icon - this.button_active = new mod_masthead.GalaxyMastheadIcon ( - { + this.button_active = new mod_masthead.GalaxyMastheadIcon({ icon : 'fa-th', tooltip : 'Enable/Disable Scratchbook', onclick : function() { self._activate(); }, @@ -44,8 +41,7 @@ Galaxy.masthead.append(this.button_active); // add load icon - this.button_load = new mod_masthead.GalaxyMastheadIcon ( - { + this.button_load = new mod_masthead.GalaxyMastheadIcon({ icon : 'fa-eye', tooltip : 'Show/Hide Scratchbook', onclick : function(e) { @@ -126,31 +122,25 @@ /** * Add and display a new frame/window based on options. */ - add: function(options) - { + add: function(options){ // open new tab - if (options.target == '_blank') - { + if (options.target == '_blank'){ window.open(options.content); return; } // reload entire window - if (options.target == '_top' || options.target == '_parent' || options.target == '_self') - { + if (options.target == '_top' || options.target == '_parent' || options.target == '_self'){ window.location = options.content; return; } // validate - if (!this.active) - { + if (!this.active){ // fix url if main frame is unavailable var $galaxy_main = $(window.parent.document).find('#galaxy_main'); - if (options.target == 'galaxy_main' || options.target == 'center') - { - if ($galaxy_main.length === 0) - { + if (options.target == 'galaxy_main' || options.target == 'center'){ + if ($galaxy_main.length === 0){ var href = options.content; if (href.indexOf('?') == -1) href += '?'; @@ -173,11 +163,9 @@ }, // activate/disable panel - _activate: function () - { + _activate: function (){ // check - if (this.active) - { + if (this.active){ // disable this.active = false; @@ -196,8 +184,7 @@ }, // update frame counter - _refresh: function() - { + _refresh: function(){ // update on screen counter this.button_load.number(this.frames.length()); diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f client/galaxy/scripts/galaxy.masthead.js --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -1,9 +1,8 @@ // dependencies define([], function() { -// masthead -var GalaxyMasthead = Backbone.View.extend( -{ +/** Masthead **/ +var GalaxyMasthead = Backbone.View.extend({ // base element el_masthead: '#everything', @@ -17,8 +16,7 @@ list: [], // initialize - initialize : function(options) - { + initialize : function(options) { // update options this.options = options; @@ -51,27 +49,23 @@ }, // configure events - events: - { + events: { 'click' : '_click', 'mousedown' : function(e) { e.preventDefault() } }, // adds a new item to the masthead - append : function(item) - { + append : function(item) { return this._add(item, true); }, // adds a new item to the masthead - prepend : function(item) - { + prepend : function(item) { return this._add(item, false); }, // activate - highlight: function(id) - { + highlight: function(id) { var current = $(this.el).find('#' + id + '> li'); if (current) { current.addClass('active'); @@ -79,11 +73,9 @@ }, // adds a new item to the masthead - _add : function(item, append) - { + _add : function(item, append) { var $loc = $(this.el).find('#' + item.location); - if ($loc) - { + if ($loc){ // create frame for new item var $current = $(item.el); @@ -106,8 +98,7 @@ }, // handle click event - _click: function(e) - { + _click: function(e) { // close all popups var $all = $(this.el).find('.popup'); if ($all) { @@ -129,8 +120,7 @@ */ // fill template - _template: function(options) - { + _template: function(options) { var brand_text = options.brand ? ("/ " + options.brand) : "" ; return '<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse">' + '<div style="position: relative; right: -50%; float: left;">' + @@ -150,12 +140,10 @@ } }); -// icon -var GalaxyMastheadIcon = Backbone.View.extend( -{ +/** Masthead icon **/ +var GalaxyMastheadIcon = Backbone.View.extend({ // icon options - options: - { + options:{ id : '', icon : 'fa-cog', tooltip : '', @@ -169,8 +157,7 @@ location: 'iconbar', // initialize - initialize: function (options) - { + initialize: function (options){ // read in defaults if (options) this.options = _.defaults(options, this.options); @@ -189,20 +176,17 @@ }, // show - show: function() - { + show: function(){ $(this.el).css({visibility : 'visible'}); }, // show - hide: function() - { + hide: function(){ $(this.el).css({visibility : 'hidden'}); }, // switch icon - icon: function (new_icon) - { + icon: function (new_icon){ // update icon class $(this.el).find('.icon').removeClass(this.options.icon) .addClass(new_icon); @@ -212,26 +196,22 @@ }, // toggle - toggle: function() - { + toggle: function(){ $(this.el).addClass('toggle'); }, // untoggle - untoggle: function() - { + untoggle: function(){ $(this.el).removeClass('toggle'); }, // set/get number - number: function(new_number) - { + number: function(new_number){ $(this.el).find('.number').text(new_number); }, // fill template icon - _template: function (options) - { + _template: function (options){ var tmpl = '<div id="' + options.id + '" class="symbol">' + '<div class="icon fa fa-2x ' + options.icon + '"></div>'; if (options.with_number) @@ -243,12 +223,10 @@ } }); -// tab -var GalaxyMastheadTab = Backbone.View.extend( -{ +/** Masthead tab **/ +var GalaxyMastheadTab = Backbone.View.extend({ // main options - options: - { + options:{ id : '', title : '', target : '_parent', @@ -268,14 +246,12 @@ $menu: null, // events - events: - { + events:{ 'click .head' : '_head' }, // initialize - initialize: function (options) - { + initialize: function (options){ // read in defaults if (options) this.options = _.defaults(options, this.options); @@ -300,20 +276,17 @@ }, // show - show: function() - { + show: function(){ $(this.el).css({visibility : 'visible'}); }, // show - hide: function() - { + hide: function(){ $(this.el).css({visibility : 'hidden'}); }, // add menu item - add: function (options) - { + add: function (options){ // menu option defaults var menuOptions = { title : 'Title', @@ -333,8 +306,7 @@ menuOptions.content = galaxy_config.root + menuOptions.content; // check if submenu element is available - if (!this.$menu) - { + if (!this.$menu){ // insert submenu element into root $(this.el).find('.root').append(this._templateMenu()); @@ -353,8 +325,7 @@ // add events var self = this; - $item.on('click', function(e) - { + $item.on('click', function(e){ // prevent default e.preventDefault(); @@ -372,8 +343,7 @@ }, // show menu on header click - _head: function(e) - { + _head: function(e){ // prevent default e.preventDefault(); @@ -387,8 +357,7 @@ } }, - _attachPopover : function() - { + _attachPopover : function(){ var $popover_element = $(this.el).find('.head'); $popover_element.popover({ html: true, @@ -402,25 +371,21 @@ }, // fill template header - _templateMenuItem: function (options) - { + _templateMenuItem: function (options){ return '<li><a href="' + options.content + '" target="' + options.target + '">' + options.title + '</a></li>'; }, // fill template header - _templateMenu: function () - { + _templateMenu: function (){ return '<ul class="popup dropdown-menu"></ul>'; }, - _templateDivider: function() - { + _templateDivider: function(){ return '<li class="divider"></li>'; }, // fill template - _template: function (options) - { + _template: function (options){ // start template var tmpl = '<ul id="' + options.id + '" class="nav navbar-nav" border="0" cellspacing="0">' + '<li class="root dropdown" style="">' + diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f client/galaxy/scripts/galaxy.menu.js --- a/client/galaxy/scripts/galaxy.menu.js +++ b/client/galaxy/scripts/galaxy.menu.js @@ -1,13 +1,8 @@ -/* - galaxy menu -*/ - // dependencies define(["galaxy.masthead"], function(mod_masthead) { -// frame manager -var GalaxyMenu = Backbone.Model.extend( -{ +/** GalaxyMenu uses the GalaxyMasthead class in order to add menu items and icons to the Masthead **/ +var GalaxyMenu = Backbone.Model.extend({ // options options: null, @@ -15,16 +10,14 @@ masthead: null, // initialize - initialize: function(options) - { + initialize: function(options) { this.options = options.config; this.masthead = options.masthead; this.create(); }, // default menu - create: function() - { + create: function(){ // // Analyze data tab. // @@ -137,8 +130,7 @@ var tab_visualization = new mod_masthead.GalaxyMastheadTab(visualization_options); - if (this.options.user.valid) //add submenu only when user is logged in - { + if (this.options.user.valid){ //add submenu only when user is logged in tab_visualization.add({ title : "New Track Browser", content : "visualization/trackster", @@ -155,8 +147,7 @@ // // Cloud menu. // - if (this.options.enable_cloud_launch) - { + if (this.options.enable_cloud_launch){ var tab_cloud = new mod_masthead.GalaxyMastheadTab({ id : "cloud", title : "Cloud", @@ -172,8 +163,7 @@ // // Admin. // - if (this.options.is_admin_user) - { + if (this.options.is_admin_user) { var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", @@ -192,8 +182,7 @@ title : "Help", title_attribute : 'Support, contact, and community hubs' }); - if (this.options.biostar_url) - { + if (this.options.biostar_url){ tab_help.add({ title : "Galaxy Biostar", content : this.options.biostar_url_redirect, @@ -235,8 +224,7 @@ content : this.options.citation_url, target : "_blank" }); - if (this.options.terms_url) - { + if (this.options.terms_url){ tab_help.add({ title : "Terms and Conditions", content : this.options.terms_url, @@ -248,8 +236,7 @@ // // User tab. // - if (!this.options.user.valid) - { + if (!this.options.user.valid){ var tab_user = new mod_masthead.GalaxyMastheadTab({ id : "user", title : "User", @@ -265,8 +252,7 @@ }); // register - if (this.options.allow_user_creation) - { + if (this.options.allow_user_creation){ tab_user.add({ title : "Register", content : "user/create", @@ -331,8 +317,7 @@ target : "galaxy_main" }); - if (this.options.use_remote_user) - { + if (this.options.use_remote_user){ tab_user.add({ title : "Public Name", content : "user/edit_username?cntrller=user", diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f client/galaxy/scripts/mvc/tools.js --- a/client/galaxy/scripts/mvc/tools.js +++ b/client/galaxy/scripts/mvc/tools.js @@ -506,7 +506,19 @@ tagName: 'div', render: function() { - this.$el.append( Handlebars.templates.tool_link(this.model.toJSON()) ); + // create element + var $link = $(Handlebars.templates.tool_link(this.model.toJSON())); + + // open upload dialog for upload tool + if (this.model.id === 'upload1') { + $link.on('click', function(e) { + e.preventDefault(); + Galaxy.upload.show(); + }); + } + + // add element + this.$el.append($link); return this; } }); diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f client/galaxy/scripts/mvc/upload/upload-view.js --- a/client/galaxy/scripts/mvc/upload/upload-view.js +++ b/client/galaxy/scripts/mvc/upload/upload-view.js @@ -96,7 +96,11 @@ label : 'Load Data', onclick : function(e) { if (e) { - self._eventShow(e) + // prevent default + e.preventDefault(); + + // show + self.show() } }, onunload : function() { @@ -168,10 +172,7 @@ // // show/hide upload frame - _eventShow : function (e) { - // prevent default - e.preventDefault(); - + show: function () { // create modal if (!this.modal) { // make modal @@ -437,8 +438,7 @@ }, // create a new file - _eventCreate : function () - { + _eventCreate : function (){ this.uploadbox.add([{ name : 'New File', size : 0, @@ -497,8 +497,7 @@ // remove all _eventReset : function() { // make sure queue is not running - if (this.counter.running == 0) - { + if (this.counter.running == 0){ // reset collection this.collection.reset(); @@ -533,8 +532,7 @@ */ // check default message - if(this.counter.announce == 0) - { + if(this.counter.announce == 0){ if (this.uploadbox.compatible()) message = 'You can Drag & Drop files into this box.'; else @@ -572,8 +570,7 @@ this.modal.disableButton('Pause'); // select upload button - if (this.counter.running == 0) - { + if (this.counter.running == 0){ this.modal.enableButton('Choose local file'); this.modal.enableButton('Choose FTP file'); this.modal.enableButton('Paste/Fetch data'); @@ -591,10 +588,11 @@ } // table visibility - if (this.counter.announce + this.counter.success + this.counter.error > 0) + if (this.counter.announce + this.counter.success + this.counter.error > 0) { $(this.el).find('#upload-table').show(); - else + } else { $(this.el).find('#upload-table').hide(); + } }, // calculate percentage of all queued uploads diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -1,9 +1,8 @@ // dependencies define(["galaxy.masthead", "mvc/ui/ui-frames"], function(mod_masthead, Frames) { -// frame manager -var GalaxyFrame = Backbone.View.extend( -{ +/** Frame manager uses the ui-frames to create the scratch book masthead icon and functionality **/ +var GalaxyFrame = Backbone.View.extend({ // base element el_main: 'body', @@ -17,8 +16,7 @@ button_load : null, // initialize - initialize : function(options) - { + initialize : function(options) { // add to masthead menu var self = this; @@ -28,8 +26,7 @@ }); // add activate icon - this.button_active = new mod_masthead.GalaxyMastheadIcon ( - { + this.button_active = new mod_masthead.GalaxyMastheadIcon({ icon : 'fa-th', tooltip : 'Enable/Disable Scratchbook', onclick : function() { self._activate(); }, @@ -44,8 +41,7 @@ Galaxy.masthead.append(this.button_active); // add load icon - this.button_load = new mod_masthead.GalaxyMastheadIcon ( - { + this.button_load = new mod_masthead.GalaxyMastheadIcon({ icon : 'fa-eye', tooltip : 'Show/Hide Scratchbook', onclick : function(e) { @@ -126,31 +122,25 @@ /** * Add and display a new frame/window based on options. */ - add: function(options) - { + add: function(options){ // open new tab - if (options.target == '_blank') - { + if (options.target == '_blank'){ window.open(options.content); return; } // reload entire window - if (options.target == '_top' || options.target == '_parent' || options.target == '_self') - { + if (options.target == '_top' || options.target == '_parent' || options.target == '_self'){ window.location = options.content; return; } // validate - if (!this.active) - { + if (!this.active){ // fix url if main frame is unavailable var $galaxy_main = $(window.parent.document).find('#galaxy_main'); - if (options.target == 'galaxy_main' || options.target == 'center') - { - if ($galaxy_main.length === 0) - { + if (options.target == 'galaxy_main' || options.target == 'center'){ + if ($galaxy_main.length === 0){ var href = options.content; if (href.indexOf('?') == -1) href += '?'; @@ -173,11 +163,9 @@ }, // activate/disable panel - _activate: function () - { + _activate: function (){ // check - if (this.active) - { + if (this.active){ // disable this.active = false; @@ -196,8 +184,7 @@ }, // update frame counter - _refresh: function() - { + _refresh: function(){ // update on screen counter this.button_load.number(this.frames.length()); diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -1,9 +1,8 @@ // dependencies define([], function() { -// masthead -var GalaxyMasthead = Backbone.View.extend( -{ +/** Masthead **/ +var GalaxyMasthead = Backbone.View.extend({ // base element el_masthead: '#everything', @@ -17,8 +16,7 @@ list: [], // initialize - initialize : function(options) - { + initialize : function(options) { // update options this.options = options; @@ -51,27 +49,23 @@ }, // configure events - events: - { + events: { 'click' : '_click', 'mousedown' : function(e) { e.preventDefault() } }, // adds a new item to the masthead - append : function(item) - { + append : function(item) { return this._add(item, true); }, // adds a new item to the masthead - prepend : function(item) - { + prepend : function(item) { return this._add(item, false); }, // activate - highlight: function(id) - { + highlight: function(id) { var current = $(this.el).find('#' + id + '> li'); if (current) { current.addClass('active'); @@ -79,11 +73,9 @@ }, // adds a new item to the masthead - _add : function(item, append) - { + _add : function(item, append) { var $loc = $(this.el).find('#' + item.location); - if ($loc) - { + if ($loc){ // create frame for new item var $current = $(item.el); @@ -106,8 +98,7 @@ }, // handle click event - _click: function(e) - { + _click: function(e) { // close all popups var $all = $(this.el).find('.popup'); if ($all) { @@ -129,8 +120,7 @@ */ // fill template - _template: function(options) - { + _template: function(options) { var brand_text = options.brand ? ("/ " + options.brand) : "" ; return '<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse">' + '<div style="position: relative; right: -50%; float: left;">' + @@ -150,12 +140,10 @@ } }); -// icon -var GalaxyMastheadIcon = Backbone.View.extend( -{ +/** Masthead icon **/ +var GalaxyMastheadIcon = Backbone.View.extend({ // icon options - options: - { + options:{ id : '', icon : 'fa-cog', tooltip : '', @@ -169,8 +157,7 @@ location: 'iconbar', // initialize - initialize: function (options) - { + initialize: function (options){ // read in defaults if (options) this.options = _.defaults(options, this.options); @@ -189,20 +176,17 @@ }, // show - show: function() - { + show: function(){ $(this.el).css({visibility : 'visible'}); }, // show - hide: function() - { + hide: function(){ $(this.el).css({visibility : 'hidden'}); }, // switch icon - icon: function (new_icon) - { + icon: function (new_icon){ // update icon class $(this.el).find('.icon').removeClass(this.options.icon) .addClass(new_icon); @@ -212,26 +196,22 @@ }, // toggle - toggle: function() - { + toggle: function(){ $(this.el).addClass('toggle'); }, // untoggle - untoggle: function() - { + untoggle: function(){ $(this.el).removeClass('toggle'); }, // set/get number - number: function(new_number) - { + number: function(new_number){ $(this.el).find('.number').text(new_number); }, // fill template icon - _template: function (options) - { + _template: function (options){ var tmpl = '<div id="' + options.id + '" class="symbol">' + '<div class="icon fa fa-2x ' + options.icon + '"></div>'; if (options.with_number) @@ -243,12 +223,10 @@ } }); -// tab -var GalaxyMastheadTab = Backbone.View.extend( -{ +/** Masthead tab **/ +var GalaxyMastheadTab = Backbone.View.extend({ // main options - options: - { + options:{ id : '', title : '', target : '_parent', @@ -268,14 +246,12 @@ $menu: null, // events - events: - { + events:{ 'click .head' : '_head' }, // initialize - initialize: function (options) - { + initialize: function (options){ // read in defaults if (options) this.options = _.defaults(options, this.options); @@ -300,20 +276,17 @@ }, // show - show: function() - { + show: function(){ $(this.el).css({visibility : 'visible'}); }, // show - hide: function() - { + hide: function(){ $(this.el).css({visibility : 'hidden'}); }, // add menu item - add: function (options) - { + add: function (options){ // menu option defaults var menuOptions = { title : 'Title', @@ -333,8 +306,7 @@ menuOptions.content = galaxy_config.root + menuOptions.content; // check if submenu element is available - if (!this.$menu) - { + if (!this.$menu){ // insert submenu element into root $(this.el).find('.root').append(this._templateMenu()); @@ -353,8 +325,7 @@ // add events var self = this; - $item.on('click', function(e) - { + $item.on('click', function(e){ // prevent default e.preventDefault(); @@ -372,8 +343,7 @@ }, // show menu on header click - _head: function(e) - { + _head: function(e){ // prevent default e.preventDefault(); @@ -387,8 +357,7 @@ } }, - _attachPopover : function() - { + _attachPopover : function(){ var $popover_element = $(this.el).find('.head'); $popover_element.popover({ html: true, @@ -402,25 +371,21 @@ }, // fill template header - _templateMenuItem: function (options) - { + _templateMenuItem: function (options){ return '<li><a href="' + options.content + '" target="' + options.target + '">' + options.title + '</a></li>'; }, // fill template header - _templateMenu: function () - { + _templateMenu: function (){ return '<ul class="popup dropdown-menu"></ul>'; }, - _templateDivider: function() - { + _templateDivider: function(){ return '<li class="divider"></li>'; }, // fill template - _template: function (options) - { + _template: function (options){ // start template var tmpl = '<ul id="' + options.id + '" class="nav navbar-nav" border="0" cellspacing="0">' + '<li class="root dropdown" style="">' + diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -1,13 +1,8 @@ -/* - galaxy menu -*/ - // dependencies define(["galaxy.masthead"], function(mod_masthead) { -// frame manager -var GalaxyMenu = Backbone.Model.extend( -{ +/** GalaxyMenu uses the GalaxyMasthead class in order to add menu items and icons to the Masthead **/ +var GalaxyMenu = Backbone.Model.extend({ // options options: null, @@ -15,16 +10,14 @@ masthead: null, // initialize - initialize: function(options) - { + initialize: function(options) { this.options = options.config; this.masthead = options.masthead; this.create(); }, // default menu - create: function() - { + create: function(){ // // Analyze data tab. // @@ -137,8 +130,7 @@ var tab_visualization = new mod_masthead.GalaxyMastheadTab(visualization_options); - if (this.options.user.valid) //add submenu only when user is logged in - { + if (this.options.user.valid){ //add submenu only when user is logged in tab_visualization.add({ title : "New Track Browser", content : "visualization/trackster", @@ -155,8 +147,7 @@ // // Cloud menu. // - if (this.options.enable_cloud_launch) - { + if (this.options.enable_cloud_launch){ var tab_cloud = new mod_masthead.GalaxyMastheadTab({ id : "cloud", title : "Cloud", @@ -172,8 +163,7 @@ // // Admin. // - if (this.options.is_admin_user) - { + if (this.options.is_admin_user) { var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", @@ -192,8 +182,7 @@ title : "Help", title_attribute : 'Support, contact, and community hubs' }); - if (this.options.biostar_url) - { + if (this.options.biostar_url){ tab_help.add({ title : "Galaxy Biostar", content : this.options.biostar_url_redirect, @@ -235,8 +224,7 @@ content : this.options.citation_url, target : "_blank" }); - if (this.options.terms_url) - { + if (this.options.terms_url){ tab_help.add({ title : "Terms and Conditions", content : this.options.terms_url, @@ -248,8 +236,7 @@ // // User tab. // - if (!this.options.user.valid) - { + if (!this.options.user.valid){ var tab_user = new mod_masthead.GalaxyMastheadTab({ id : "user", title : "User", @@ -265,8 +252,7 @@ }); // register - if (this.options.allow_user_creation) - { + if (this.options.allow_user_creation){ tab_user.add({ title : "Register", content : "user/create", @@ -331,8 +317,7 @@ target : "galaxy_main" }); - if (this.options.use_remote_user) - { + if (this.options.use_remote_user){ tab_user.add({ title : "Public Name", content : "user/edit_username?cntrller=user", diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -506,7 +506,19 @@ tagName: 'div', render: function() { - this.$el.append( Handlebars.templates.tool_link(this.model.toJSON()) ); + // create element + var $link = $(Handlebars.templates.tool_link(this.model.toJSON())); + + // open upload dialog for upload tool + if (this.model.id === 'upload1') { + $link.on('click', function(e) { + e.preventDefault(); + Galaxy.upload.show(); + }); + } + + // add element + this.$el.append($link); return this; } }); diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -96,7 +96,11 @@ label : 'Load Data', onclick : function(e) { if (e) { - self._eventShow(e) + // prevent default + e.preventDefault(); + + // show + self.show() } }, onunload : function() { @@ -168,10 +172,7 @@ // // show/hide upload frame - _eventShow : function (e) { - // prevent default - e.preventDefault(); - + show: function () { // create modal if (!this.modal) { // make modal @@ -437,8 +438,7 @@ }, // create a new file - _eventCreate : function () - { + _eventCreate : function (){ this.uploadbox.add([{ name : 'New File', size : 0, @@ -497,8 +497,7 @@ // remove all _eventReset : function() { // make sure queue is not running - if (this.counter.running == 0) - { + if (this.counter.running == 0){ // reset collection this.collection.reset(); @@ -533,8 +532,7 @@ */ // check default message - if(this.counter.announce == 0) - { + if(this.counter.announce == 0){ if (this.uploadbox.compatible()) message = 'You can Drag & Drop files into this box.'; else @@ -572,8 +570,7 @@ this.modal.disableButton('Pause'); // select upload button - if (this.counter.running == 0) - { + if (this.counter.running == 0){ this.modal.enableButton('Choose local file'); this.modal.enableButton('Choose FTP file'); this.modal.enableButton('Paste/Fetch data'); @@ -591,10 +588,11 @@ } // table visibility - if (this.counter.announce + this.counter.success + this.counter.error > 0) + if (this.counter.announce + this.counter.success + this.counter.error > 0) { $(this.el).find('#upload-table').show(); - else + } else { $(this.el).find('#upload-table').hide(); + } }, // calculate percentage of all queued uploads diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){this.$el.append(Handlebars.templates.tool_link(this.model.toJSON()));return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data"],function(x,a,y){var g={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(z){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},set_value:function(z){this.set("value",z||"")}});var i=Backbone.Collection.extend({model:e});var k=e.extend({});var d=e.extend({set_value:function(z){this.set("value",parseInt(z,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}});var f=d.extend({set_value:function(z){this.set("value",parseFloat(z))}});var t=e.extend({get_samples:function(){return x.map(this.get("options"),function(z){return z[0]})}});e.subModelTypes={integer:d,"float":f,data:k,select:t};var j=Backbone.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:galaxy_config.root+"api/tools",initialize:function(z){this.set("inputs",new i(x.map(z.inputs,function(A){var B=e.subModelTypes[A.type]||e;return new B(A)})))},toJSON:function(){var z=Backbone.Model.prototype.toJSON.call(this);z.inputs=this.get("inputs").map(function(A){return A.toJSON()});return z},remove_inputs:function(A){var z=this,B=z.get("inputs").filter(function(C){return(A.indexOf(C.get("type"))!==-1)});z.get("inputs").remove(B)},copy:function(A){var B=new j(this.toJSON());if(A){var z=new Backbone.Collection();B.get("inputs").each(function(C){if(C.get_samples()){z.push(C)}});B.set("inputs",z)}return B},apply_search_results:function(z){(x.indexOf(z,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(z,A){this.get("inputs").find(function(B){return B.get("name")===z}).set("value",A)},set_input_values:function(A){var z=this;x.each(x.keys(A),function(B){z.set_input_value(B,A[B])})},run:function(){return this._run()},rerun:function(A,z){return this._run({action:"rerun",target_dataset_id:A.id,regions:z})},get_inputs_dict:function(){var z={};this.get("inputs").each(function(A){z[A.get("name")]=A.get("value")});return z},_run:function(B){var C=x.extend({tool_id:this.id,inputs:this.get_inputs_dict()},B);var A=$.Deferred(),z=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(C),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(D){return D!=="pending"}});$.when(z.go()).then(function(D){A.resolve(new y.DatasetCollection().reset(D))});return A}});x.extend(j.prototype,g);var q=Backbone.View.extend({});var n=Backbone.Collection.extend({model:j});var v=Backbone.Model.extend(g);var l=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){x.each(this.attributes.elems,function(z){z.show()});this.show();this.set("open",false)},apply_search_results:function(A){var B=true,z;x.each(this.attributes.elems,function(C){if(C instanceof v){z=C;z.hide()}else{if(C instanceof j){if(C.apply_search_results(A)){B=false;if(z){z.show()}}}}});if(B){this.hide()}else{this.show();this.set("open",true)}}});x.extend(l.prototype,g);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var B=this.attributes.query;if(B.length<this.attributes.min_chars_for_search){this.set("results",null);return}var A=B+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var z=this;this.timer=setTimeout(function(){$.get(z.attributes.search_url,{query:A},function(C){z.set("results",C);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});x.extend(c.prototype,g);var o=Backbone.Model.extend({initialize:function(z){this.attributes.tool_search=z.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=z.tools;this.attributes.layout=new Backbone.Collection(this.parse(z.layout))},parse:function(A){var z=this,B=function(E){var D=E.model_class;if(D.indexOf("Tool")===D.length-4){return z.attributes.tools.get(E.id)}else{if(D==="ToolSection"){var C=x.map(E.elems,B);E.elems=C;return new l(E)}else{if(D==="ToolSectionLabel"){return new v(E)}}}};return x.map(A,B)},clear_search_results:function(){this.get("layout").each(function(z){if(z instanceof l){z.clear_search_results()}else{z.show()}})},apply_search_results:function(){var A=this.get("tool_search").get("results");if(A===null){this.clear_search_results();return}var z=null;this.get("layout").each(function(B){if(B instanceof v){z=B;z.hide()}else{if(B instanceof j){if(B.apply_search_results(A)){if(z){z.show()}}}else{z=null;B.apply_search_results(A)}}})}});var s=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var m=s.extend({tagName:"div",render:function(){var z=$(Handlebars.templates.tool_link(this.model.toJSON()));if(this.model.id==="upload1"){z.on("click",function(A){A.preventDefault();Galaxy.upload.show()})}this.$el.append(z);return this}});var b=s.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var r=s.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){s.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(Handlebars.templates.panel_section(this.model.toJSON()));var z=this.$el.find(".toolSectionBody");x.each(this.model.attributes.elems,function(A){if(A instanceof j){var B=new m({model:A,className:"toolTitle"});B.render();z.append(B.$el)}else{if(A instanceof v){var C=new b({model:A});C.render();z.append(C.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var p=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(Handlebars.templates.tool_search(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find("[title]").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(z){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===z.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var w=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var z=this;var A=new p({model:this.model.get("tool_search")});A.render();z.$el.append(A.$el);this.model.get("layout").each(function(C){if(C instanceof l){var B=new r({model:C});B.render();z.$el.append(B.$el)}else{if(C instanceof j){var D=new m({model:C,className:"toolTitleNoSection"});D.render();z.$el.append(D.$el)}else{if(C instanceof v){var E=new b({model:C});E.render();z.$el.append(E.$el)}}}});z.$el.find("a.tool-link").click(function(D){var C=$(this).attr("class").split(/\s+/)[0],B=z.model.get("tools").get(C);z.trigger("tool_link_click",D,B)});return this},handle_search_results:function(){var z=this.model.get("tool_search").get("results");if(z&&z.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var u=Backbone.View.extend({className:"toolForm",render:function(){this.$el.children().remove();this.$el.append(Handlebars.templates.tool_form(this.model.toJSON()))}});var h=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new w({collection:this.collection});this.tool_form_view=new u()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var z=this;this.tool_panel_view.on("tool_link_click",function(B,A){B.preventDefault();z.show_tool(A)})},show_tool:function(A){var z=this;A.fetch().done(function(){z.tool_form_view.model=A;z.tool_form_view.render();z.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,SelectToolParameter:t,Tool:j,ToolCollection:n,ToolSearch:c,ToolPanel:o,ToolPanelView:w,ToolFormView:u}}); \ No newline at end of file diff -r cf1550da899848378f9c5e5ca00818c029c3a1bb -r b8efe7496a7e591450722765cdca0307ffad957f static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],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."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.get(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui/ui-modal","mvc/ui","utils/uploadbox"],function(f,e,c,b,g,d,a){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],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."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){j.preventDefault();h.show()}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.get(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.get(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},show:function(){if(!this.modal){var h=this;this.modal=new a.View({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(j,k,l){h._eventAnnounce(j,k,l)},initialize:function(j,k,l){return h._eventInitialize(j,k,l)},progress:function(j,k,l){h._eventProgress(j,k,l)},success:function(j,k,l){h._eventSuccess(j,k,l)},error:function(j,k,l){h._eventError(j,k,l)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshContents()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: List panel, history panels: allow keyboard shortcut for selection of sub-view: ALT+clicking the title bar of history contents will not expand the details but select the content and show the multiselect controls
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf1550da8998/ Changeset: cf1550da8998 User: carlfeberhard Date: 2014-09-29 16:36:20+00:00 Summary: List panel, history panels: allow keyboard shortcut for selection of sub-view: ALT+clicking the title bar of history contents will not expand the details but select the content and show the multiselect controls Affected #: 6 files diff -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 -r cf1550da899848378f9c5e5ca00818c029c3a1bb client/galaxy/scripts/mvc/list/list-item.js --- a/client/galaxy/scripts/mvc/list/list-item.js +++ b/client/galaxy/scripts/mvc/list/list-item.js @@ -261,7 +261,14 @@ /** expand when the title bar is clicked */ _clickTitleBar : function( event ){ event.stopPropagation(); - this.toggleExpanded(); + if( event.altKey ){ + this.toggleSelect( event ); + if( !this.selectable ){ + this.showSelector(); + } + } else { + this.toggleExpanded(); + } }, /** expand when the title bar is in focus and enter or space is pressed */ diff -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 -r cf1550da899848378f9c5e5ca00818c029c3a1bb client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -191,6 +191,8 @@ if( lastSelectedView ){ this.selectRange( view, lastSelectedView ); } + } else if( ev && ev.altKey && !this.selecting ){ + this.showSelectors(); } this.selected.push( view.model.id ); this.lastSelected = view.model.id; diff -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 -r cf1550da899848378f9c5e5ca00818c029c3a1bb static/scripts/mvc/list/list-item.js --- a/static/scripts/mvc/list/list-item.js +++ b/static/scripts/mvc/list/list-item.js @@ -261,7 +261,14 @@ /** expand when the title bar is clicked */ _clickTitleBar : function( event ){ event.stopPropagation(); - this.toggleExpanded(); + if( event.altKey ){ + this.toggleSelect( event ); + if( !this.selectable ){ + this.showSelector(); + } + } else { + this.toggleExpanded(); + } }, /** expand when the title bar is in focus and enter or space is pressed */ diff -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 -r cf1550da899848378f9c5e5ca00818c029c3a1bb static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -191,6 +191,8 @@ if( lastSelectedView ){ this.selectRange( view, lastSelectedView ); } + } else if( ev && ev.altKey && !this.selecting ){ + this.showSelectors(); } this.selected.push( view.model.id ); this.lastSelected = view.model.id; diff -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 -r cf1550da899848378f9c5e5ca00818c029c3a1bb static/scripts/packed/mvc/list/list-item.js --- a/static/scripts/packed/mvc/list/list-item.js +++ b/static/scripts/packed/mvc/list/list-item.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(b,d){var e=Backbone.View.extend(b.LoggableMixin).extend({initialize:function(f){this.expanded=f.expanded||false;this.fxSpeed=f.fxSpeed||this.fxSpeed},fxSpeed:"fast",render:function(g){var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){var f=$(this.templates.el(this.model.toJSON(),this));if(this.expanded){this.$details(f).replaceWith(this._renderDetails().show())}return f},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){this.trigger("rendered",f);i()}])},_swapNewRender:function(f){return this.$el.empty().attr("class",this.className).append(f.children())},_setUpBehaviors:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},$details:function(f){f=f||this.$el;return f.find("> .details")},_renderDetails:function(){var f=$(this.templates.details(this.model.toJSON(),this));this._setUpBehaviors(f);return f},toggleExpanded:function(f){f=(f===undefined)?(!this.expanded):(f);if(f){this.expand()}else{this.collapse()}return this},expand:function(){var f=this;return f._fetchModelDetails().always(function(){var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})})},_fetchModelDetails:function(){if(!this.model.hasDetails()){return this.model.fetch()}return jQuery.when()},collapse:function(){this.debug(this+"(ExpandableView).collapse");var f=this;f.expanded=false;this.$details().slideUp(f.fxSpeed,function(){f.trigger("collapsed",f)})}});var a=e.extend(b.mixin(b.SelectableViewMixin,b.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(f){e.prototype.initialize.call(this,f);b.SelectableViewMixin.initialize.call(this,f);b.DraggableViewMixin.initialize.call(this,f);this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}},this);return this},_buildNewRender:function(){var f=e.prototype._buildNewRender.call(this);f.children(".warnings").replaceWith(this._renderWarnings());f.children(".title-bar").replaceWith(this._renderTitleBar());f.children(".primary-actions").append(this._renderPrimaryActions());f.find(".title-bar .subtitle").replaceWith(this._renderSubtitle());return f},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.selectable){this.showSelector(0)}if(this.draggable){this.draggableOn()}return this.$el},_renderWarnings:function(){var f=this,h=$('<div class="warnings"></div>'),g=f.model.toJSON();_.each(f.templates.warnings,function(i){h.append($(i(g,f)))});return h},_renderTitleBar:function(){return $(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(f){f.stopPropagation();this.toggleExpanded()},_keyDownTitleBar:function(h){var f=32,g=13;if(h&&(h.type==="keydown")&&(h.keyCode===f||h.keyCode===g)){this.toggleExpanded();h.stopPropagation();return false}return true},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"ListItemView("+f+")"}}));a.prototype.templates=(function(){var h=b.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var f={};var i=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");var j=b.wrapTemplate(['<div class="subtitle"></div>']);var g=b.wrapTemplate(['<div class="details"></div>']);return{el:h,warnings:f,titleBar:i,subtitle:j,details:g}}());var c=a.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(f){a.prototype.initialize.call(this,f);if(this.foldoutStyle==="drilldown"){this.expanded=false}this.foldoutStyle=f.foldoutStyle||this.foldoutStyle;this.foldoutPanelClass=f.foldoutPanelClass||this.foldoutPanelClass},_renderDetails:function(){if(this.foldoutStyle==="drilldown"){return $()}var f=a.prototype._renderDetails.call(this);return this._attachFoldout(this._createFoldoutPanel(),f)},_createFoldoutPanel:function(){var h=this.model;var i=this._getFoldoutPanelClass(h),g=this._getFoldoutPanelOptions(h),f=new i(_.extend(g,{model:h}));return f},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle}},_attachFoldout:function(f,g){g=g||this.$("> .details");this.foldout=f.render(0);f.$("> .controls").hide();return g.append(f.$el)},expand:function(){var f=this;return f._fetchModelDetails().always(function(){if(f.foldoutStyle==="foldout"){f._expandByFoldout()}else{if(f.foldoutStyle==="drilldown"){f._expandByDrilldown()}}})},_expandByFoldout:function(){var f=this;var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})},_expandByDrilldown:function(){var f=this;f.foldout=this._createFoldoutPanel();f.foldout.on("close",function(){f.trigger("collapsed:drilldown",f,f.foldout)});f.trigger("expanded:drilldown",f,f.foldout)}});c.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="details">',"</div>"],"collection");return _.extend({},a.prototype.templates,{details:f})}());return{ExpandableView:e,ListItemView:a,FoldoutListItemView:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(b,d){var e=Backbone.View.extend(b.LoggableMixin).extend({initialize:function(f){this.expanded=f.expanded||false;this.fxSpeed=f.fxSpeed||this.fxSpeed},fxSpeed:"fast",render:function(g){var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){var f=$(this.templates.el(this.model.toJSON(),this));if(this.expanded){this.$details(f).replaceWith(this._renderDetails().show())}return f},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){this.trigger("rendered",f);i()}])},_swapNewRender:function(f){return this.$el.empty().attr("class",this.className).append(f.children())},_setUpBehaviors:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},$details:function(f){f=f||this.$el;return f.find("> .details")},_renderDetails:function(){var f=$(this.templates.details(this.model.toJSON(),this));this._setUpBehaviors(f);return f},toggleExpanded:function(f){f=(f===undefined)?(!this.expanded):(f);if(f){this.expand()}else{this.collapse()}return this},expand:function(){var f=this;return f._fetchModelDetails().always(function(){var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})})},_fetchModelDetails:function(){if(!this.model.hasDetails()){return this.model.fetch()}return jQuery.when()},collapse:function(){this.debug(this+"(ExpandableView).collapse");var f=this;f.expanded=false;this.$details().slideUp(f.fxSpeed,function(){f.trigger("collapsed",f)})}});var a=e.extend(b.mixin(b.SelectableViewMixin,b.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(f){e.prototype.initialize.call(this,f);b.SelectableViewMixin.initialize.call(this,f);b.DraggableViewMixin.initialize.call(this,f);this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}},this);return this},_buildNewRender:function(){var f=e.prototype._buildNewRender.call(this);f.children(".warnings").replaceWith(this._renderWarnings());f.children(".title-bar").replaceWith(this._renderTitleBar());f.children(".primary-actions").append(this._renderPrimaryActions());f.find(".title-bar .subtitle").replaceWith(this._renderSubtitle());return f},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.selectable){this.showSelector(0)}if(this.draggable){this.draggableOn()}return this.$el},_renderWarnings:function(){var f=this,h=$('<div class="warnings"></div>'),g=f.model.toJSON();_.each(f.templates.warnings,function(i){h.append($(i(g,f)))});return h},_renderTitleBar:function(){return $(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return $(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(f){f.stopPropagation();if(f.altKey){this.toggleSelect(f);if(!this.selectable){this.showSelector()}}else{this.toggleExpanded()}},_keyDownTitleBar:function(h){var f=32,g=13;if(h&&(h.type==="keydown")&&(h.keyCode===f||h.keyCode===g)){this.toggleExpanded();h.stopPropagation();return false}return true},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"ListItemView("+f+")"}}));a.prototype.templates=(function(){var h=b.wrapTemplate(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]);var f={};var i=b.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");var j=b.wrapTemplate(['<div class="subtitle"></div>']);var g=b.wrapTemplate(['<div class="details"></div>']);return{el:h,warnings:f,titleBar:i,subtitle:j,details:g}}());var c=a.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(f){a.prototype.initialize.call(this,f);if(this.foldoutStyle==="drilldown"){this.expanded=false}this.foldoutStyle=f.foldoutStyle||this.foldoutStyle;this.foldoutPanelClass=f.foldoutPanelClass||this.foldoutPanelClass},_renderDetails:function(){if(this.foldoutStyle==="drilldown"){return $()}var f=a.prototype._renderDetails.call(this);return this._attachFoldout(this._createFoldoutPanel(),f)},_createFoldoutPanel:function(){var h=this.model;var i=this._getFoldoutPanelClass(h),g=this._getFoldoutPanelOptions(h),f=new i(_.extend(g,{model:h}));return f},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle}},_attachFoldout:function(f,g){g=g||this.$("> .details");this.foldout=f.render(0);f.$("> .controls").hide();return g.append(f.$el)},expand:function(){var f=this;return f._fetchModelDetails().always(function(){if(f.foldoutStyle==="foldout"){f._expandByFoldout()}else{if(f.foldoutStyle==="drilldown"){f._expandByDrilldown()}}})},_expandByFoldout:function(){var f=this;var g=f._renderDetails();f.$details().replaceWith(g);f.expanded=true;f.$details().slideDown(f.fxSpeed,function(){f.trigger("expanded",f)})},_expandByDrilldown:function(){var f=this;f.foldout=this._createFoldoutPanel();f.foldout.on("close",function(){f.trigger("collapsed:drilldown",f,f.foldout)});f.trigger("expanded:drilldown",f,f.foldout)}});c.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="details">',"</div>"],"collection");return _.extend({},a.prototype.templates,{details:f})}());return{ExpandableView:e,ListItemView:a,FoldoutListItemView:c}}); \ No newline at end of file diff -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 -r cf1550da899848378f9c5e5ca00818c029c3a1bb static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.dragItems=f.dragItems||false;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},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);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragItems}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});g.on("draggable:dragstart",function(k,h){var i={},j=this.getSelectedModels();if(j.length){i=j.toJSON()}else{i=[h.model.toJSON()]}k.dataTransfer.setData("text",JSON.stringify(i))},this);return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g._attachView(f);k()}]);return f},_attachView:function(g){var f=this;f.views.push(g);f.$list().append(g.render(0).$el.hide());g.$el.slideDown(f.fxSpeed)},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.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)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();this.$("> .controls .search-query").val(f);return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.dragItems=f.dragItems||false;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},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);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}else{if(g&&g.altKey&&!this.selecting){this.showSelectors()}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragItems}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});g.on("draggable:dragstart",function(k,h){var i={},j=this.getSelectedModels();if(j.length){i=j.toJSON()}else{i=[h.model.toJSON()]}k.dataTransfer.setData("text",JSON.stringify(i))},this);return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g._attachView(f);k()}]);return f},_attachView:function(g){var f=this;f.views.push(g);f.$list().append(g.render(0).$el.hide());g.$el.slideDown(f.fxSpeed)},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.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)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();this.$("> .controls .search-query").val(f);return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();this.$("> .controls .search-query").val("");return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file 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commit/galaxy-central: jgoecks: Remove references to global var.
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31a059dcc381/ Changeset: 31a059dcc381 User: jgoecks Date: 2014-09-29 16:24:51+00:00 Summary: Remove references to global var. Affected #: 3 files diff -r 991cd029642f477f3596ca6035d0830fd2c117ed -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 client/galaxy/scripts/viz/trackster/tracks.js --- a/client/galaxy/scripts/viz/trackster/tracks.js +++ b/client/galaxy/scripts/viz/trackster/tracks.js @@ -1152,9 +1152,9 @@ // Update location. Only update when there is a valid chrom; when loading vis, there may // not be a valid chrom. - var chrom = view.chrom_select.val(); + var chrom = this.chrom_select.val(); if (chrom !== "") { - this.trigger_navigate(chrom, view.low, view.high, true); + this.trigger_navigate(chrom, this.low, this.high, true); } }, diff -r 991cd029642f477f3596ca6035d0830fd2c117ed -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ak=Math.floor(Q*af),ac=Math.floor(al/ak),am,ah,ai=[],ao=[];while((ac*ak)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ac*ak,end:Math.min((ac+1)*ak,this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=Math.floor((ac-ae.low)/af*ah);ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=this.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,this.low,this.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ak=Math.floor(Q*af),ac=Math.floor(al/ak),am,ah,ai=[],ao=[];while((ac*ak)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ac*ak,end:Math.min((ac+1)*ak,this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=Math.floor((ac-ae.low)/af*ah);ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var 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ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top 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d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 991cd029642f477f3596ca6035d0830fd2c117ed -r 31a059dcc3814365a8dd3b5a56fc0d38de4f6d59 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1152,9 +1152,9 @@ // Update location. Only update when there is a valid chrom; when loading vis, there may // not be a valid chrom. - var chrom = view.chrom_select.val(); + var chrom = this.chrom_select.val(); if (chrom !== "") { - this.trigger_navigate(chrom, view.low, view.high, true); + this.trigger_navigate(chrom, this.low, this.high, true); } }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History multi-view, Histories: allow searching/filtering of histories by low-level adv. search (name, tags, annotation), remove delay on column render
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/991cd029642f/ Changeset: 991cd029642f User: carlfeberhard Date: 2014-09-29 16:16:00+00:00 Summary: History multi-view, Histories: allow searching/filtering of histories by low-level adv. search (name, tags, annotation), remove delay on column render Affected #: 9 files diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed client/galaxy/scripts/mvc/history/history-model.js --- a/client/galaxy/scripts/mvc/history/history-model.js +++ b/client/galaxy/scripts/mvc/history/history-model.js @@ -14,7 +14,7 @@ * @constructs */ var History = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( -/** @lends History.prototype */{ + BASE_MVC.mixin( BASE_MVC.SearchableModelMixin, /** @lends History.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, @@ -117,6 +117,18 @@ return _.reduce( _.values( this.get( 'state_details' ) ), function( memo, num ){ return memo + num; }, 0 ); }, + // ........................................................................ search + /** What model fields to search with */ + searchAttributes : [ + 'name', 'annotation', 'tags' + ], + + /** Adding title and singular tag */ + searchAliases : { + title : 'name', + tag : 'tags' + }, + // ........................................................................ updates /** does the contents collection indicate they're still running and need to be updated later? * delay + update if needed @@ -252,7 +264,7 @@ toString : function(){ return 'History(' + this.get( 'id' ) + ',' + this.get( 'name' ) + ')'; } -}); +})); //------------------------------------------------------------------------------ CLASS VARS /** When the history has running hdas, diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -69,13 +69,14 @@ /* ============================================================================== TODO: + rendering/delayed rendering is a mess + may not need to render columns in renderColumns (just moving them/attaching them may be enough) copy places old current in wrong location sort by size is confusing (but correct) - nice_size shows actual disk usage, !== size handle delete current currently manual by user - delete then create new - make one step render move all columns over as one (agg. then html()) - loading indicator on startup performance rendering columns could be better lazy load history list (for large numbers) @@ -808,7 +809,11 @@ /** Render a single column using the non-blocking setTimeout( 0 ) pattern */ renderColumn : function( column, speed ){ speed = speed !== undefined? speed: this.fxSpeed; - return _.delay( function(){ return column.render( speed ); }, 0 ); + return column.render( speed ); + //TODO: causes weirdness + //return _.delay( function(){ + // return column.render( speed ); + //}, 0 ); }, //TODO: combine the following two more sensibly @@ -922,12 +927,13 @@ onsearch : function( searchFor ){ multipanel.searchFor = searchFor; multipanel.filters = [ function(){ - return this.model.get( 'name' ).indexOf( multipanel.searchFor ) !== -1; + return this.model.matchesAll( multipanel.searchFor ); }]; multipanel.renderColumns( 0 ); }, onclear : function( searchFor ){ multipanel.searchFor = null; +//TODO: remove specifically not just reset multipanel.filters = []; multipanel.renderColumns( 0 ); } @@ -949,7 +955,7 @@ }); multipanel.hdaQueue.progress( function( progress ){ multipanel.renderInfo([ - _l( 'loading' ), ( progress.curr + 1 ), _l( 'of' ), progress.total + _l( 'searching' ), ( progress.curr + 1 ), _l( 'of' ), progress.total ].join( ' ' )); }); multipanel.hdaQueue.deferred.done( function(){ diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed client/galaxy/scripts/mvc/ui.js --- a/client/galaxy/scripts/mvc/ui.js +++ b/client/galaxy/scripts/mvc/ui.js @@ -692,7 +692,6 @@ } }) .on( 'change', function( event ){ - console.info( 'changed', $( this ), event ); search.call( this, event, $( this ).val() ); }) .val( options.initialVal ); diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -14,7 +14,7 @@ * @constructs */ var History = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( -/** @lends History.prototype */{ + BASE_MVC.mixin( BASE_MVC.SearchableModelMixin, /** @lends History.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, @@ -117,6 +117,18 @@ return _.reduce( _.values( this.get( 'state_details' ) ), function( memo, num ){ return memo + num; }, 0 ); }, + // ........................................................................ search + /** What model fields to search with */ + searchAttributes : [ + 'name', 'annotation', 'tags' + ], + + /** Adding title and singular tag */ + searchAliases : { + title : 'name', + tag : 'tags' + }, + // ........................................................................ updates /** does the contents collection indicate they're still running and need to be updated later? * delay + update if needed @@ -252,7 +264,7 @@ toString : function(){ return 'History(' + this.get( 'id' ) + ',' + this.get( 'name' ) + ')'; } -}); +})); //------------------------------------------------------------------------------ CLASS VARS /** When the history has running hdas, diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -69,13 +69,14 @@ /* ============================================================================== TODO: + rendering/delayed rendering is a mess + may not need to render columns in renderColumns (just moving them/attaching them may be enough) copy places old current in wrong location sort by size is confusing (but correct) - nice_size shows actual disk usage, !== size handle delete current currently manual by user - delete then create new - make one step render move all columns over as one (agg. then html()) - loading indicator on startup performance rendering columns could be better lazy load history list (for large numbers) @@ -808,7 +809,11 @@ /** Render a single column using the non-blocking setTimeout( 0 ) pattern */ renderColumn : function( column, speed ){ speed = speed !== undefined? speed: this.fxSpeed; - return _.delay( function(){ return column.render( speed ); }, 0 ); + return column.render( speed ); + //TODO: causes weirdness + //return _.delay( function(){ + // return column.render( speed ); + //}, 0 ); }, //TODO: combine the following two more sensibly @@ -922,12 +927,13 @@ onsearch : function( searchFor ){ multipanel.searchFor = searchFor; multipanel.filters = [ function(){ - return this.model.get( 'name' ).indexOf( multipanel.searchFor ) !== -1; + return this.model.matchesAll( multipanel.searchFor ); }]; multipanel.renderColumns( 0 ); }, onclear : function( searchFor ){ multipanel.searchFor = null; +//TODO: remove specifically not just reset multipanel.filters = []; multipanel.renderColumns( 0 ); } @@ -949,7 +955,7 @@ }); multipanel.hdaQueue.progress( function( progress ){ multipanel.renderInfo([ - _l( 'loading' ), ( progress.curr + 1 ), _l( 'of' ), progress.total + _l( 'searching' ), ( progress.curr + 1 ), _l( 'of' ), progress.total ].join( ' ' )); }); multipanel.hdaQueue.deferred.done( function(){ diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -692,7 +692,6 @@ } }) .on( 'change', function( event ){ - console.info( 'changed', $( this ), event ); search.call( this, event, $( this ).val() ); }) .val( options.initialVal ); diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file +define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue"],function(d,l,z,a){window.HISTORY_MODEL=d;function g(H,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return H.copy()}var F=H.get("name"),C="Copy of '"+F+"'";function D(J){if(!J){if(!Galaxy.modal.$("#invalid-title").size()){var I=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(I)}return false}return J}function G(I){var J=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(J);H.copy(true,I).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){var I=Galaxy.modal.$("#copy-modal-title").val();if(!D(I)){return}G(I)}}},E));$("#copy-modal-title").focus().select()}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',D.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var C=this,D;if(this.model.get("deleted")){D=this.model.undelete()}else{D=this.model._delete()}D.fail(function(G,E,F){alert(_l("Could not delete the history")+":\n"+F)}).done(function(E){C.render()})},"click .copy-history.btn":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.template(C.options));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},template:function w(C){C=C||{};var D=[];if(this.options.headerHeight){D=D.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}D=D.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(D.join(""))},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return _.delay(function(){return C.render(D)},0)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":function(){window.location="/"},"click .create-new.btn":"create","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")}},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var D=this;D.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(D.includeDeletedHistories,D)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(D.excludeDeletedHistories,D)}]});D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.get("name").indexOf(D.searchFor)!==-1}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("loading"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});D.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowDeleted(E,false)},F*200)})});D.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowHidden(E,false)},F*200)})});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:m}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue"],function(d,l,z,a){window.HISTORY_MODEL=d;function g(H,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return H.copy()}var F=H.get("name"),C="Copy of '"+F+"'";function D(J){if(!J){if(!Galaxy.modal.$("#invalid-title").size()){var I=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(I)}return false}return J}function G(I){var J=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(J);H.copy(true,I).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){var I=Galaxy.modal.$("#copy-modal-title").val();if(!D(I)){return}G(I)}}},E));$("#copy-modal-title").focus().select()}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',D.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var C=this,D;if(this.model.get("deleted")){D=this.model.undelete()}else{D=this.model._delete()}D.fail(function(G,E,F){alert(_l("Could not delete the history")+":\n"+F)}).done(function(E){C.render()})},"click .copy-history.btn":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.template(C.options));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},template:function w(C){C=C||{};var D=[];if(this.options.headerHeight){D=D.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}D=D.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(D.join(""))},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return C.render(D)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":function(){window.location="/"},"click .create-new.btn":"create","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")}},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var D=this;D.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(D.includeDeletedHistories,D)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(D.excludeDeletedHistories,D)}]});D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.matchesAll(D.searchFor)}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("searching"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});D.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowDeleted(E,false)},F*200)})});D.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowHidden(E,false)},F*200)})});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:m}}); \ No newline at end of file diff -r ff5d57faf17d38d345105300097fc7d196f3527e -r 991cd029642f477f3596ca6035d0830fd2c117ed static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.create=function _create(b,a){return new PopupMenu(b,a)};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((!a.disabled&&a.target)?(' target="'+a.target+'"'):("")),' href="',((!a.disabled&&a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";a.parent().find(".loading-indicator").remove();b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}(function(){var b=window._l||function(d){return d};function a(k,q){var e=27,n=13,d=$(k),f=true,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(r){},minSearchLen:0,escWillClear:true,oninit:function(){}};function j(r){var s=$(this).parent().children("input");s.focus().val("").trigger("clear:searchInput");q.onclear()}function p(s,r){$(this).trigger("search:searchInput",r);if(typeof q.onfirstsearch==="function"&&f){f=false;q.onfirstsearch(r)}else{q.onsearch(r)}}function g(){return['<input type="text" name="',q.name,'" placeholder="',q.placeholder,'" ','class="search-query ',q.classes,'" ',"/>"].join("")}function m(){return $(g()).focus(function(r){$(this).select()}).keyup(function(s){s.preventDefault();s.stopPropagation();if(!$(this).val()){$(this).blur()}if(s.which===e&&q.escWillClear){j.call(this,s)}else{var r=$(this).val();if((s.which===n)||(q.minSearchLen&&r.length>=q.minSearchLen)){p.call(this,s,r)}else{if(!r.length){j.call(this,s)}}}}).on("change",function(r){console.info("changed",$(this),r);p.call(this,r,$(this).val())}).val(q.initialVal)}function l(){return $(['<span class="search-clear fa fa-times-circle" ','title="',b("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(r){j.call(this,r)})}function o(){return $(['<span class="search-loading fa fa-spinner fa-spin" ','title="',b("loading..."),'"></span>'].join("")).hide().tooltip({placement:"bottom"})}function i(){d.find(".search-loading").toggle();d.find(".search-clear").toggle()}if(jQuery.type(q)==="string"){if(q==="toggle-loading"){i()}return d}if(jQuery.type(q)==="object"){q=jQuery.extend(true,{},h,q)}return d.addClass("search-input").prepend([m(),l(),o()])}jQuery.fn.extend({searchInput:function c(d){return this.each(function(){return a(this,d)})}})}());(function(){function c(o,n){this.currModeIndex=0;return this._init(o,n)}c.prototype.DATA_KEY="mode-button";c.prototype.defaults={switchModesOnClick:true};c.prototype._init=function j(o,n){n=n||{};this.$element=$(o);this.options=jQuery.extend(true,{},this.defaults,n);if(!n.modes){throw new Error('ModeButton requires a "modes" array')}var q=this;this.$element.click(function p(r){q.callModeFn();if(q.options.switchModesOnClick){q._incModeIndex()}$(this).html(q.options.modes[q.currModeIndex].html)});return this.reset()};c.prototype._incModeIndex=function l(){this.currModeIndex+=1;if(this.currModeIndex>=this.options.modes.length){this.currModeIndex=0}return this};c.prototype._getModeIndex=function f(n){for(var o=0;o<this.options.modes.length;o+=1){if(this.options.modes[o].mode===n){return o}}throw new Error("mode not found: "+n)};c.prototype._setModeByIndex=function m(n){var o=this.options.modes[n];if(!o){throw new Error("mode index not found: 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r=$(this);r.data("mode-button",new c(r,n));return this})}var p=$(this[0]),o=p.data("mode-button");if(!o){throw new Error("modeButton needs an options object or string name of a function")}if(o&&jQuery.type(n)==="string"){var q=n;if(o&&jQuery.type(o[q])==="function"){return o[q].apply(o,jQuery.makeArray(arguments).slice(1))}}return o}})}());function dropDownSelect(b,c){c=c||((!_.isEmpty(b))?(b[0]):(""));var a=$(['<div class="dropdown-select btn-group">','<button type="button" class="btn btn-default">','<span class="dropdown-select-selected">'+c+"</span>","</button>","</div>"].join("\n"));if(b&&b.length>1){a.find("button").addClass("dropdown-toggle").attr("data-toggle","dropdown").append(' <span class="caret"></span>');a.append(['<ul class="dropdown-menu" role="menu">',_.map(b,function(e){return['<li><a href="javascript:void(0)">',e,"</a></li>"].join("")}).join("\n"),"</ul>"].join("\n"))}function d(g){var h=$(this),f=h.parents(".dropdown-select"),e=h.text();f.find(".dropdown-select-selected").text(e);f.trigger("change.dropdown-select",e)}a.find("a").click(d);return a}(function(){function e(k,j){return this.init(k,j)}e.prototype.DATA_KEY="filter-control";e.prototype.init=function g(k,j){j=j||{filters:[]};this.$element=$(k).addClass("filter-control btn-group");this.options=jQuery.extend(true,{},this.defaults,j);this.currFilter=this.options.filters[0];return this.render()};e.prototype.render=function d(){this.$element.empty().append([this._renderKeySelect(),this._renderOpSelect(),this._renderValueInput()]);return this};e.prototype._renderKeySelect=function a(){var j=this;var k=this.options.filters.map(function(l){return l.key});this.$keySelect=dropDownSelect(k,this.currFilter.key).addClass("filter-control-key").on("change.dropdown-select",function(m,l){j.currFilter=_.findWhere(j.options.filters,{key:l});j.render()._triggerChange()});return this.$keySelect};e.prototype._renderOpSelect=function i(){var j=this,k=this.currFilter.ops;this.$opSelect=dropDownSelect(k,k[0]).addClass("filter-control-op").on("change.dropdown-select",function(m,l){j._triggerChange()});return this.$opSelect};e.prototype._renderValueInput=function c(){var j=this;if(this.currFilter.values){this.$valueSelect=dropDownSelect(this.currFilter.values,this.currFilter.values[0]).on("change.dropdown-select",function(l,k){j._triggerChange()})}else{this.$valueSelect=$("<input/>").addClass("form-control").on("change",function(k,l){j._triggerChange()})}this.$valueSelect.addClass("filter-control-value");return this.$valueSelect};e.prototype.val=function b(){var k=this.$element.find(".filter-control-key .dropdown-select-selected").text(),m=this.$element.find(".filter-control-op 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g={renameColumns:false,columnNames:[],commentChar:"#",hideCommentRows:false,includePrompts:true,topLeftContent:"Columns:"},s="peek-control.change",t="peek-control.rename",l="peek-control",v="control",f="control-prompt",c="selected",n="disabled",u="button",q="renamable-header",p="column-index",a="column-name";function i(w){if(w.disabled&&jQuery.type(w.disabled)!=="array"){throw new Error('"disabled" must be defined as an array of indeces: '+JSON.stringify(w))}if(w.multiselect&&w.selected&&jQuery.type(w.selected)!=="array"){throw new Error('Mulitselect rows need an array for "selected": '+JSON.stringify(w))}if(!w.label||!w.id){throw new Error("Peek controls need a label and id for each control row: "+JSON.stringify(w))}if(w.disabled&&w.disabled.indexOf(w.selected)!==-1){throw new Error("Selected column is in the list of disabled columns: "+JSON.stringify(w))}return w}function o(x,w){return $("<div/>").addClass(u).text(x.label)}function k(x,w){var y=$("<td/>").html(o(x,w)).attr("data-"+p,w);if(x.disabled&&x.disabled.indexOf(w)!==-1){y.addClass(n)}return y}function e(y,z,w){var x=y.children("."+u);if(y.hasClass(c)){x.html((z.selectedText!==undefined)?(z.selectedText):(z.label))}else{x.html((z.unselectedText!==undefined)?(z.unselectedText):(z.label))}}function h(z,x){var y=k(z,x);if(z.selected===x){y.addClass(c)}e(y,z,x);if(!y.hasClass(n)){y.click(function w(D){var E=$(this);if(!E.hasClass(c)){var A=E.parent().children("."+c).removeClass(c);A.each(function(){e($(this),z,x)});E.addClass(c);e(E,z,x);var C={},B=E.parent().attr("id"),F=E.data(p);C[B]=F;E.parents(".peek").trigger(s,C)}})}return y}function m(z,x){var y=k(z,x);if(z.selected&&z.selected.indexOf(x)!==-1){y.addClass(c)}e(y,z,x);if(!y.hasClass(n)){y.click(function w(D){var E=$(this);E.toggleClass(c);e(E,z,x);var C=E.parent().find("."+c).map(function(G,H){return $(H).data(p)});var 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H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var 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c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var 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g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";a.parent().find(".loading-indicator").remove();b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}(function(){var b=window._l||function(d){return 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h=$(this),f=h.parents(".dropdown-select"),e=h.text();f.find(".dropdown-select-selected").text(e);f.trigger("change.dropdown-select",e)}a.find("a").click(d);return a}(function(){function e(k,j){return this.init(k,j)}e.prototype.DATA_KEY="filter-control";e.prototype.init=function g(k,j){j=j||{filters:[]};this.$element=$(k).addClass("filter-control btn-group");this.options=jQuery.extend(true,{},this.defaults,j);this.currFilter=this.options.filters[0];return this.render()};e.prototype.render=function d(){this.$element.empty().append([this._renderKeySelect(),this._renderOpSelect(),this._renderValueInput()]);return this};e.prototype._renderKeySelect=function a(){var j=this;var k=this.options.filters.map(function(l){return l.key});this.$keySelect=dropDownSelect(k,this.currFilter.key).addClass("filter-control-key").on("change.dropdown-select",function(m,l){j.currFilter=_.findWhere(j.options.filters,{key:l});j.render()._triggerChange()});return 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g={renameColumns:false,columnNames:[],commentChar:"#",hideCommentRows:false,includePrompts:true,topLeftContent:"Columns:"},s="peek-control.change",t="peek-control.rename",l="peek-control",v="control",f="control-prompt",c="selected",n="disabled",u="button",q="renamable-header",p="column-index",a="column-name";function i(w){if(w.disabled&&jQuery.type(w.disabled)!=="array"){throw new Error('"disabled" must be defined as an array of indeces: '+JSON.stringify(w))}if(w.multiselect&&w.selected&&jQuery.type(w.selected)!=="array"){throw new Error('Mulitselect rows need an array for "selected": '+JSON.stringify(w))}if(!w.label||!w.id){throw new Error("Peek controls need a label and id for each control row: "+JSON.stringify(w))}if(w.disabled&&w.disabled.indexOf(w.selected)!==-1){throw new Error("Selected column is in the list of disabled columns: "+JSON.stringify(w))}return w}function o(x,w){return $("<div/>").addClass(u).text(x.label)}function k(x,w){var 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commit/galaxy-central: carlfeberhard: History multi-view: documentation and some cleanup
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff5d57faf17d/ Changeset: ff5d57faf17d User: carlfeberhard Date: 2014-09-29 14:54:01+00:00 Summary: History multi-view: documentation and some cleanup Affected #: 3 files diff -r 633b4212806d850135a28966d9759da3157b22e8 -r ff5d57faf17d38d345105300097fc7d196f3527e client/galaxy/scripts/mvc/history/multi-panel.js --- a/client/galaxy/scripts/mvc/history/multi-panel.js +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -30,6 +30,7 @@ } return name; } + function copyHistory( name ){ var $copyIndicator = $( '<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>' ) .css( 'margin-top', '8px' ); @@ -69,21 +70,16 @@ /* ============================================================================== TODO: copy places old current in wrong location - size not updating on dnd - sort by size is broken + sort by size is confusing (but correct) - nice_size shows actual disk usage, !== size handle delete current currently manual by user - delete then create new - make one step render move all columns over as one (agg. then html()) loading indicator on startup - loading indicators on histories (while queueHdaLoading) - __panelPatchRenderEmptyMsg performance - page load takes a while - renders where blocking each other - used _.delay( 0 ) - sort takes a while rendering columns could be better - lazy load history list + lazy load history list (for large numbers) + req. API limit/offset move in-view from pubsub handle errors @@ -103,10 +99,11 @@ privatize non-interface fns search for and drag and drop - should reset after dataset is loaded (or alt. clear search) - better ajax error handling ?columns should be a panel, not have a panel ============================================================================== */ +/** @class A container for a history panel that renders controls for that history (delete, copy, etc.) + */ var HistoryPanelColumn = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ //TODO: extend from panel? (instead of aggregating) @@ -120,7 +117,7 @@ }, // ------------------------------------------------------------------------ set up - /** */ + /** set up passed-in panel (if any) and listeners */ initialize : function initialize( options ){ options = options || {}; @@ -132,7 +129,7 @@ this.setUpListeners(); }, - /** */ + /** create a history panel for this column */ createPanel : function createPanel( panelOptions ){ panelOptions = _.extend({ model : this.model, @@ -148,7 +145,8 @@ }, //TODO: needs work - /** */ +//TODO: move to stub-class to avoid monkey-patching + /** the function monkey-patched into panels to show contents loading state */ __patch_renderEmptyMessage : function( $whereTo ){ var panel = this, hdaCount = _.chain( this.model.get( 'state_ids' ) ).values().flatten().value().length, @@ -170,7 +168,7 @@ return $emptyMsg; }, - /** */ + /** set up reflexive listeners */ setUpListeners : function setUpListeners(){ var column = this; //this.log( 'setUpListeners', this ); @@ -180,7 +178,7 @@ this.setUpPanelListeners(); }, - /** */ + /** set listeners needed for panel */ setUpPanelListeners : function setUpPanelListeners(){ var column = this; this.listenTo( this.panel, { @@ -193,7 +191,7 @@ }, this ); }, - /** */ + /** do the dimensions of this column overlap the given (horizontal) browser coords? */ inView : function( viewLeft, viewRight ){ //TODO: offset is expensive var columnLeft = this.$el.offset().left, @@ -203,13 +201,13 @@ return true; }, - /** */ + /** shortcut to the panel */ $panel : function $panel(){ return this.$( '.history-panel' ); }, // ------------------------------------------------------------------------ render - /** */ + /** render ths column, its panel, and set up plugins */ render : function render( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); //this.log( this + '.render', this.$el, this.el ); @@ -225,14 +223,14 @@ return this; }, - /** */ + /** set up plugins */ setUpBehaviors : function setUpBehaviors(){ //this.log( 'setUpBehaviors:', this ); //var column = this; // on panel size change, ... }, - /** */ + /** column body template with inner div for panel based on data (model json) */ template : function template( data ){ data = data || {}; var html = [ @@ -253,6 +251,7 @@ return $( html ); }, + /** controls template displaying controls above the panel based on this.currentHistory */ controlsLeftTemplate : function(){ return ( this.currentHistory )? [ @@ -267,7 +266,7 @@ ].join( '' ); }, - /** */ + /** render the panel contained in the column using speed for fx speed */ renderPanel : function renderPanel( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); this.panel.setElement( this.$panel() ).render( speed ); @@ -275,9 +274,11 @@ }, // ------------------------------------------------------------------------ behaviors and events - /** */ + /** event map */ events : { + // will make this the current history 'click .switch-to.btn' : function(){ this.model.setAsCurrent(); }, + // toggles deleted here and on the server and re-renders 'click .delete-history.btn' : function(){ var column = this, xhr; @@ -294,17 +295,18 @@ column.render(); }); }, + // will copy this history and make the copy the current history 'click .copy-history.btn' : 'copy' }, // ------------------------------------------------------------------------ non-current controls - /** */ + /** Open a modal to get a new history name, copy it (if not canceled), and makes the copy current */ copy : function copy(){ historyCopyDialog( this.model ); }, // ------------------------------------------------------------------------ misc - /** */ + /** String rep */ toString : function(){ return 'HistoryPanelColumn(' + ( this.panel? this.panel : '' ) + ')'; } @@ -312,13 +314,14 @@ //============================================================================== -// a multi-history view that displays histories in full +/** @class A view of a HistoryCollection and displays histories similarly to the current history panel. + */ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ //logger : console, // ------------------------------------------------------------------------ set up - /** */ + /** Set up internals, history collection, and columns to display the history */ initialize : function initialize( options ){ options = options || {}; this.log( this + '.init', options ); @@ -352,8 +355,6 @@ this.collection = null; this.setCollection( options.histories || [] ); - ///** the column views of histories */ - //this.columns = []; /** model id to column map */ this.columnMap = {}; //TODO: why create here? @@ -362,14 +363,16 @@ this.setUpListeners(); }, - /** */ + /** Set up reflexive listeners */ setUpListeners : function setUpListeners(){ //var multipanel = this; //multipanel.log( 'setUpListeners', multipanel ); }, // ------------------------------------------------------------------------ collection - /** */ + /** Set up a (new) history collection, sorting and adding listeners + * @fires 'new-collection' when set with this view as the arg + */ setCollection : function setCollection( models ){ var multipanel = this; multipanel.stopListening( multipanel.collection ); @@ -383,6 +386,7 @@ return multipanel; }, + /** Set up listeners for the collection - handling: added histories, change of current, deletion, and sorting */ setUpCollectionListeners : function(){ var multipanel = this, collection = multipanel.collection; @@ -394,15 +398,16 @@ // handle deleting a history (depends on whether panels is including deleted or not) 'change:deleted': multipanel.handleDeletedHistory, - 'sort' : function(){ multipanel.renderColumns( 0 ); }, + 'sort' : function(){ multipanel.renderColumns( 0 ); } + // debugging //'all' : function(){ // console.info( 'collection:', arguments ); //} }); }, - /** */ + /** Re-render and set currentHistoryId to reflect a new current history */ setCurrentHistory : function setCurrentHistory( history ){ var oldCurrentColumn = this.columnMap[ this.currentHistoryId ]; if( oldCurrentColumn ){ @@ -425,7 +430,9 @@ return newCurrentColumn; }, - /** */ + /** Either remove a deleted history or re-render it to show the deleted message + * based on collection.includeDeleted + */ handleDeletedHistory : function handleDeletedHistory( history ){ if( history.get( 'deleted' ) ){ this.log( 'handleDeletedHistory', this.collection.includeDeleted, history ); @@ -446,7 +453,9 @@ } }, - /** */ + /** Sort this collection based on order (defaulting to this.order) a string key + * (sorting the collection will re-render the panel) + */ sortCollection : function( order, options ){ order = order || this.order; var currentHistoryId = this.currentHistoryId; @@ -477,7 +486,7 @@ return this.collection; }, - /** */ + /** Set the sort order and re-sort */ setOrder : function( order ){ if( [ 'update', 'name', 'size' ].indexOf( order ) === -1 ){ order = 'update'; @@ -487,12 +496,12 @@ return this; }, - /** */ + /** create a new history and set it to current */ create : function( ev ){ return this.collection.create({ current: true }); }, - ///** */ + ///** delete the current history */ //deleteCurrent : function deleteCurrent(){ // var multipanel = this, // currentColumn = multipanel.columnMap[ multipanel.currentHistoryId ]; @@ -515,7 +524,7 @@ }); }, - /** */ + /** create a column and its panel and set up any listeners to them */ createColumn : function createColumn( history, options ){ // options passed can be re-used, so extend them before adding the model to prevent pollution for the next options = _.extend( {}, options, { model: history }); @@ -525,10 +534,6 @@ return column; }, - columnMapLength : function(){ - return Object.keys( this.columnMap ).length; - }, - sortedFilteredColumns : function( filters ){ filters = filters || this.filters; if( !filters || !filters.length ){ @@ -598,7 +603,7 @@ }); }, - /** */ + /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ var multipanel = this; multipanel.listenTo( column, { @@ -641,8 +646,13 @@ }, + /** conv. fn to count the columns in columnMap */ + columnMapLength : function(){ + return Object.keys( this.columnMap ).length; + }, + // ------------------------------------------------------------------------ render - /** */ + /** Render this view, columns, and set up view plugins */ render : function render( speed ){ speed = speed !== undefined? speed: this.fxSpeed; var multipanel = this; @@ -660,14 +670,16 @@ return multipanel; }, - /** */ + /** Template - overall structure relies on flex-boxes and is 3 components: header, middle, footer */ template : function template( options ){ options = options || {}; var html = []; if( this.options.headerHeight ){ html = html.concat([ + // a loading overlay '<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>', '<div class="header flex-column-container">', + // page & history controls '<div class="header-control header-control-left flex-column">', '<button class="done btn btn-default">', _l( 'Done' ), '</button>', '<button class="include-deleted btn btn-default"></button>', @@ -689,10 +701,12 @@ '</div>', '<div id="search-histories" class="header-search"></div>', '</div>', + // feedback '<div class="header-control header-control-center flex-column">', '<div class="header-info">', '</div>', '</div>', + // dataset controls '<div class="header-control header-control-right flex-column">', '<div id="search-datasets" class="header-search"></div>', '<button id="toggle-deleted" class="btn btn-default">', @@ -707,15 +721,17 @@ } html = html.concat([ + // middle - where the columns go '<div class="outer-middle flex-row flex-row-container">', '<div class="middle flex-column-container flex-row"></div>', '</div>', + // footer '<div class="footer flex-column-container">','</div>' ]); return $( html.join( '' ) ); }, - /** */ + /** Render the columns and panels */ renderColumns : function renderColumns( speed ){ speed = speed !== undefined? speed: this.fxSpeed; //this.log( 'renderColumns:', speed ); @@ -780,14 +796,16 @@ if( this.searchFor && sortedAndFiltered.length <= 1 ){ } else { + // check for in-view, hda lazy-loading if so multipanel.checkColumnsInView(); + // the first, current column has position: fixed and flex css will not apply - adjust height manually this._recalcFirstColumnHeight(); } return sortedAndFiltered; }, - /** */ + /** Render a single column using the non-blocking setTimeout( 0 ) pattern */ renderColumn : function( column, speed ){ speed = speed !== undefined? speed: this.fxSpeed; return _.delay( function(){ return column.render( speed ); }, 0 ); @@ -796,7 +814,9 @@ //TODO: combine the following two more sensibly //TODO: could have HistoryContents.haveDetails return false // if column.model.contents.length === 0 && !column.model.get( 'empty' ) then just check that - /** */ + /** Get the *summary* contents of a column's history (and details on any expanded contents), + * queueing the ajax call and using a named queue to prevent the call being sent twice + */ queueHdaFetch : function queueHdaFetch( column ){ //this.log( 'queueHdaFetch:', column ); // if the history model says it has hdas but none are present, queue an ajax req for them @@ -822,7 +842,7 @@ } }, - /** */ + /** Get the *detailed* json for *all* of a column's history's contents - req'd for searching */ queueHdaFetchDetails : function( column ){ if( ( column.model.contents.length === 0 && !column.model.get( 'empty' ) ) || ( !column.model.contents.haveDetails() ) ){ @@ -841,11 +861,7 @@ } }, - /** */ - allColumns : function allColumns(){ - return [ this.currentColumn ].concat( this.columns ); - }, - + /** put a text msg in the header */ renderInfo : function( msg ){ this.$( '.header .header-info' ).text( msg ); }, @@ -853,9 +869,13 @@ // ------------------------------------------------------------------------ events/behaviors /** */ events : { + // will move to the server root (gen. Analyze data) 'click .done.btn' : function(){ window.location = '/'; }, + //TODO:?? could just go back - but that's not always correct/desired behav. //'click .done.btn' : function(){ window.history.back(); }, + // creates a new empty history and makes it current 'click .create-new.btn' : 'create', + // these change the collection and column sort order 'click .order .order-update' : function( e ){ this.setOrder( 'update' ); }, 'click .order .order-name' : function( e ){ this.setOrder( 'name' ); }, 'click .order .order-size' : function( e ){ this.setOrder( 'size' ); } @@ -863,22 +883,25 @@ //'dragstart .list-item .title-bar' : function( e ){ console.debug( 'ok' ); } }, + /** Include deleted histories in the collection */ includeDeletedHistories : function(){ //TODO: better through API/limit+offset window.location += ( /\?/.test( window.location.toString() ) )?( '&' ):( '?' ) + 'include_deleted_histories=True'; }, + /** Show only non-deleted histories */ excludeDeletedHistories : function(){ //TODO: better through API/limit+offset window.location = window.location.toString().replace( /[&\?]include_deleted_histories=True/g, '' ); }, - /** */ + /** Set up any view plugins */ setUpBehaviors : function(){ var multipanel = this; //TODO: currently doesn't need to be a mode button + // toggle button for include deleted multipanel.$( '.include-deleted' ).modeButton({ initialMode : this.collection.includeDeleted? 'exclude' : 'include', switchModesOnClick : false, @@ -949,6 +972,7 @@ }); //TODO: each panel stores the hidden/deleted state - and that isn't reflected in the buttons + // toggle button for showing deleted history contents multipanel.$( '#toggle-deleted' ).modeButton({ initialMode : 'include', modes: [ @@ -964,6 +988,7 @@ }); }); + // toggle button for showing hidden history contents multipanel.$( '#toggle-hidden' ).modeButton({ initialMode : 'include', modes: [ @@ -990,33 +1015,26 @@ this.$( '.middle' ).parent().scroll( debouncedInView ); }, + ///** Put the in-view columns then the other columns in a queue, rendering each one at a time */ //panelRenderQueue : function( columns, fn, args, renderEventName ){ //}, + /** Adjust the height of the first, current column since flex-boxes won't work with fixed postiion elements */ _recalcFirstColumnHeight : function(){ - //var currentColumn = this.columnMap[ this.currentHistoryId ]; - //if( !currentColumn ){ return; } var $firstColumn = this.$( '.history-column' ).first(), middleHeight = this.$( '.middle' ).height(), controlHeight = $firstColumn.find( '.panel-controls' ).height(); $firstColumn.height( middleHeight ) .find( '.inner' ).height( middleHeight - controlHeight ); - -//console.debug( '$firstColumn:', $firstColumn ); - //var currentColumn = this.columnMap[ this.currentHistoryId ]; - //if( !currentColumn ){ return; } - //var middleHeight = this.$( '.middle' ).height(), - // controlHeight = currentColumn.$( '.panel-controls' ).height(); - //currentColumn.$el.height( middleHeight ) - // .find( '.inner' ).height( middleHeight - controlHeight ); }, + /** Get the left and right pixel coords of the middle element */ _viewport : function(){ var viewLeft = this.$( '.middle' ).parent().offset().left; return { left: viewLeft, right: viewLeft + this.$( '.middle' ).parent().width() }; }, - /** */ + /** returns the columns currently in the viewport */ columnsInView : function(){ //TODO: uses offset which is render intensive //TODO: 2N - could use arg filter (sortedFilteredColumns( filter )) instead @@ -1027,15 +1045,16 @@ }, //TODO: sortByInView - return cols in view, then others - /** */ + /** trigger in-view from columns in-view */ checkColumnsInView : function(){ +//TODO: assbackward //console.debug( 'checking columns in view', this.columnsInView() ); this.columnsInView().forEach( function( column ){ column.trigger( 'in-view', column ); }); }, - /** */ + /** Show and enable the current columns drop target */ currentColumnDropTargetOn : function(){ var currentColumn = this.columnMap[ this.currentHistoryId ]; if( !currentColumn ){ return; } @@ -1044,7 +1063,7 @@ currentColumn.panel.dropTargetOn(); }, - /** */ + /** Hide and disable the current columns drop target */ currentColumnDropTargetOff : function(){ var currentColumn = this.columnMap[ this.currentHistoryId ]; if( !currentColumn ){ return; } @@ -1053,7 +1072,7 @@ }, // ------------------------------------------------------------------------ misc - /** */ + /** String rep */ toString : function(){ return 'MultiPanelColumns(' + ( this.columns? this.columns.length : 0 ) + ')'; } diff -r 633b4212806d850135a28966d9759da3157b22e8 -r ff5d57faf17d38d345105300097fc7d196f3527e static/scripts/mvc/history/multi-panel.js --- a/static/scripts/mvc/history/multi-panel.js +++ b/static/scripts/mvc/history/multi-panel.js @@ -30,6 +30,7 @@ } return name; } + function copyHistory( name ){ var $copyIndicator = $( '<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>' ) .css( 'margin-top', '8px' ); @@ -69,21 +70,16 @@ /* ============================================================================== TODO: copy places old current in wrong location - size not updating on dnd - sort by size is broken + sort by size is confusing (but correct) - nice_size shows actual disk usage, !== size handle delete current currently manual by user - delete then create new - make one step render move all columns over as one (agg. then html()) loading indicator on startup - loading indicators on histories (while queueHdaLoading) - __panelPatchRenderEmptyMsg performance - page load takes a while - renders where blocking each other - used _.delay( 0 ) - sort takes a while rendering columns could be better - lazy load history list + lazy load history list (for large numbers) + req. API limit/offset move in-view from pubsub handle errors @@ -103,10 +99,11 @@ privatize non-interface fns search for and drag and drop - should reset after dataset is loaded (or alt. clear search) - better ajax error handling ?columns should be a panel, not have a panel ============================================================================== */ +/** @class A container for a history panel that renders controls for that history (delete, copy, etc.) + */ var HistoryPanelColumn = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ //TODO: extend from panel? (instead of aggregating) @@ -120,7 +117,7 @@ }, // ------------------------------------------------------------------------ set up - /** */ + /** set up passed-in panel (if any) and listeners */ initialize : function initialize( options ){ options = options || {}; @@ -132,7 +129,7 @@ this.setUpListeners(); }, - /** */ + /** create a history panel for this column */ createPanel : function createPanel( panelOptions ){ panelOptions = _.extend({ model : this.model, @@ -148,7 +145,8 @@ }, //TODO: needs work - /** */ +//TODO: move to stub-class to avoid monkey-patching + /** the function monkey-patched into panels to show contents loading state */ __patch_renderEmptyMessage : function( $whereTo ){ var panel = this, hdaCount = _.chain( this.model.get( 'state_ids' ) ).values().flatten().value().length, @@ -170,7 +168,7 @@ return $emptyMsg; }, - /** */ + /** set up reflexive listeners */ setUpListeners : function setUpListeners(){ var column = this; //this.log( 'setUpListeners', this ); @@ -180,7 +178,7 @@ this.setUpPanelListeners(); }, - /** */ + /** set listeners needed for panel */ setUpPanelListeners : function setUpPanelListeners(){ var column = this; this.listenTo( this.panel, { @@ -193,7 +191,7 @@ }, this ); }, - /** */ + /** do the dimensions of this column overlap the given (horizontal) browser coords? */ inView : function( viewLeft, viewRight ){ //TODO: offset is expensive var columnLeft = this.$el.offset().left, @@ -203,13 +201,13 @@ return true; }, - /** */ + /** shortcut to the panel */ $panel : function $panel(){ return this.$( '.history-panel' ); }, // ------------------------------------------------------------------------ render - /** */ + /** render ths column, its panel, and set up plugins */ render : function render( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); //this.log( this + '.render', this.$el, this.el ); @@ -225,14 +223,14 @@ return this; }, - /** */ + /** set up plugins */ setUpBehaviors : function setUpBehaviors(){ //this.log( 'setUpBehaviors:', this ); //var column = this; // on panel size change, ... }, - /** */ + /** column body template with inner div for panel based on data (model json) */ template : function template( data ){ data = data || {}; var html = [ @@ -253,6 +251,7 @@ return $( html ); }, + /** controls template displaying controls above the panel based on this.currentHistory */ controlsLeftTemplate : function(){ return ( this.currentHistory )? [ @@ -267,7 +266,7 @@ ].join( '' ); }, - /** */ + /** render the panel contained in the column using speed for fx speed */ renderPanel : function renderPanel( speed ){ speed = ( speed !== undefined )?( speed ):( 'fast' ); this.panel.setElement( this.$panel() ).render( speed ); @@ -275,9 +274,11 @@ }, // ------------------------------------------------------------------------ behaviors and events - /** */ + /** event map */ events : { + // will make this the current history 'click .switch-to.btn' : function(){ this.model.setAsCurrent(); }, + // toggles deleted here and on the server and re-renders 'click .delete-history.btn' : function(){ var column = this, xhr; @@ -294,17 +295,18 @@ column.render(); }); }, + // will copy this history and make the copy the current history 'click .copy-history.btn' : 'copy' }, // ------------------------------------------------------------------------ non-current controls - /** */ + /** Open a modal to get a new history name, copy it (if not canceled), and makes the copy current */ copy : function copy(){ historyCopyDialog( this.model ); }, // ------------------------------------------------------------------------ misc - /** */ + /** String rep */ toString : function(){ return 'HistoryPanelColumn(' + ( this.panel? this.panel : '' ) + ')'; } @@ -312,13 +314,14 @@ //============================================================================== -// a multi-history view that displays histories in full +/** @class A view of a HistoryCollection and displays histories similarly to the current history panel. + */ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ //logger : console, // ------------------------------------------------------------------------ set up - /** */ + /** Set up internals, history collection, and columns to display the history */ initialize : function initialize( options ){ options = options || {}; this.log( this + '.init', options ); @@ -352,8 +355,6 @@ this.collection = null; this.setCollection( options.histories || [] ); - ///** the column views of histories */ - //this.columns = []; /** model id to column map */ this.columnMap = {}; //TODO: why create here? @@ -362,14 +363,16 @@ this.setUpListeners(); }, - /** */ + /** Set up reflexive listeners */ setUpListeners : function setUpListeners(){ //var multipanel = this; //multipanel.log( 'setUpListeners', multipanel ); }, // ------------------------------------------------------------------------ collection - /** */ + /** Set up a (new) history collection, sorting and adding listeners + * @fires 'new-collection' when set with this view as the arg + */ setCollection : function setCollection( models ){ var multipanel = this; multipanel.stopListening( multipanel.collection ); @@ -383,6 +386,7 @@ return multipanel; }, + /** Set up listeners for the collection - handling: added histories, change of current, deletion, and sorting */ setUpCollectionListeners : function(){ var multipanel = this, collection = multipanel.collection; @@ -394,15 +398,16 @@ // handle deleting a history (depends on whether panels is including deleted or not) 'change:deleted': multipanel.handleDeletedHistory, - 'sort' : function(){ multipanel.renderColumns( 0 ); }, + 'sort' : function(){ multipanel.renderColumns( 0 ); } + // debugging //'all' : function(){ // console.info( 'collection:', arguments ); //} }); }, - /** */ + /** Re-render and set currentHistoryId to reflect a new current history */ setCurrentHistory : function setCurrentHistory( history ){ var oldCurrentColumn = this.columnMap[ this.currentHistoryId ]; if( oldCurrentColumn ){ @@ -425,7 +430,9 @@ return newCurrentColumn; }, - /** */ + /** Either remove a deleted history or re-render it to show the deleted message + * based on collection.includeDeleted + */ handleDeletedHistory : function handleDeletedHistory( history ){ if( history.get( 'deleted' ) ){ this.log( 'handleDeletedHistory', this.collection.includeDeleted, history ); @@ -446,7 +453,9 @@ } }, - /** */ + /** Sort this collection based on order (defaulting to this.order) a string key + * (sorting the collection will re-render the panel) + */ sortCollection : function( order, options ){ order = order || this.order; var currentHistoryId = this.currentHistoryId; @@ -477,7 +486,7 @@ return this.collection; }, - /** */ + /** Set the sort order and re-sort */ setOrder : function( order ){ if( [ 'update', 'name', 'size' ].indexOf( order ) === -1 ){ order = 'update'; @@ -487,12 +496,12 @@ return this; }, - /** */ + /** create a new history and set it to current */ create : function( ev ){ return this.collection.create({ current: true }); }, - ///** */ + ///** delete the current history */ //deleteCurrent : function deleteCurrent(){ // var multipanel = this, // currentColumn = multipanel.columnMap[ multipanel.currentHistoryId ]; @@ -515,7 +524,7 @@ }); }, - /** */ + /** create a column and its panel and set up any listeners to them */ createColumn : function createColumn( history, options ){ // options passed can be re-used, so extend them before adding the model to prevent pollution for the next options = _.extend( {}, options, { model: history }); @@ -525,10 +534,6 @@ return column; }, - columnMapLength : function(){ - return Object.keys( this.columnMap ).length; - }, - sortedFilteredColumns : function( filters ){ filters = filters || this.filters; if( !filters || !filters.length ){ @@ -598,7 +603,7 @@ }); }, - /** */ + /** set up listeners for a column and it's panel - handling: hda lazy-loading, drag and drop */ setUpColumnListeners : function setUpColumnListeners( column ){ var multipanel = this; multipanel.listenTo( column, { @@ -641,8 +646,13 @@ }, + /** conv. fn to count the columns in columnMap */ + columnMapLength : function(){ + return Object.keys( this.columnMap ).length; + }, + // ------------------------------------------------------------------------ render - /** */ + /** Render this view, columns, and set up view plugins */ render : function render( speed ){ speed = speed !== undefined? speed: this.fxSpeed; var multipanel = this; @@ -660,14 +670,16 @@ return multipanel; }, - /** */ + /** Template - overall structure relies on flex-boxes and is 3 components: header, middle, footer */ template : function template( options ){ options = options || {}; var html = []; if( this.options.headerHeight ){ html = html.concat([ + // a loading overlay '<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>', '<div class="header flex-column-container">', + // page & history controls '<div class="header-control header-control-left flex-column">', '<button class="done btn btn-default">', _l( 'Done' ), '</button>', '<button class="include-deleted btn btn-default"></button>', @@ -689,10 +701,12 @@ '</div>', '<div id="search-histories" class="header-search"></div>', '</div>', + // feedback '<div class="header-control header-control-center flex-column">', '<div class="header-info">', '</div>', '</div>', + // dataset controls '<div class="header-control header-control-right flex-column">', '<div id="search-datasets" class="header-search"></div>', '<button id="toggle-deleted" class="btn btn-default">', @@ -707,15 +721,17 @@ } html = html.concat([ + // middle - where the columns go '<div class="outer-middle flex-row flex-row-container">', '<div class="middle flex-column-container flex-row"></div>', '</div>', + // footer '<div class="footer flex-column-container">','</div>' ]); return $( html.join( '' ) ); }, - /** */ + /** Render the columns and panels */ renderColumns : function renderColumns( speed ){ speed = speed !== undefined? speed: this.fxSpeed; //this.log( 'renderColumns:', speed ); @@ -780,14 +796,16 @@ if( this.searchFor && sortedAndFiltered.length <= 1 ){ } else { + // check for in-view, hda lazy-loading if so multipanel.checkColumnsInView(); + // the first, current column has position: fixed and flex css will not apply - adjust height manually this._recalcFirstColumnHeight(); } return sortedAndFiltered; }, - /** */ + /** Render a single column using the non-blocking setTimeout( 0 ) pattern */ renderColumn : function( column, speed ){ speed = speed !== undefined? speed: this.fxSpeed; return _.delay( function(){ return column.render( speed ); }, 0 ); @@ -796,7 +814,9 @@ //TODO: combine the following two more sensibly //TODO: could have HistoryContents.haveDetails return false // if column.model.contents.length === 0 && !column.model.get( 'empty' ) then just check that - /** */ + /** Get the *summary* contents of a column's history (and details on any expanded contents), + * queueing the ajax call and using a named queue to prevent the call being sent twice + */ queueHdaFetch : function queueHdaFetch( column ){ //this.log( 'queueHdaFetch:', column ); // if the history model says it has hdas but none are present, queue an ajax req for them @@ -822,7 +842,7 @@ } }, - /** */ + /** Get the *detailed* json for *all* of a column's history's contents - req'd for searching */ queueHdaFetchDetails : function( column ){ if( ( column.model.contents.length === 0 && !column.model.get( 'empty' ) ) || ( !column.model.contents.haveDetails() ) ){ @@ -841,11 +861,7 @@ } }, - /** */ - allColumns : function allColumns(){ - return [ this.currentColumn ].concat( this.columns ); - }, - + /** put a text msg in the header */ renderInfo : function( msg ){ this.$( '.header .header-info' ).text( msg ); }, @@ -853,9 +869,13 @@ // ------------------------------------------------------------------------ events/behaviors /** */ events : { + // will move to the server root (gen. Analyze data) 'click .done.btn' : function(){ window.location = '/'; }, + //TODO:?? could just go back - but that's not always correct/desired behav. //'click .done.btn' : function(){ window.history.back(); }, + // creates a new empty history and makes it current 'click .create-new.btn' : 'create', + // these change the collection and column sort order 'click .order .order-update' : function( e ){ this.setOrder( 'update' ); }, 'click .order .order-name' : function( e ){ this.setOrder( 'name' ); }, 'click .order .order-size' : function( e ){ this.setOrder( 'size' ); } @@ -863,22 +883,25 @@ //'dragstart .list-item .title-bar' : function( e ){ console.debug( 'ok' ); } }, + /** Include deleted histories in the collection */ includeDeletedHistories : function(){ //TODO: better through API/limit+offset window.location += ( /\?/.test( window.location.toString() ) )?( '&' ):( '?' ) + 'include_deleted_histories=True'; }, + /** Show only non-deleted histories */ excludeDeletedHistories : function(){ //TODO: better through API/limit+offset window.location = window.location.toString().replace( /[&\?]include_deleted_histories=True/g, '' ); }, - /** */ + /** Set up any view plugins */ setUpBehaviors : function(){ var multipanel = this; //TODO: currently doesn't need to be a mode button + // toggle button for include deleted multipanel.$( '.include-deleted' ).modeButton({ initialMode : this.collection.includeDeleted? 'exclude' : 'include', switchModesOnClick : false, @@ -949,6 +972,7 @@ }); //TODO: each panel stores the hidden/deleted state - and that isn't reflected in the buttons + // toggle button for showing deleted history contents multipanel.$( '#toggle-deleted' ).modeButton({ initialMode : 'include', modes: [ @@ -964,6 +988,7 @@ }); }); + // toggle button for showing hidden history contents multipanel.$( '#toggle-hidden' ).modeButton({ initialMode : 'include', modes: [ @@ -990,33 +1015,26 @@ this.$( '.middle' ).parent().scroll( debouncedInView ); }, + ///** Put the in-view columns then the other columns in a queue, rendering each one at a time */ //panelRenderQueue : function( columns, fn, args, renderEventName ){ //}, + /** Adjust the height of the first, current column since flex-boxes won't work with fixed postiion elements */ _recalcFirstColumnHeight : function(){ - //var currentColumn = this.columnMap[ this.currentHistoryId ]; - //if( !currentColumn ){ return; } var $firstColumn = this.$( '.history-column' ).first(), middleHeight = this.$( '.middle' ).height(), controlHeight = $firstColumn.find( '.panel-controls' ).height(); $firstColumn.height( middleHeight ) .find( '.inner' ).height( middleHeight - controlHeight ); - -//console.debug( '$firstColumn:', $firstColumn ); - //var currentColumn = this.columnMap[ this.currentHistoryId ]; - //if( !currentColumn ){ return; } - //var middleHeight = this.$( '.middle' ).height(), - // controlHeight = currentColumn.$( '.panel-controls' ).height(); - //currentColumn.$el.height( middleHeight ) - // .find( '.inner' ).height( middleHeight - controlHeight ); }, + /** Get the left and right pixel coords of the middle element */ _viewport : function(){ var viewLeft = this.$( '.middle' ).parent().offset().left; return { left: viewLeft, right: viewLeft + this.$( '.middle' ).parent().width() }; }, - /** */ + /** returns the columns currently in the viewport */ columnsInView : function(){ //TODO: uses offset which is render intensive //TODO: 2N - could use arg filter (sortedFilteredColumns( filter )) instead @@ -1027,15 +1045,16 @@ }, //TODO: sortByInView - return cols in view, then others - /** */ + /** trigger in-view from columns in-view */ checkColumnsInView : function(){ +//TODO: assbackward //console.debug( 'checking columns in view', this.columnsInView() ); this.columnsInView().forEach( function( column ){ column.trigger( 'in-view', column ); }); }, - /** */ + /** Show and enable the current columns drop target */ currentColumnDropTargetOn : function(){ var currentColumn = this.columnMap[ this.currentHistoryId ]; if( !currentColumn ){ return; } @@ -1044,7 +1063,7 @@ currentColumn.panel.dropTargetOn(); }, - /** */ + /** Hide and disable the current columns drop target */ currentColumnDropTargetOff : function(){ var currentColumn = this.columnMap[ this.currentHistoryId ]; if( !currentColumn ){ return; } @@ -1053,7 +1072,7 @@ }, // ------------------------------------------------------------------------ misc - /** */ + /** String rep */ toString : function(){ return 'MultiPanelColumns(' + ( this.columns? this.columns.length : 0 ) + ')'; } diff -r 633b4212806d850135a28966d9759da3157b22e8 -r ff5d57faf17d38d345105300097fc7d196f3527e static/scripts/packed/mvc/history/multi-panel.js --- a/static/scripts/packed/mvc/history/multi-panel.js +++ b/static/scripts/packed/mvc/history/multi-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue"],function(d,m,A,a){window.HISTORY_MODEL=d;function g(I,F){F=F||{};if(!(Galaxy&&Galaxy.modal)){return I.copy()}var G=I.get("name"),D="Copy of '"+G+"'";function E(K){if(!K){if(!Galaxy.modal.$("#invalid-title").size()){var J=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(J)}return false}return K}function H(J){var K=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(K);I.copy(true,J).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+G+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',D,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){var J=Galaxy.modal.$("#copy-modal-title").val();if(!E(J)){return}H(J)}}},F));$("#copy-modal-title").focus().select()}var C=Backbone.View.extend(A.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function r(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(D){D=D||{};this.panel=D.panel||this.createPanel(D);this.setUpListeners()},createPanel:function v(E){E=_.extend({model:this.model,dragItems:true},E);var D=new m.HistoryPanelEdit(E);D._renderEmptyMessage=this.__patch_renderEmptyMessage;return D},__patch_renderEmptyMessage:function(F){var E=this,G=_.chain(this.model.get("state_ids")).values().flatten().value().length,D=E.$emptyMessage(F);if(!_.isEmpty(E.hdaViews)){D.hide()}else{if(G&&!this.model.contents.length){D.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(E.searchFor){D.text(E.noneFoundMsg).show()}else{D.text(E.emptyMsg).show()}}}return D},setUpListeners:function f(){var D=this;this.once("rendered",function(){D.trigger("rendered:initial",D)});this.setUpPanelListeners()},setUpPanelListeners:function l(){var D=this;this.listenTo(this.panel,{rendered:function(){D.trigger("rendered",D)}},this)},inView:function(D,E){var G=this.$el.offset().left,F=G+this.$el.width();if(F<D){return false}if(G>E){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function B(E){E=(E!==undefined)?(E):("fast");var D=this.model?this.model.toJSON():{};this.$el.html(this.template(D));this.renderPanel(E);this.setUpBehaviors();return this},setUpBehaviors:function w(){},template:function x(E){E=E||{};var D=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',E.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',E.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(D)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function i(D){D=(D!==undefined)?(D):("fast");this.panel.setElement(this.$panel()).render(D);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var D=this,E;if(this.model.get("deleted")){E=this.model.undelete()}else{E=this.model._delete()}E.fail(function(H,F,G){alert(_l("Could not delete the history")+":\n"+G)}).done(function(F){D.render()})},"click .copy-history.btn":"copy"},copy:function t(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var n=Backbone.View.extend(A.LoggableMixin).extend({initialize:function c(D){D=D||{};this.log(this+".init",D);if(!D.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=D.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=D.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(D.histories||[]);this.columnMap={};this.createColumns(D.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function z(E){var D=this;D.stopListening(D.collection);D.collection=E;D.sortCollection(D.order,{silent:true});D.setUpCollectionListeners();D.trigger("new-collection",D);return D},setUpCollectionListeners:function(){var D=this,E=D.collection;D.listenTo(E,{add:D.addAsCurrentColumn,"set-as-current":D.setCurrentHistory,"change:deleted":D.handleDeletedHistory,sort:function(){D.renderColumns(0)},})},setCurrentHistory:function q(E){var D=this.columnMap[this.currentHistoryId];if(D){D.currentHistory=false;D.$el.height("")}this.currentHistoryId=E.id;var F=this.columnMap[this.currentHistoryId];F.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return F},handleDeletedHistory:function b(E){if(E.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,E);var D=this;column=D.columnMap[E.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!D.collection.includeDeleted){D.removeColumn(column)}}}},sortCollection:function(D,E){D=D||this.order;var F=this.currentHistoryId;switch(D){case"name":this.collection.comparator=function(G){return[G.id!==F,G.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(G){return[G.id!==F,G.get("size")]};break;default:this.collection.comparator=function(G){return[G.id!==F,Date(G.get("update_time"))]}}this.collection.sort(E);return this.collection},setOrder:function(D){if(["update","name","size"].indexOf(D)===-1){D="update"}this.order=D;this.sortCollection();return this},create:function(D){return this.collection.create({current:true})},createColumns:function s(E){E=E||{};var D=this;this.columnMap={};D.collection.each(function(F,G){var H=D.createColumn(F,E);D.columnMap[F.id]=H})},createColumn:function u(F,D){D=_.extend({},D,{model:F});var E=new C(D);if(F.id===this.currentHistoryId){E.currentHistory=true}this.setUpColumnListeners(E);return E},columnMapLength:function(){return Object.keys(this.columnMap).length},sortedFilteredColumns:function(D){D=D||this.filters;if(!D||!D.length){return this.sortedColumns()}var E=this;return E.sortedColumns().filter(function(H,G){var F=H.currentHistory||_.every(D.map(function(I){return I.call(H)}));return F})},sortedColumns:function(){var E=this;var D=this.collection.map(function(G,F){return E.columnMap[G.id]});return D},addColumn:function p(F,D){D=D!==undefined?D:true;var E=this.createColumn(F);this.columnMap[F.id]=E;if(D){this.renderColumns()}return E},addAsCurrentColumn:function p(F){var E=this,D=this.addColumn(F,false);this.setCurrentHistory(F);D.once("rendered",function(){E.queueHdaFetch(D)});return D},removeColumn:function y(F,E){E=E!==undefined?E:true;this.log("removeColumn",F);if(!F){return}var G=this,D=this.options.columnWidth+this.options.columnGap;F.$el.fadeOut("fast",function(){if(E){$(this).remove();G.$(".middle").width(G.$(".middle").width()-D);G.checkColumnsInView();G._recalcFirstColumnHeight()}G.stopListening(F.panel);G.stopListening(F);delete G.columnMap[F.model.id];F.remove()})},setUpColumnListeners:function o(D){var E=this;E.listenTo(D,{"in-view":E.queueHdaFetch});E.listenTo(D.panel,{"view:draggable:dragstart":function(I,G,F,H){E._dropData=JSON.parse(I.dataTransfer.getData("text"));E.currentColumnDropTargetOn()},"view:draggable:dragend":function(I,G,F,H){E._dropData=null;E.currentColumnDropTargetOff()},"droptarget:drop":function(H,I,G){var J=E._dropData.filter(function(K){return(_.isObject(K)&&K.id&&K.model_class==="HistoryDatasetAssociation")});E._dropData=null;var F=new a.NamedAjaxQueue();J.forEach(function(K){F.add({name:"copy-"+K.id,fn:function(){return G.model.contents.copy(K.id)}})});F.start();F.done(function(K){G.model.fetch()})}})},render:function B(E){E=E!==undefined?E:this.fxSpeed;var D=this;D.log(D+".render");D.$el.html(D.template(D.options));D.renderColumns(E);D.setUpBehaviors();D.trigger("rendered",D);return D},template:function x(D){D=D||{};var E=[];if(this.options.headerHeight){E=E.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}E=E.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(E.join(""))},renderColumns:function k(G){G=G!==undefined?G:this.fxSpeed;var F=this,D=F.sortedFilteredColumns();F.$(".middle").width(D.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var E=F.$(".middle");E.empty();D.forEach(function(I,H){I.$el.appendTo(E);I.delegateEvents();F.renderColumn(I,G)});if(this.searchFor&&D.length<=1){}else{F.checkColumnsInView();this._recalcFirstColumnHeight()}return D},renderColumn:function(D,E){E=E!==undefined?E:this.fxSpeed;return _.delay(function(){return D.render(E)},0)},queueHdaFetch:function j(F){if(F.model.contents.length===0&&!F.model.get("empty")){var D={},E=_.values(F.panel.storage.get("expandedIds")).join();if(E){D.dataset_details=E}this.hdaQueue.add({name:F.model.id,fn:function(){var G=F.model.contents.fetch({data:D,silent:true});return G.done(function(H){F.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(D){if((D.model.contents.length===0&&!D.model.get("empty"))||(!D.model.contents.haveDetails())){this.hdaQueue.add({name:D.model.id,fn:function(){var E=D.model.contents.fetch({data:{details:"all"},silent:true});return E.done(function(F){D.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},allColumns:function h(){return[this.currentColumn].concat(this.columns)},renderInfo:function(D){this.$(".header .header-info").text(D)},events:{"click .done.btn":function(){window.location="/"},"click .create-new.btn":"create","click .order .order-update":function(D){this.setOrder("update")},"click .order .order-name":function(D){this.setOrder("name")},"click .order .order-size":function(D){this.setOrder("size")}},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var E=this;E.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(E.includeDeletedHistories,E)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(E.excludeDeletedHistories,E)}]});E.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(F){E.searchFor=F;E.filters=[function(){return this.model.get("name").indexOf(E.searchFor)!==-1}];E.renderColumns(0)},onclear:function(F){E.searchFor=null;E.filters=[];E.renderColumns(0)}});E.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(F){E.hdaQueue.clear();E.$("#search-datasets").searchInput("toggle-loading");E.searchFor=F;E.sortedFilteredColumns().forEach(function(G){G.panel.searchItems(F);E.queueHdaFetchDetails(G)});E.hdaQueue.progress(function(G){E.renderInfo([_l("loading"),(G.curr+1),_l("of"),G.total].join(" "))});E.hdaQueue.deferred.done(function(){E.renderInfo("");E.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(F){E.searchFor=F;E.sortedFilteredColumns().forEach(function(G){G.panel.searchItems(F)})},onclear:function(F){E.searchFor=null;E.sortedFilteredColumns().forEach(function(G){G.panel.clearSearch()})}});E.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var F=$(this).modeButton("getMode").mode==="exclude";E.sortedFilteredColumns().forEach(function(H,G){_.delay(function(){H.panel.toggleShowDeleted(F,false)},G*200)})});E.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var F=$(this).modeButton("getMode").mode==="exclude";E.sortedFilteredColumns().forEach(function(H,G){_.delay(function(){H.panel.toggleShowHidden(F,false)},G*200)})});$(window).resize(function(){E._recalcFirstColumnHeight()});var D=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(D)},_recalcFirstColumnHeight:function(){var D=this.$(".history-column").first(),F=this.$(".middle").height(),E=D.find(".panel-controls").height();D.height(F).find(".inner").height(F-E)},_viewport:function(){var D=this.$(".middle").parent().offset().left;return{left:D,right:D+this.$(".middle").parent().width()}},columnsInView:function(){var D=this._viewport();return this.sortedFilteredColumns().filter(function(E){return E.currentHistory||E.inView(D.left,D.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(D){D.trigger("in-view",D)})},currentColumnDropTargetOn:function(){var D=this.columnMap[this.currentHistoryId];if(!D){return}D.panel.dataDropped=function(E){};D.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var D=this.columnMap[this.currentHistoryId];if(!D){return}D.panel.dataDropped=m.HistoryPanelEdit.prototype.dataDrop;D.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:n}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/base-mvc","utils/ajax-queue"],function(d,l,z,a){window.HISTORY_MODEL=d;function g(H,E){E=E||{};if(!(Galaxy&&Galaxy.modal)){return H.copy()}var F=H.get("name"),C="Copy of '"+F+"'";function D(J){if(!J){if(!Galaxy.modal.$("#invalid-title").size()){var I=$("<p/>").attr("id","invalid-title").css({color:"red","margin-top":"8px"}).addClass("bg-danger").text(_l("Please enter a valid history title"));Galaxy.modal.$(".modal-body").append(I)}return false}return J}function G(I){var J=$('<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>').css("margin-top","8px");Galaxy.modal.$(".modal-body").append(J);H.copy(true,I).fail(function(){alert(_l("History could not be copied. Please contact a Galaxy administrator"))}).always(function(){Galaxy.modal.hide()})}Galaxy.modal.show(_.extend({title:_l("Copying history")+' "'+F+'"',body:$(['<label for="copy-modal-title">',_l("Enter a title for the copied history"),":","</label><br />",'<input id="copy-modal-title" class="form-control" style="width: 100%" value="',C,'" />'].join("")),buttons:{Cancel:function(){Galaxy.modal.hide()},Copy:function(){var I=Galaxy.modal.$("#copy-modal-title").val();if(!D(I)){return}G(I)}}},E));$("#copy-modal-title").focus().select()}var B=Backbone.View.extend(z.LoggableMixin).extend({tagName:"div",className:"history-column flex-column flex-row-container",id:function q(){if(!this.model){return""}return"history-column-"+this.model.get("id")},initialize:function c(C){C=C||{};this.panel=C.panel||this.createPanel(C);this.setUpListeners()},createPanel:function u(D){D=_.extend({model:this.model,dragItems:true},D);var C=new l.HistoryPanelEdit(D);C._renderEmptyMessage=this.__patch_renderEmptyMessage;return C},__patch_renderEmptyMessage:function(E){var D=this,F=_.chain(this.model.get("state_ids")).values().flatten().value().length,C=D.$emptyMessage(E);if(!_.isEmpty(D.hdaViews)){C.hide()}else{if(F&&!this.model.contents.length){C.empty().append($('<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>')).show()}else{if(D.searchFor){C.text(D.noneFoundMsg).show()}else{C.text(D.emptyMsg).show()}}}return C},setUpListeners:function f(){var C=this;this.once("rendered",function(){C.trigger("rendered:initial",C)});this.setUpPanelListeners()},setUpPanelListeners:function k(){var C=this;this.listenTo(this.panel,{rendered:function(){C.trigger("rendered",C)}},this)},inView:function(C,D){var F=this.$el.offset().left,E=F+this.$el.width();if(E<C){return false}if(F>D){return false}return true},$panel:function e(){return this.$(".history-panel")},render:function A(D){D=(D!==undefined)?(D):("fast");var C=this.model?this.model.toJSON():{};this.$el.html(this.template(C));this.renderPanel(D);this.setUpBehaviors();return this},setUpBehaviors:function v(){},template:function w(D){D=D||{};var C=['<div class="panel-controls clear flex-row">',this.controlsLeftTemplate(),'<div class="pull-right">','<button class="delete-history btn btn-default">',D.deleted?_l("Undelete"):_l("Delete"),"</button>",'<button class="copy-history btn btn-default">',_l("Copy"),"</button>","</div>","</div>",'<div class="inner flex-row flex-column-container">','<div id="history-',D.id,'" class="history-column history-panel flex-column"></div>',"</div>"].join("");return $(C)},controlsLeftTemplate:function(){return(this.currentHistory)?['<div class="pull-left">','<button class="create-new btn btn-default">',_l("Create new"),"</button> ","</div>"].join(""):['<div class="pull-left">','<button class="switch-to btn btn-default">',_l("Switch to"),"</button>","</div>"].join("")},renderPanel:function h(C){C=(C!==undefined)?(C):("fast");this.panel.setElement(this.$panel()).render(C);return this},events:{"click .switch-to.btn":function(){this.model.setAsCurrent()},"click .delete-history.btn":function(){var C=this,D;if(this.model.get("deleted")){D=this.model.undelete()}else{D=this.model._delete()}D.fail(function(G,E,F){alert(_l("Could not delete the history")+":\n"+F)}).done(function(E){C.render()})},"click .copy-history.btn":"copy"},copy:function s(){g(this.model)},toString:function(){return"HistoryPanelColumn("+(this.panel?this.panel:"")+")"}});var m=Backbone.View.extend(z.LoggableMixin).extend({initialize:function c(C){C=C||{};this.log(this+".init",C);if(!C.currentHistoryId){throw new Error(this+" requires a currentHistoryId in the options")}this.currentHistoryId=C.currentHistoryId;this.options={columnWidth:312,borderWidth:1,columnGap:8,headerHeight:29,footerHeight:0,controlsHeight:20};this.order=C.order||"update";this.hdaQueue=new a.NamedAjaxQueue([],false);this.collection=null;this.setCollection(C.histories||[]);this.columnMap={};this.createColumns(C.columnOptions);this.setUpListeners()},setUpListeners:function f(){},setCollection:function y(D){var C=this;C.stopListening(C.collection);C.collection=D;C.sortCollection(C.order,{silent:true});C.setUpCollectionListeners();C.trigger("new-collection",C);return C},setUpCollectionListeners:function(){var C=this,D=C.collection;C.listenTo(D,{add:C.addAsCurrentColumn,"set-as-current":C.setCurrentHistory,"change:deleted":C.handleDeletedHistory,sort:function(){C.renderColumns(0)}})},setCurrentHistory:function p(D){var C=this.columnMap[this.currentHistoryId];if(C){C.currentHistory=false;C.$el.height("")}this.currentHistoryId=D.id;var E=this.columnMap[this.currentHistoryId];E.currentHistory=true;this.sortCollection();multipanel._recalcFirstColumnHeight();return E},handleDeletedHistory:function b(D){if(D.get("deleted")){this.log("handleDeletedHistory",this.collection.includeDeleted,D);var C=this;column=C.columnMap[D.id];if(!column){return}if(column.model.id===this.currentHistoryId){}else{if(!C.collection.includeDeleted){C.removeColumn(column)}}}},sortCollection:function(C,D){C=C||this.order;var E=this.currentHistoryId;switch(C){case"name":this.collection.comparator=function(F){return[F.id!==E,F.get("name").toLowerCase()]};break;case"size":this.collection.comparator=function(F){return[F.id!==E,F.get("size")]};break;default:this.collection.comparator=function(F){return[F.id!==E,Date(F.get("update_time"))]}}this.collection.sort(D);return this.collection},setOrder:function(C){if(["update","name","size"].indexOf(C)===-1){C="update"}this.order=C;this.sortCollection();return this},create:function(C){return this.collection.create({current:true})},createColumns:function r(D){D=D||{};var C=this;this.columnMap={};C.collection.each(function(E,F){var G=C.createColumn(E,D);C.columnMap[E.id]=G})},createColumn:function t(E,C){C=_.extend({},C,{model:E});var D=new B(C);if(E.id===this.currentHistoryId){D.currentHistory=true}this.setUpColumnListeners(D);return D},sortedFilteredColumns:function(C){C=C||this.filters;if(!C||!C.length){return this.sortedColumns()}var D=this;return D.sortedColumns().filter(function(G,F){var E=G.currentHistory||_.every(C.map(function(H){return H.call(G)}));return E})},sortedColumns:function(){var D=this;var C=this.collection.map(function(F,E){return D.columnMap[F.id]});return C},addColumn:function o(E,C){C=C!==undefined?C:true;var D=this.createColumn(E);this.columnMap[E.id]=D;if(C){this.renderColumns()}return D},addAsCurrentColumn:function o(E){var D=this,C=this.addColumn(E,false);this.setCurrentHistory(E);C.once("rendered",function(){D.queueHdaFetch(C)});return C},removeColumn:function x(E,D){D=D!==undefined?D:true;this.log("removeColumn",E);if(!E){return}var F=this,C=this.options.columnWidth+this.options.columnGap;E.$el.fadeOut("fast",function(){if(D){$(this).remove();F.$(".middle").width(F.$(".middle").width()-C);F.checkColumnsInView();F._recalcFirstColumnHeight()}F.stopListening(E.panel);F.stopListening(E);delete F.columnMap[E.model.id];E.remove()})},setUpColumnListeners:function n(C){var D=this;D.listenTo(C,{"in-view":D.queueHdaFetch});D.listenTo(C.panel,{"view:draggable:dragstart":function(H,F,E,G){D._dropData=JSON.parse(H.dataTransfer.getData("text"));D.currentColumnDropTargetOn()},"view:draggable:dragend":function(H,F,E,G){D._dropData=null;D.currentColumnDropTargetOff()},"droptarget:drop":function(G,H,F){var I=D._dropData.filter(function(J){return(_.isObject(J)&&J.id&&J.model_class==="HistoryDatasetAssociation")});D._dropData=null;var E=new a.NamedAjaxQueue();I.forEach(function(J){E.add({name:"copy-"+J.id,fn:function(){return F.model.contents.copy(J.id)}})});E.start();E.done(function(J){F.model.fetch()})}})},columnMapLength:function(){return Object.keys(this.columnMap).length},render:function A(D){D=D!==undefined?D:this.fxSpeed;var C=this;C.log(C+".render");C.$el.html(C.template(C.options));C.renderColumns(D);C.setUpBehaviors();C.trigger("rendered",C);return C},template:function w(C){C=C||{};var D=[];if(this.options.headerHeight){D=D.concat(['<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>','<div class="header flex-column-container">','<div class="header-control header-control-left flex-column">','<button class="done btn btn-default">',_l("Done"),"</button>",'<button class="include-deleted btn btn-default"></button>','<div class="order btn-group">','<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">',_l("Order histories by")+'... <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="javascript:void(0);" class="order-update">',_l("Time of last update"),"</a></li>",'<li><a href="javascript:void(0);" class="order-name">',_l("Name"),"</a></li>",'<li><a href="javascript:void(0);" class="order-size">',_l("Size"),"</a></li>","</ul>","</div>",'<div id="search-histories" class="header-search"></div>',"</div>",'<div class="header-control header-control-center flex-column">','<div class="header-info">',"</div>","</div>",'<div class="header-control header-control-right flex-column">','<div id="search-datasets" class="header-search"></div>','<button id="toggle-deleted" class="btn btn-default">',_l("Include deleted datasets"),"</button>",'<button id="toggle-hidden" class="btn btn-default">',_l("Include hidden datasets"),"</button>","</div>","</div>"])}D=D.concat(['<div class="outer-middle flex-row flex-row-container">','<div class="middle flex-column-container flex-row"></div>',"</div>",'<div class="footer flex-column-container">',"</div>"]);return $(D.join(""))},renderColumns:function j(F){F=F!==undefined?F:this.fxSpeed;var E=this,C=E.sortedFilteredColumns();E.$(".middle").width(C.length*(this.options.columnWidth+this.options.columnGap)+this.options.columnGap+16);var D=E.$(".middle");D.empty();C.forEach(function(H,G){H.$el.appendTo(D);H.delegateEvents();E.renderColumn(H,F)});if(this.searchFor&&C.length<=1){}else{E.checkColumnsInView();this._recalcFirstColumnHeight()}return C},renderColumn:function(C,D){D=D!==undefined?D:this.fxSpeed;return _.delay(function(){return C.render(D)},0)},queueHdaFetch:function i(E){if(E.model.contents.length===0&&!E.model.get("empty")){var C={},D=_.values(E.panel.storage.get("expandedIds")).join();if(D){C.dataset_details=D}this.hdaQueue.add({name:E.model.id,fn:function(){var F=E.model.contents.fetch({data:C,silent:true});return F.done(function(G){E.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},queueHdaFetchDetails:function(C){if((C.model.contents.length===0&&!C.model.get("empty"))||(!C.model.contents.haveDetails())){this.hdaQueue.add({name:C.model.id,fn:function(){var D=C.model.contents.fetch({data:{details:"all"},silent:true});return D.done(function(E){C.panel.renderItems()})}});if(!this.hdaQueue.running){this.hdaQueue.start()}}},renderInfo:function(C){this.$(".header .header-info").text(C)},events:{"click .done.btn":function(){window.location="/"},"click .create-new.btn":"create","click .order .order-update":function(C){this.setOrder("update")},"click .order .order-name":function(C){this.setOrder("name")},"click .order .order-size":function(C){this.setOrder("size")}},includeDeletedHistories:function(){window.location+=(/\?/.test(window.location.toString()))?("&"):("?")+"include_deleted_histories=True"},excludeDeletedHistories:function(){window.location=window.location.toString().replace(/[&\?]include_deleted_histories=True/g,"")},setUpBehaviors:function(){var D=this;D.$(".include-deleted").modeButton({initialMode:this.collection.includeDeleted?"exclude":"include",switchModesOnClick:false,modes:[{mode:"include",html:_l("Include deleted histories"),onclick:_.bind(D.includeDeletedHistories,D)},{mode:"exclude",html:_l("Exclude deleted histories"),onclick:_.bind(D.excludeDeletedHistories,D)}]});D.$("#search-histories").searchInput({name:"search-histories",placeholder:_l("search histories"),onsearch:function(E){D.searchFor=E;D.filters=[function(){return this.model.get("name").indexOf(D.searchFor)!==-1}];D.renderColumns(0)},onclear:function(E){D.searchFor=null;D.filters=[];D.renderColumns(0)}});D.$("#search-datasets").searchInput({name:"search-datasets",placeholder:_l("search all datasets"),onfirstsearch:function(E){D.hdaQueue.clear();D.$("#search-datasets").searchInput("toggle-loading");D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E);D.queueHdaFetchDetails(F)});D.hdaQueue.progress(function(F){D.renderInfo([_l("loading"),(F.curr+1),_l("of"),F.total].join(" "))});D.hdaQueue.deferred.done(function(){D.renderInfo("");D.$("#search-datasets").searchInput("toggle-loading")})},onsearch:function(E){D.searchFor=E;D.sortedFilteredColumns().forEach(function(F){F.panel.searchItems(E)})},onclear:function(E){D.searchFor=null;D.sortedFilteredColumns().forEach(function(F){F.panel.clearSearch()})}});D.$("#toggle-deleted").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude deleted datasets")},{mode:"include",html:_l("Include deleted datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowDeleted(E,false)},F*200)})});D.$("#toggle-hidden").modeButton({initialMode:"include",modes:[{mode:"exclude",html:_l("Exclude hidden datasets")},{mode:"include",html:_l("Include hidden datasets")}]}).click(function(){var E=$(this).modeButton("getMode").mode==="exclude";D.sortedFilteredColumns().forEach(function(G,F){_.delay(function(){G.panel.toggleShowHidden(E,false)},F*200)})});$(window).resize(function(){D._recalcFirstColumnHeight()});var C=_.debounce(_.bind(this.checkColumnsInView,this),100);this.$(".middle").parent().scroll(C)},_recalcFirstColumnHeight:function(){var C=this.$(".history-column").first(),E=this.$(".middle").height(),D=C.find(".panel-controls").height();C.height(E).find(".inner").height(E-D)},_viewport:function(){var C=this.$(".middle").parent().offset().left;return{left:C,right:C+this.$(".middle").parent().width()}},columnsInView:function(){var C=this._viewport();return this.sortedFilteredColumns().filter(function(D){return D.currentHistory||D.inView(C.left,C.right)})},checkColumnsInView:function(){this.columnsInView().forEach(function(C){C.trigger("in-view",C)})},currentColumnDropTargetOn:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=function(D){};C.panel.dropTargetOn()},currentColumnDropTargetOff:function(){var C=this.columnMap[this.currentHistoryId];if(!C){return}C.panel.dataDropped=l.HistoryPanelEdit.prototype.dataDrop;C.panel.dropTargetOff()},toString:function(){return"MultiPanelColumns("+(this.columns?this.columns.length:0)+")"}});return{MultiPanelColumns:m}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History multi-view: initial commit of page to show all user histories in panel form (the page is currently orphaned/unwired - go to <root>/history/view_multiple to see the page)
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/633b4212806d/ Changeset: 633b4212806d User: carlfeberhard Date: 2014-09-29 13:47:18+00:00 Summary: History multi-view: initial commit of page to show all user histories in panel form (the page is currently orphaned/unwired - go to <root>/history/view_multiple to see the page) Affected #: 30 files diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/base-mvc.js --- a/client/galaxy/scripts/mvc/base-mvc.js +++ b/client/galaxy/scripts/mvc/base-mvc.js @@ -380,11 +380,6 @@ /** allow the view to be dragged, set up event handlers */ draggableOn : function(){ this.draggable = true; - //TODO: I have no idea why this doesn't work with the events hash or jq.on()... - //this.$el.find( '.title-bar' ) - // .attr( 'draggable', true ) - // .bind( 'dragstart', this.dragStartHandler, false ) - // .bind( 'dragend', this.dragEndHandler, false ); this.dragStartHandler = _.bind( this._dragStartHandler, this ); this.dragEndHandler = _.bind( this._dragEndHandler, this ); @@ -402,23 +397,22 @@ }, /** sets the dataTransfer data to the model's toJSON - * @fires dragstart (bbone event) which is passed this view + * @fires draggable:dragstart (bbone event) which is passed the event and this view */ _dragStartHandler : function( event ){ - //this.debug( 'dragStartHandler:', this, event, arguments ) - this.trigger( 'dragstart', this ); event.dataTransfer.effectAllowed = 'move'; + //ASSUMES: this.model //TODO: all except IE: should be 'application/json', IE: must be 'text' event.dataTransfer.setData( 'text', JSON.stringify( this.model.toJSON() ) ); + this.trigger( 'draggable:dragstart', event, this ); return false; }, /** handle the dragend - * @fires dragend (bbone event) which is passed this view + * @fires draggable:dragend (bbone event) which is passed the event and this view */ _dragEndHandler : function( event ){ - this.trigger( 'dragend', this ); - //this.debug( 'dragEndHandler:', event ) + this.trigger( 'draggable:dragend', event, this ); return false; } }; diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/dataset/dataset-li-edit.js --- a/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li-edit.js @@ -181,6 +181,8 @@ } var $visualizations = $( this.templates.visualizations( visualizations, this ) ); + //HACK: need to re-write those directed at galaxy_main with linkTarget + $visualizations.find( '[target="galaxy_main"]').attr( 'target', this.linkTarget ); // use addBack here to include the root $visualizations elem (for the case of 1 visualization) this._addScratchBookFn( $visualizations.find( '.visualization-link' ).addBack( '.visualization-link' ) ); return $visualizations; @@ -188,6 +190,7 @@ /** add scratchbook functionality to visualization links */ _addScratchBookFn : function( $links ){ + var li = this; $links.click( function( ev ){ if( Galaxy.frame && Galaxy.frame.active ){ Galaxy.frame.add({ diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/dataset/dataset-model.js --- a/client/galaxy/scripts/mvc/dataset/dataset-model.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js @@ -359,74 +359,11 @@ Backbone.Collection.prototype.set.call( this, models, options ); }, -// /** Convert this ad-hoc collection of hdas to a formal collection tracked -// by the server. -// **/ -// promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ -////TODO: seems like this would be better in mvc/collections -// options = options || {}; -// options.url = this.url(); -// options.type = "POST"; -// var full_collection_type = collection_type; -// var element_identifiers = [], -// name = null; -// -// // This mechanism is rough - no error handling, allows invalid selections, no way -// // for user to pick/override element identifiers. This is only really meant -// if( collection_type === "list" ) { -// this.chain().each( function( hda ) { -// // TODO: Handle duplicate names. -// var name = hda.attributes.name; -// var id = hda.get('id'); -// var content_type = hda.attributes.history_content_type; -// if( content_type === "dataset" ) { -// if( full_collection_type !== "list" ) { -// this.log( "Invalid collection type" ); -// } -// element_identifiers.push( { name: name, src: "hda", id: id } ); -// } else { -// if( full_collection_type === "list" ) { -// full_collection_type = "list:" + hda.attributes.collection_type; -// } else { -// if( full_collection_type !== "list:" + hda.attributes.collection_type ) { -// this.log( "Invalid collection type" ); -// } -// } -// element_identifiers.push( { name: name, src: "hdca", id: id } ); -// } -// }); -// name = "New Dataset List"; -// } else if( collection_type === "paired" ) { -// var ids = this.ids(); -// if( ids.length !== 2 ){ -// // TODO: Do something... -// } -// element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } ); -// element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } ); -// name = "New Dataset Pair"; -// } -// options.data = { -// type: "dataset_collection", -// name: name, -// collection_type: full_collection_type, -// element_identifiers: JSON.stringify( element_identifiers ) -// }; -// -// var xhr = jQuery.ajax( options ); -// xhr.done( function( message, status, responseObj ){ -// history.refresh( ); -// }); -// xhr.fail( function( xhr, status, message ){ -// if( xhr.responseJSON && xhr.responseJSON.error ){ -// error = xhr.responseJSON.error; -// } else { -// error = xhr.responseJSON; -// } -// xhr.responseText = error; -// // Do something? -// }); -// return xhr; -// }, + ///** Convert this ad-hoc collection of hdas to a formal collection tracked + // by the server. + //**/ + //promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ + //}, /** String representation. */ toString : function(){ diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/history/history-contents.js --- a/client/galaxy/scripts/mvc/history/history-contents.js +++ b/client/galaxy/scripts/mvc/history/history-contents.js @@ -187,6 +187,7 @@ /** copy an existing, accessible hda into this collection */ copy : function( id ){ +//TODO: incorp collections var collection = this, xhr = jQuery.post( this.url(), { source : 'hda', diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/history/history-model.js --- a/client/galaxy/scripts/mvc/history/history-model.js +++ b/client/galaxy/scripts/mvc/history/history-model.js @@ -117,7 +117,7 @@ return _.reduce( _.values( this.get( 'state_details' ) ), function( memo, num ){ return memo + num; }, 0 ); }, - // ........................................................................ ajax + // ........................................................................ updates /** does the contents collection indicate they're still running and need to be updated later? * delay + update if needed * @param {Function} onReadyCallback function to run when all contents are in the ready state @@ -187,6 +187,18 @@ return xhr; }, + // ........................................................................ ajax + /** save this history, _Mark_ing it as deleted (just a flag) */ + _delete : function( options ){ + if( this.get( 'deleted' ) ){ return jQuery.when(); } + return this.save( { deleted: true }, options ); + }, + /** save this history, _Mark_ing it as undeleted */ + undelete : function( options ){ + if( !this.get( 'deleted' ) ){ return jQuery.when(); } + return this.save( { deleted: false }, options ); + }, + /** Make a copy of this history on the server * @param {Boolean} current if true, set the copy as the new current history (default: true) * @param {String} name name of new history (default: none - server sets to: Copy of <current name>) @@ -210,9 +222,28 @@ //TODO:?? all datasets? var history = this, - xhr = jQuery.post( this.urlRoot, postData ); - xhr.done( function( newData ){ - history.trigger( 'copied', history, newData ); + copy = jQuery.post( this.urlRoot, postData ); + // if current - queue to setAsCurrent before firing 'copied' + if( current ){ + return copy.then( function( response ){ + var newHistory = new History( response ); + return newHistory.setAsCurrent() + .done( function(){ + history.trigger( 'copied', history, response ); + }); + }); + } + return copy.done( function( response ){ + history.trigger( 'copied', history, response ); + }); + }, + + setAsCurrent : function(){ + var history = this, + xhr = jQuery.getJSON( '/history/set_as_current?id=' + this.id ); + + xhr.done( function(){ + history.trigger( 'set-as-current', history ); }); return xhr; }, @@ -351,12 +382,15 @@ create : function create( data, hdas, historyOptions, xhrOptions ){ var collection = this, - history = new History( data || {}, hdas || [], historyOptions || {} ); - return history.save( xhrOptions ).done( function( newData ){ + xhr = jQuery.getJSON( galaxy_config.root + 'history/create_new_current' ); + return xhr.done( function( newData ){ + var history = new History( newData, [], historyOptions || {} ); // new histories go in the front //TODO: (implicit ordering by update time...) collection.unshift( history ); + collection.trigger( 'new-current' ); }); +//TODO: move back to using history.save (via Deferred.then w/ set_as_current) }, toString: function toString(){ diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/history/history-panel-edit.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js @@ -69,6 +69,17 @@ this.multiselectActions = attributes.multiselectActions || this._getActions(); }, + /** Override to handle history as drag-drop target */ + _setUpListeners : function(){ + _super.prototype._setUpListeners.call( this ); + + this.on( 'drop', function( ev, data ){ + this.dataDropped( data ); + // remove the drop target + this.dropTargetOff(); + }); + }, + // ------------------------------------------------------------------------ listeners /** listening for collection events */ _setUpCollectionListeners : function(){ @@ -296,6 +307,13 @@ return options; }, + ///** Override to alter data in drag based on multiselection */ + //_setUpItemViewListeners : function( view ){ + // var panel = this; + // _super.prototype._setUpItemViewListeners.call( panel, view ); + // + //}, + /** If this item is deleted and we're not showing deleted items, remove the view * @param {Model} the item model to check */ @@ -346,6 +364,132 @@ this.$el.find( '.history-size' ).text( this.model.get( 'nice_size' ) ); }, + // ------------------------------------------------------------------------ as drop target + /** */ + dropTargetOn : function(){ + if( this.dropTarget ){ return this; } + this.dropTarget = true; + + //TODO: to init + var dropHandlers = { + 'dragenter' : _.bind( this.dragenter, this ), + 'dragover' : _.bind( this.dragover, this ), + 'dragleave' : _.bind( this.dragleave, this ), + 'drop' : _.bind( this.drop, this ) + }; +//TODO: scroll to top + var $dropTarget = this._renderDropTarget(); + this.$list().before([ this._renderDropTargetHelp(), $dropTarget ]); + for( var evName in dropHandlers ){ + if( dropHandlers.hasOwnProperty( evName ) ){ + //console.debug( evName, dropHandlers[ evName ] ); + $dropTarget.on( evName, dropHandlers[ evName ] ); + } + } + return this; + }, + + /** */ + _renderDropTarget : function(){ + return $( '<div/>' ).addClass( 'history-drop-target' ) + .css({ + 'height': '64px', + 'margin': '0px 10px 10px 10px', + 'border': '1px dashed black', + 'border-radius' : '3px' + }); + }, + + /** */ + _renderDropTargetHelp : function(){ + return $( '<div/>' ).addClass( 'history-drop-target-help' ) + .css({ + 'margin' : '10px 10px 4px 10px', + 'color' : 'grey', + 'font-size' : '80%', + 'font-style' : 'italic' + }) + .text( _l( 'Drag datasets here to copy them to the current history' ) ); + }, + + /** */ + dropTargetOff : function(){ + if( !this.dropTarget ){ return this; } + //this.log( 'dropTargetOff' ); + this.dropTarget = false; + // + //var dropTarget = this.$( '.history-drop-target' ).get(0); + //for( var evName in this._dropHandlers ){ + // if( this._dropHandlers.hasOwnProperty( evName ) ){ + // console.debug( evName, this._dropHandlers[ evName ] ); + // dropTarget.off( evName, this._dropHandlers[ evName ] ); + // } + //} + this.$( '.history-drop-target' ).remove(); + this.$( '.history-drop-target-help' ).remove(); + return this; + }, + /** */ + dropTargetToggle : function(){ + if( this.dropTarget ){ + this.dropTargetOff(); + } else { + this.dropTargetOn(); + } + return this; + }, + + /** */ + dragenter : function( ev ){ + //console.debug( 'dragenter:', this, ev ); + ev.preventDefault(); + ev.stopPropagation(); + this.$( '.history-drop-target' ).css( 'border', '2px solid black' ); + }, + /** */ + dragover : function( ev ){ + ev.preventDefault(); + ev.stopPropagation(); + }, + /** */ + dragleave : function( ev ){ + //console.debug( 'dragleave:', this, ev ); + ev.preventDefault(); + ev.stopPropagation(); + this.$( '.history-drop-target' ).css( 'border', '1px dashed black' ); + }, + /** */ + drop : function( ev ){ + //console.warn( 'dataTransfer:', ev.dataTransfer.getData( 'text' ) ); + //console.warn( 'dataTransfer:', ev.originalEvent.dataTransfer.getData( 'text' ) ); + ev.preventDefault(); + //ev.stopPropagation(); + ev.dataTransfer.dropEffect = 'move'; + + //console.debug( 'ev.dataTransfer:', ev.dataTransfer ); + + var panel = this, + data = ev.dataTransfer.getData( "text" ); + try { + data = JSON.parse( data ); + + } catch( err ){ + this.warn( 'error parsing JSON from drop:', data ); + } + this.trigger( 'droptarget:drop', ev, data, panel ); + return false; + }, + + /** */ + dataDropped : function( data ){ + var panel = this; + // HDA: dropping will copy it to the history + if( _.isObject( data ) && data.model_class === 'HistoryDatasetAssociation' && data.id ){ + return panel.model.contents.copy( data.id ); + } + return jQuery.when(); + }, + // ........................................................................ misc /** Return a string rep of the history */ toString : function(){ diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/history/multi-panel.js --- /dev/null +++ b/client/galaxy/scripts/mvc/history/multi-panel.js @@ -0,0 +1,1067 @@ +define([ + "mvc/history/history-model", + "mvc/history/history-panel-edit", + "mvc/base-mvc", + "utils/ajax-queue" +], function( HISTORY_MODEL, HPANEL_EDIT, baseMVC, ajaxQueue ){ +window.HISTORY_MODEL = HISTORY_MODEL; +//============================================================================== +/** */ +function historyCopyDialog( history, options ){ + options = options || {}; + // fall back to un-notifying copy + if( !( Galaxy && Galaxy.modal ) ){ + return history.copy(); + } + + // maybe better as multiselect dialog? + var historyName = history.get( 'name' ), + defaultCopyName = "Copy of '" + historyName + "'"; + + function validateName( name ){ + if( !name ){ + if( !Galaxy.modal.$( '#invalid-title' ).size() ){ + var $invalidTitle = $( '<p/>' ).attr( 'id', 'invalid-title' ) + .css({ color: 'red', 'margin-top': '8px' }) + .addClass( 'bg-danger' ).text( _l( 'Please enter a valid history title' ) ); + Galaxy.modal.$( '.modal-body' ).append( $invalidTitle ); + } + return false; + } + return name; + } + function copyHistory( name ){ + var $copyIndicator = $( '<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>' ) + .css( 'margin-top', '8px' ); + Galaxy.modal.$( '.modal-body' ).append( $copyIndicator ); + history.copy( true, name ) +//TODO: make this unneccessary with pub-sub error + .fail( function(){ + alert( _l( 'History could not be copied. Please contact a Galaxy administrator' ) ); + }) + .always( function(){ + Galaxy.modal.hide(); + }); + } + + Galaxy.modal.show( _.extend({ + title : _l( 'Copying history' ) + ' "' + historyName + '"', + body : $([ + '<label for="copy-modal-title">', + _l( 'Enter a title for the copied history' ), ':', + '</label><br />', + '<input id="copy-modal-title" class="form-control" style="width: 100%" value="', + defaultCopyName, '" />' + ].join('')), + buttons : { + 'Cancel' : function(){ Galaxy.modal.hide(); }, + 'Copy' : function(){ + var name = Galaxy.modal.$( '#copy-modal-title' ).val(); + if( !validateName( name ) ){ return; } + copyHistory( name ); + } + } + }, options )); + $( '#copy-modal-title' ).focus().select(); +} + + +/* ============================================================================== +TODO: + copy places old current in wrong location + size not updating on dnd + sort by size is broken + handle delete current + currently manual by user - delete then create new - make one step + render + move all columns over as one (agg. then html()) + loading indicator on startup + loading indicators on histories (while queueHdaLoading) + __panelPatchRenderEmptyMsg + performance + page load takes a while + renders where blocking each other - used _.delay( 0 ) + sort takes a while + rendering columns could be better + lazy load history list + move in-view from pubsub + + handle errors + handle no histories + handle no histories found + + handle anon + no button + error message on loading url direct + include hidden/deleted + allow toggling w/o setting in storage + reloading with expanded collections doesn't get details of that collection + + change includeDeleted to an ajax call + + better narrowing + + privatize non-interface fns + search for and drag and drop - should reset after dataset is loaded (or alt. clear search) + better ajax error handling + ?columns should be a panel, not have a panel + +============================================================================== */ +var HistoryPanelColumn = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ +//TODO: extend from panel? (instead of aggregating) + + //logger : console, + + tagName : 'div', + className : 'history-column flex-column flex-row-container', + id : function id(){ + if( !this.model ){ return ''; } + return 'history-column-' + this.model.get( 'id' ); + }, + + // ------------------------------------------------------------------------ set up + /** */ + initialize : function initialize( options ){ + options = options || {}; + + //this.log( this + '.init', options ); + // if model, set up model + // create panel sub-view +//TODO: use current-history-panel for current + this.panel = options.panel || this.createPanel( options ); + this.setUpListeners(); + }, + + /** */ + createPanel : function createPanel( panelOptions ){ + panelOptions = _.extend({ + model : this.model, + //el : this.$panel(), + // non-current panels should set their hdas to draggable + dragItems : true + }, panelOptions ); + //this.log( 'panelOptions:', panelOptions ); +//TODO: use current-history-panel for current + var panel = new HPANEL_EDIT.HistoryPanelEdit( panelOptions ); + panel._renderEmptyMessage = this.__patch_renderEmptyMessage; + return panel; + }, + +//TODO: needs work + /** */ + __patch_renderEmptyMessage : function( $whereTo ){ + var panel = this, + hdaCount = _.chain( this.model.get( 'state_ids' ) ).values().flatten().value().length, + $emptyMsg = panel.$emptyMessage( $whereTo ); + + if( !_.isEmpty( panel.hdaViews ) ){ + $emptyMsg.hide(); + + } else if( hdaCount && !this.model.contents.length ){ + $emptyMsg.empty() + .append( $( '<span class="fa fa-spinner fa-spin"></span><i>loading datasets...</i>' ) ).show(); + + } else if( panel.searchFor ){ + $emptyMsg.text( panel.noneFoundMsg ).show(); + + } else { + $emptyMsg.text( panel.emptyMsg ).show(); + } + return $emptyMsg; + }, + + /** */ + setUpListeners : function setUpListeners(){ + var column = this; + //this.log( 'setUpListeners', this ); + this.once( 'rendered', function(){ + column.trigger( 'rendered:initial', column ); + }); + this.setUpPanelListeners(); + }, + + /** */ + setUpPanelListeners : function setUpPanelListeners(){ + var column = this; + this.listenTo( this.panel, { + //'all': function(){ console.info( 'panel of ' + this, arguments ); }, + + // assumes panel will take the longest to render + 'rendered': function(){ + column.trigger( 'rendered', column ); + } + }, this ); + }, + + /** */ + inView : function( viewLeft, viewRight ){ +//TODO: offset is expensive + var columnLeft = this.$el.offset().left, + columnRight = columnLeft + this.$el.width(); + if( columnRight < viewLeft ){ return false; } + if( columnLeft > viewRight ){ return false; } + return true; + }, + + /** */ + $panel : function $panel(){ + return this.$( '.history-panel' ); + }, + + // ------------------------------------------------------------------------ render + /** */ + render : function render( speed ){ + speed = ( speed !== undefined )?( speed ):( 'fast' ); + //this.log( this + '.render', this.$el, this.el ); +//TODO: not needed + var modelData = this.model? this.model.toJSON(): {}; + this.$el.html( this.template( modelData ) ); + this.renderPanel( speed ); + // if model and not children + // template + // render controls + this.setUpBehaviors(); + // add panel + return this; + }, + + /** */ + setUpBehaviors : function setUpBehaviors(){ + //this.log( 'setUpBehaviors:', this ); + //var column = this; + // on panel size change, ... + }, + + /** */ + template : function template( data ){ + data = data || {}; + var html = [ + '<div class="panel-controls clear flex-row">', + this.controlsLeftTemplate(), + //'<button class="btn btn-default">Herp</button>', + '<div class="pull-right">', + '<button class="delete-history btn btn-default">', + data.deleted? _l( 'Undelete' ): _l( 'Delete' ), + '</button>', + '<button class="copy-history btn btn-default">', _l( 'Copy' ), '</button>', + '</div>', + '</div>', + '<div class="inner flex-row flex-column-container">', + '<div id="history-', data.id, '" class="history-column history-panel flex-column"></div>', + '</div>' + ].join( '' ); + return $( html ); + }, + + controlsLeftTemplate : function(){ + return ( this.currentHistory )? + [ + '<div class="pull-left">', + '<button class="create-new btn btn-default">', _l( 'Create new' ), '</button> ', + '</div>' + ].join( '' ) + :[ + '<div class="pull-left">', + '<button class="switch-to btn btn-default">', _l( 'Switch to' ), '</button>', + '</div>' + ].join( '' ); + }, + + /** */ + renderPanel : function renderPanel( speed ){ + speed = ( speed !== undefined )?( speed ):( 'fast' ); + this.panel.setElement( this.$panel() ).render( speed ); + return this; + }, + + // ------------------------------------------------------------------------ behaviors and events + /** */ + events : { + 'click .switch-to.btn' : function(){ this.model.setAsCurrent(); }, + 'click .delete-history.btn' : function(){ + var column = this, + xhr; + if( this.model.get( 'deleted' ) ){ + xhr = this.model.undelete(); + } else { + xhr = this.model._delete(); + } +//TODO: better error handler + xhr.fail( function( xhr, status, error ){ + alert( _l( 'Could not delete the history' ) + ':\n' + error ); + }) + .done( function( data ){ + column.render(); + }); + }, + 'click .copy-history.btn' : 'copy' + }, + + // ------------------------------------------------------------------------ non-current controls + /** */ + copy : function copy(){ + historyCopyDialog( this.model ); + }, + + // ------------------------------------------------------------------------ misc + /** */ + toString : function(){ + return 'HistoryPanelColumn(' + ( this.panel? this.panel : '' ) + ')'; + } +}); + + +//============================================================================== +// a multi-history view that displays histories in full +var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ + + //logger : console, + + // ------------------------------------------------------------------------ set up + /** */ + initialize : function initialize( options ){ + options = options || {}; + this.log( this + '.init', options ); + + // --- instance vars + if( !options.currentHistoryId ){ + throw new Error( this + ' requires a currentHistoryId in the options' ); + } + this.currentHistoryId = options.currentHistoryId; + +//TODO: move these to some defaults + this.options = { + columnWidth : 312, + borderWidth : 1, + columnGap : 8, + + headerHeight : 29, + footerHeight : 0, + + controlsHeight : 20 + }; + + /** the order that the collection is rendered in */ + this.order = options.order || 'update'; + + /** named ajax queue for loading hdas */ + this.hdaQueue = new ajaxQueue.NamedAjaxQueue( [], false ); + + // --- set up models, sub-views, and listeners + /** the original unfiltered and unordered collection of histories */ + this.collection = null; + this.setCollection( options.histories || [] ); + + ///** the column views of histories */ + //this.columns = []; + /** model id to column map */ + this.columnMap = {}; +//TODO: why create here? + this.createColumns( options.columnOptions ); + + this.setUpListeners(); + }, + + /** */ + setUpListeners : function setUpListeners(){ + //var multipanel = this; + //multipanel.log( 'setUpListeners', multipanel ); + }, + + // ------------------------------------------------------------------------ collection + /** */ + setCollection : function setCollection( models ){ + var multipanel = this; + multipanel.stopListening( multipanel.collection ); + multipanel.collection = models; +//TODO: slow... esp. on start up + //if( multipanel.order !== 'update' ){ + multipanel.sortCollection( multipanel.order, { silent: true }); + //} + multipanel.setUpCollectionListeners(); + multipanel.trigger( 'new-collection', multipanel ); + return multipanel; + }, + + setUpCollectionListeners : function(){ + var multipanel = this, + collection = multipanel.collection; + multipanel.listenTo( collection, { + // handle addition of histories, triggered by column copy and create new + 'add': multipanel.addAsCurrentColumn, + // handle setting a history as current, triggered by history.setAsCurrent + 'set-as-current': multipanel.setCurrentHistory, + // handle deleting a history (depends on whether panels is including deleted or not) + 'change:deleted': multipanel.handleDeletedHistory, + + 'sort' : function(){ multipanel.renderColumns( 0 ); }, + + //'all' : function(){ + // console.info( 'collection:', arguments ); + //} + }); + }, + + /** */ + setCurrentHistory : function setCurrentHistory( history ){ + var oldCurrentColumn = this.columnMap[ this.currentHistoryId ]; + if( oldCurrentColumn ){ + oldCurrentColumn.currentHistory = false; + oldCurrentColumn.$el.height( '' ); + } + + this.currentHistoryId = history.id; + var newCurrentColumn = this.columnMap[ this.currentHistoryId ]; + newCurrentColumn.currentHistory = true; + + this.sortCollection(); + +////TODO: this actually means these render twice (1st from setCollection) - good enough for now + //if( oldCurrentColumn ){ oldCurrentColumn.render().delegateEvents(); } + //TODO:?? this occasionally causes race with hdaQueue + //newCurrentColumn.panel.render( 'fast' ).delegateEvents(); + + multipanel._recalcFirstColumnHeight(); + return newCurrentColumn; + }, + + /** */ + handleDeletedHistory : function handleDeletedHistory( history ){ + if( history.get( 'deleted' ) ){ + this.log( 'handleDeletedHistory', this.collection.includeDeleted, history ); + var multipanel = this; + column = multipanel.columnMap[ history.id ]; + if( !column ){ return; } + + // if it's the current column, create a new, empty history as the new current + if( column.model.id === this.currentHistoryId ){ +//TODO: figuring out the order of async here is tricky - for now let the user handle the two step process + //multipanel.collection.create().done( function(){ + // if( !multipanel.collection.includeDeleted ){ multipanel.removeColumn( column, false ); } + //}); + } else if( !multipanel.collection.includeDeleted ){ + multipanel.removeColumn( column ); + } +//TODO: prob. be done better + } + }, + + /** */ + sortCollection : function( order, options ){ + order = order || this.order; + var currentHistoryId = this.currentHistoryId; + + //note: h.id !== currentHistoryId allows the sort to put the current history first + switch( order ){ + case 'name': + //TODO: we can use a 2 arg version and return 1/0/-1 + //this.collection.comparator = function( h1, h2 ){ + this.collection.comparator = function( h ){ +//TODO: this won't do reverse order well + return [ h.id !== currentHistoryId, h.get( 'name' ).toLowerCase() ]; + }; + break; + case 'size': + this.collection.comparator = function( h ){ +//console.debug( 'name sort', arguments ) + return [ h.id !== currentHistoryId, h.get( 'size' ) ]; + }; + break; + default: + this.collection.comparator = function( h ){ + return [ h.id !== currentHistoryId, Date( h.get( 'update_time' ) ) ]; + }; + } + //NOTE: auto fires 'sort' from collection + this.collection.sort( options ); + return this.collection; + }, + + /** */ + setOrder : function( order ){ + if( [ 'update', 'name', 'size' ].indexOf( order ) === -1 ){ + order = 'update'; + } + this.order = order; + this.sortCollection(); + return this; + }, + + /** */ + create : function( ev ){ + return this.collection.create({ current: true }); + }, + + ///** */ + //deleteCurrent : function deleteCurrent(){ + // var multipanel = this, + // currentColumn = multipanel.columnMap[ multipanel.currentHistoryId ]; + // currentColumn.model._delete() + // .done( function(){ + // multipanel.create(); + // }); + //}, + + // ------------------------------------------------------------------------ columns + /** create columns from collection */ + createColumns : function createColumns( columnOptions ){ + columnOptions = columnOptions || {}; + var multipanel = this; + // clear column map + this.columnMap = {}; + multipanel.collection.each( function( model, i ){ + var column = multipanel.createColumn( model, columnOptions ); + multipanel.columnMap[ model.id ] = column; + }); + }, + + /** */ + createColumn : function createColumn( history, options ){ + // options passed can be re-used, so extend them before adding the model to prevent pollution for the next + options = _.extend( {}, options, { model: history }); + var column = new HistoryPanelColumn( options ); + if( history.id === this.currentHistoryId ){ column.currentHistory = true; } + this.setUpColumnListeners( column ); + return column; + }, + + columnMapLength : function(){ + return Object.keys( this.columnMap ).length; + }, + + sortedFilteredColumns : function( filters ){ + filters = filters || this.filters; + if( !filters || !filters.length ){ + return this.sortedColumns(); + } + var multipanel = this; + return multipanel.sortedColumns().filter( function( column, index ){ + var filtered = column.currentHistory || _.every( filters.map( function( filter ){ + return filter.call( column ); + })); + return filtered; + }); + }, + + sortedColumns : function(){ + var multipanel = this; + var sorted = this.collection.map( function( history, index ){ + return multipanel.columnMap[ history.id ]; + }); + return sorted; + }, + + /** */ + addColumn : function add( history, render ){ +//console.debug( 'adding column for:', history ); + render = render !== undefined? render: true; + var newColumn = this.createColumn( history ); + this.columnMap[ history.id ] = newColumn; + if( render ){ + this.renderColumns(); + } + return newColumn; + }, + + /** */ + addAsCurrentColumn : function add( history ){ +//console.log( 'adding current column for:', history ); + var multipanel = this, + newColumn = this.addColumn( history, false ); + this.setCurrentHistory( history ); + newColumn.once( 'rendered', function(){ + multipanel.queueHdaFetch( newColumn ); + }); + return newColumn; + }, + + /** */ + removeColumn : function remove( column, render ){ + render = render !== undefined? render : true; + this.log( 'removeColumn', column ); + if( !column ){ return; } + var multipanel = this, + widthToRemove = this.options.columnWidth + this.options.columnGap; + column.$el.fadeOut( 'fast', function(){ + if( render ){ + $( this ).remove(); + multipanel.$( '.middle' ).width( multipanel.$( '.middle' ).width() - widthToRemove ); + multipanel.checkColumnsInView(); + multipanel._recalcFirstColumnHeight(); + } + +//TODO: to freeColumn (where Columns have freePanel) + multipanel.stopListening( column.panel ); + multipanel.stopListening( column ); + delete multipanel.columnMap[ column.model.id ]; + column.remove(); + }); + }, + + /** */ + setUpColumnListeners : function setUpColumnListeners( column ){ + var multipanel = this; + multipanel.listenTo( column, { + //'all': function(){ console.info( 'column ' + column + ':', arguments ) }, + 'in-view': multipanel.queueHdaFetch + }); + + multipanel.listenTo( column.panel, { + //'all': function(){ console.info( 'panel ' + column.panel + ':', arguments ) }, + + 'view:draggable:dragstart': function( ev, view, panel, column ){ + multipanel._dropData = JSON.parse( ev.dataTransfer.getData( 'text' ) ); + multipanel.currentColumnDropTargetOn(); + }, + 'view:draggable:dragend': function( ev, view, panel, column ){ + multipanel._dropData = null; + multipanel.currentColumnDropTargetOff(); + }, + 'droptarget:drop': function( ev, data, panel ){ + var toCopy = multipanel._dropData.filter( function( json ){ + return ( _.isObject( json ) && json.id && json.model_class === 'HistoryDatasetAssociation' ); + }); + multipanel._dropData = null; + + var queue = new ajaxQueue.NamedAjaxQueue(); + toCopy.forEach( function( hda ){ + queue.add({ + name : 'copy-' + hda.id, + fn : function(){ + return panel.model.contents.copy( hda.id ); + } + }); + }); + queue.start(); + queue.done( function( responses ){ + panel.model.fetch(); + }); + } + }); + + }, + + // ------------------------------------------------------------------------ render + /** */ + render : function render( speed ){ + speed = speed !== undefined? speed: this.fxSpeed; + var multipanel = this; + + multipanel.log( multipanel + '.render' ); + multipanel.$el.html( multipanel.template( multipanel.options ) ); + //console.debug( multipanel.$( '.loading-overlay' ).fadeIn( 0 ) ); + multipanel.renderColumns( speed ); + //console.debug( multipanel.$( '.loading-overlay' ).fadeOut( 'fast' ) ); + + // set the columns to full height allowed and set up behaviors for thie multipanel + multipanel.setUpBehaviors(); +//TODO: wrong - has to wait for columns to render + multipanel.trigger( 'rendered', multipanel ); + return multipanel; + }, + + /** */ + template : function template( options ){ + options = options || {}; + var html = []; + if( this.options.headerHeight ){ + html = html.concat([ + '<div class="loading-overlay flex-row"><div class="loading-overlay-message">loading...</div></div>', + '<div class="header flex-column-container">', + '<div class="header-control header-control-left flex-column">', + '<button class="done btn btn-default">', _l( 'Done' ), '</button>', + '<button class="include-deleted btn btn-default"></button>', + '<div class="order btn-group">', + '<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'Order histories by' ) + '... <span class="caret"></span>', + '</button>', + '<ul class="dropdown-menu" role="menu">', + '<li><a href="javascript:void(0);" class="order-update">', + _l( 'Time of last update' ), + '</a></li>', + '<li><a href="javascript:void(0);" class="order-name">', + _l( 'Name' ), + '</a></li>', + '<li><a href="javascript:void(0);" class="order-size">', + _l( 'Size' ), + '</a></li>', + '</ul>', + '</div>', + '<div id="search-histories" class="header-search"></div>', + '</div>', + '<div class="header-control header-control-center flex-column">', + '<div class="header-info">', + '</div>', + '</div>', + '<div class="header-control header-control-right flex-column">', + '<div id="search-datasets" class="header-search"></div>', + '<button id="toggle-deleted" class="btn btn-default">', + _l( 'Include deleted datasets' ), + '</button>', + '<button id="toggle-hidden" class="btn btn-default">', + _l( 'Include hidden datasets' ), + '</button>', + '</div>', + '</div>' + ]); + } + + html = html.concat([ + '<div class="outer-middle flex-row flex-row-container">', + '<div class="middle flex-column-container flex-row"></div>', + '</div>', + '<div class="footer flex-column-container">','</div>' + ]); + return $( html.join( '' ) ); + }, + + /** */ + renderColumns : function renderColumns( speed ){ + speed = speed !== undefined? speed: this.fxSpeed; + //this.log( 'renderColumns:', speed ); + // render columns and track the total number rendered, firing an event when all are rendered + var multipanel = this, + sortedAndFiltered = multipanel.sortedFilteredColumns(); +//console.log( '\t columnMapLength:', this.columnMapLength(), this.columnMap ); + //this.log( '\t sortedAndFiltered:', sortedAndFiltered ); + + // set up width based on collection size +//console.debug( '(render) width before:', multipanel.$( '.middle' ).width() ) + multipanel.$( '.middle' ).width( sortedAndFiltered.length + //TODO: magic number 16 === the amount that safely prevents stacking of columns when adding a new one + * ( this.options.columnWidth + this.options.columnGap ) + this.options.columnGap + 16 ); +//console.debug( '(render) width now:', multipanel.$( '.middle' ).width() ) + +//console.debug( 'sortedAndFiltered:', sortedAndFiltered ) + //multipanel.$( '.middle' ).empty(); + +// this.$( '.middle' ).html( sortedAndFiltered.map( function( column, i ){ +// return column.$el.hide(); +// })); +// sortedAndFiltered.forEach( function( column, i ){ +////console.debug( 'rendering:', column, i ) +// //multipanel.$( '.middle' ).append( column.$el.hide() ); +// column.delegateEvents(); +////TODO: current column in-view is never fired +// multipanel.renderColumn( column, speed ).$el.show(); +// }); + +// var $els = sortedAndFiltered.map( function( column, i ){ +////console.debug( 'rendering:', column, i ) +// multipanel.renderColumn( column, speed ); +// return column.$el; +// }); +//// this breaks the event map +// //this.$( '.middle' ).html( $els ); +//// this doesn't +// this.$( '.middle' ).append( $els ); + + var $middle = multipanel.$( '.middle' ); + $middle.empty(); + sortedAndFiltered.forEach( function( column, i ){ +//console.debug( 'rendering:', column, i, column.panel ) + + column.$el.appendTo( $middle ); + column.delegateEvents(); + multipanel.renderColumn( column, speed ); + + //column.$el.hide().appendTo( $middle ); + //multipanel.renderColumn( column, speed ); + // //.panel.on( 'all', function(){ + // // console.debug( 'column rendered:', arguments ); + // //}); + //// this won't work until we checkColumnsInView after the render + ////column.$el.fadeIn( speed ); + //column.$el.show(); + }); + //this.log( 'column rendering done' ); + +//TODO: event columns-rendered + + if( this.searchFor && sortedAndFiltered.length <= 1 ){ + } else { + multipanel.checkColumnsInView(); + this._recalcFirstColumnHeight(); + } + + return sortedAndFiltered; + }, + + /** */ + renderColumn : function( column, speed ){ + speed = speed !== undefined? speed: this.fxSpeed; + return _.delay( function(){ return column.render( speed ); }, 0 ); + }, + +//TODO: combine the following two more sensibly +//TODO: could have HistoryContents.haveDetails return false +// if column.model.contents.length === 0 && !column.model.get( 'empty' ) then just check that + /** */ + queueHdaFetch : function queueHdaFetch( column ){ + //this.log( 'queueHdaFetch:', column ); + // if the history model says it has hdas but none are present, queue an ajax req for them + if( column.model.contents.length === 0 && !column.model.get( 'empty' ) ){ + //this.log( '\t fetch needed:', column ); + var xhrData = {}, + ids = _.values( column.panel.storage.get( 'expandedIds' ) ).join(); + if( ids ){ + xhrData.dataset_details = ids; + } + // this uses a 'named' queue so that duplicate requests are ignored + this.hdaQueue.add({ + name : column.model.id, + fn : function(){ + var xhr = column.model.contents.fetch({ data: xhrData, silent: true }); + return xhr.done( function( response ){ + column.panel.renderItems(); + }); + } + }); + // the queue is re-used, so if it's not processing requests - start it again + if( !this.hdaQueue.running ){ this.hdaQueue.start(); } + } + }, + + /** */ + queueHdaFetchDetails : function( column ){ + if( ( column.model.contents.length === 0 && !column.model.get( 'empty' ) ) + || ( !column.model.contents.haveDetails() ) ){ + // this uses a 'named' queue so that duplicate requests are ignored + this.hdaQueue.add({ + name : column.model.id, + fn : function(){ + var xhr = column.model.contents.fetch({ data: { details: 'all' }, silent: true }); + return xhr.done( function( response ){ + column.panel.renderItems(); + }); + } + }); + // the queue is re-used, so if it's not processing requests - start it again + if( !this.hdaQueue.running ){ this.hdaQueue.start(); } + } + }, + + /** */ + allColumns : function allColumns(){ + return [ this.currentColumn ].concat( this.columns ); + }, + + renderInfo : function( msg ){ + this.$( '.header .header-info' ).text( msg ); + }, + + // ------------------------------------------------------------------------ events/behaviors + /** */ + events : { + 'click .done.btn' : function(){ window.location = '/'; }, + //'click .done.btn' : function(){ window.history.back(); }, + 'click .create-new.btn' : 'create', + 'click .order .order-update' : function( e ){ this.setOrder( 'update' ); }, + 'click .order .order-name' : function( e ){ this.setOrder( 'name' ); }, + 'click .order .order-size' : function( e ){ this.setOrder( 'size' ); } + + //'dragstart .list-item .title-bar' : function( e ){ console.debug( 'ok' ); } + }, + + includeDeletedHistories : function(){ + //TODO: better through API/limit+offset + window.location += ( /\?/.test( window.location.toString() ) )?( '&' ):( '?' ) + + 'include_deleted_histories=True'; + }, + + excludeDeletedHistories : function(){ + //TODO: better through API/limit+offset + window.location = window.location.toString().replace( /[&\?]include_deleted_histories=True/g, '' ); + }, + + /** */ + setUpBehaviors : function(){ + var multipanel = this; + +//TODO: currently doesn't need to be a mode button + multipanel.$( '.include-deleted' ).modeButton({ + initialMode : this.collection.includeDeleted? 'exclude' : 'include', + switchModesOnClick : false, + modes: [ + { mode: 'include', html: _l( 'Include deleted histories' ), + onclick: _.bind( multipanel.includeDeletedHistories, multipanel ) + }, + { mode: 'exclude', html: _l( 'Exclude deleted histories' ), + onclick: _.bind( multipanel.excludeDeletedHistories, multipanel ) + } + ] + }); + + // input to search histories + multipanel.$( '#search-histories' ).searchInput({ + name : 'search-histories', + placeholder : _l( 'search histories' ), + onsearch : function( searchFor ){ + multipanel.searchFor = searchFor; + multipanel.filters = [ function(){ + return this.model.get( 'name' ).indexOf( multipanel.searchFor ) !== -1; + }]; + multipanel.renderColumns( 0 ); + }, + onclear : function( searchFor ){ + multipanel.searchFor = null; + multipanel.filters = []; + multipanel.renderColumns( 0 ); + } + }); + + // input to search datasets + multipanel.$( '#search-datasets' ).searchInput({ + name : 'search-datasets', + placeholder : _l( 'search all datasets' ), + + onfirstsearch : function( searchFor ){ + multipanel.hdaQueue.clear(); + multipanel.$( '#search-datasets' ).searchInput( 'toggle-loading' ); + multipanel.searchFor = searchFor; + multipanel.sortedFilteredColumns().forEach( function( column ){ + column.panel.searchItems( searchFor ); + // load details for them that need + multipanel.queueHdaFetchDetails( column ); + }); + multipanel.hdaQueue.progress( function( progress ){ + multipanel.renderInfo([ + _l( 'loading' ), ( progress.curr + 1 ), _l( 'of' ), progress.total + ].join( ' ' )); + }); + multipanel.hdaQueue.deferred.done( function(){ + multipanel.renderInfo( '' ); + multipanel.$( '#search-datasets' ).searchInput( 'toggle-loading' ); + }); + }, + onsearch : function( searchFor ){ + multipanel.searchFor = searchFor; + multipanel.sortedFilteredColumns().forEach( function( column ){ + column.panel.searchItems( searchFor ); + }); + }, + onclear : function( searchFor ){ + multipanel.searchFor = null; + multipanel.sortedFilteredColumns().forEach( function( column ){ + column.panel.clearSearch(); + }); + } + }); + +//TODO: each panel stores the hidden/deleted state - and that isn't reflected in the buttons + multipanel.$( '#toggle-deleted' ).modeButton({ + initialMode : 'include', + modes: [ + { mode: 'exclude', html: _l( 'Exclude deleted datasets' ) }, + { mode: 'include', html: _l( 'Include deleted datasets' ) } + ] + }).click( function(){ + var show = $( this ).modeButton( 'getMode' ).mode === 'exclude'; + multipanel.sortedFilteredColumns().forEach( function( column, i ){ + _.delay( function(){ + column.panel.toggleShowDeleted( show, false ); + }, i * 200 ); + }); + }); + + multipanel.$( '#toggle-hidden' ).modeButton({ + initialMode : 'include', + modes: [ + { mode: 'exclude', html: _l( 'Exclude hidden datasets' ) }, + { mode: 'include', html: _l( 'Include hidden datasets' ) } + ] + }).click( function(){ + var show = $( this ).modeButton( 'getMode' ).mode === 'exclude'; + multipanel.sortedFilteredColumns().forEach( function( column, i ){ + _.delay( function(){ + column.panel.toggleShowHidden( show, false ); + }, i * 200 ); + }); + }); + + // resize first (fixed position) column on page resize + $( window ).resize( function(){ + multipanel._recalcFirstColumnHeight(); + }); + + // when scrolling - check for histories now in view: they will fire 'in-view' and queueHdaLoading if necc. +//TODO:?? might be able to simplify and not use pub-sub + var debouncedInView = _.debounce( _.bind( this.checkColumnsInView, this ), 100 ); + this.$( '.middle' ).parent().scroll( debouncedInView ); + }, + + //panelRenderQueue : function( columns, fn, args, renderEventName ){ + //}, + + _recalcFirstColumnHeight : function(){ + //var currentColumn = this.columnMap[ this.currentHistoryId ]; + //if( !currentColumn ){ return; } + var $firstColumn = this.$( '.history-column' ).first(), + middleHeight = this.$( '.middle' ).height(), + controlHeight = $firstColumn.find( '.panel-controls' ).height(); + $firstColumn.height( middleHeight ) + .find( '.inner' ).height( middleHeight - controlHeight ); + +//console.debug( '$firstColumn:', $firstColumn ); + //var currentColumn = this.columnMap[ this.currentHistoryId ]; + //if( !currentColumn ){ return; } + //var middleHeight = this.$( '.middle' ).height(), + // controlHeight = currentColumn.$( '.panel-controls' ).height(); + //currentColumn.$el.height( middleHeight ) + // .find( '.inner' ).height( middleHeight - controlHeight ); + }, + + _viewport : function(){ + var viewLeft = this.$( '.middle' ).parent().offset().left; + return { left: viewLeft, right: viewLeft + this.$( '.middle' ).parent().width() }; + }, + + /** */ + columnsInView : function(){ + //TODO: uses offset which is render intensive +//TODO: 2N - could use arg filter (sortedFilteredColumns( filter )) instead + var vp = this._viewport(); + return this.sortedFilteredColumns().filter( function( column ){ + return column.currentHistory || column.inView( vp.left, vp.right ); + }); + }, + +//TODO: sortByInView - return cols in view, then others + /** */ + checkColumnsInView : function(){ +//console.debug( 'checking columns in view', this.columnsInView() ); + this.columnsInView().forEach( function( column ){ + column.trigger( 'in-view', column ); + }); + }, + + /** */ + currentColumnDropTargetOn : function(){ + var currentColumn = this.columnMap[ this.currentHistoryId ]; + if( !currentColumn ){ return; } +//TODO: fix this - shouldn't need monkeypatch + currentColumn.panel.dataDropped = function( data ){}; + currentColumn.panel.dropTargetOn(); + }, + + /** */ + currentColumnDropTargetOff : function(){ + var currentColumn = this.columnMap[ this.currentHistoryId ]; + if( !currentColumn ){ return; } + currentColumn.panel.dataDropped = HPANEL_EDIT.HistoryPanelEdit.prototype.dataDrop; + currentColumn.panel.dropTargetOff(); + }, + + // ------------------------------------------------------------------------ misc + /** */ + toString : function(){ + return 'MultiPanelColumns(' + ( this.columns? this.columns.length : 0 ) + ')'; + } +}); + + +//============================================================================== + return { + MultiPanelColumns : MultiPanelColumns + }; +}); diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -80,6 +80,9 @@ /** the last selected item.model.id */ this.lastSelected = null; + /** are sub-views draggable */ + this.dragItems = attributes.dragItems || false; + /** list item view class (when passed models) */ this.viewClass = attributes.viewClass || this.viewClass; @@ -317,6 +320,7 @@ //TODO: free prev. views? panel.views = panel._filterCollection().map( function( itemModel ){ //TODO: creates views each time - not neccessarily good +//TODO: pass speed here return panel._createItemView( itemModel ).render( 0 ); }); //panel.debug( item$els ); @@ -377,7 +381,7 @@ expanded : false, selectable : this.selecting, selected : _.contains( this.selected, model.id ), - draggable : this.dragging + draggable : this.dragItems }; }, @@ -391,6 +395,19 @@ panel.trigger.apply( panel, args ); }); + // drag multiple - hijack ev.setData to add all selected datasets + view.on( 'draggable:dragstart', function( ev, v ){ + //TODO: set multiple drag data here + var json = {}, + selected = this.getSelectedModels(); + if( selected.length ){ + json = selected.toJSON(); + } else { + json = [ v.model.toJSON() ]; + } + ev.dataTransfer.setData( 'text', JSON.stringify( json ) ); + }, this ); + // debugging //if( this.logger ){ // view.on( 'all', function( event ){ @@ -567,6 +584,7 @@ this.searchFor = searchFor; this.trigger( 'search:searching', searchFor, this ); this.renderItems(); + this.$( '> .controls .search-query' ).val( searchFor ); return this; }, @@ -576,6 +594,7 @@ this.searchFor = ''; this.trigger( 'search:clear', this ); this.renderItems(); + this.$( '> .controls .search-query' ).val( '' ); return this; }, diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/mvc/ui.js --- a/client/galaxy/scripts/mvc/ui.js +++ b/client/galaxy/scripts/mvc/ui.js @@ -691,6 +691,10 @@ } } }) + .on( 'change', function( event ){ + console.info( 'changed', $( this ), event ); + search.call( this, event, $( this ).val() ); + }) .val( options.initialVal ); } diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 client/galaxy/scripts/utils/ajax-queue.js --- a/client/galaxy/scripts/utils/ajax-queue.js +++ b/client/galaxy/scripts/utils/ajax-queue.js @@ -46,10 +46,11 @@ this.numToProcess += 1; this.queue.push( function(){ - var xhr = fn(); + var fnIndex = index, + xhr = fn(); // if successful, notify using the deferred to allow tracking progress xhr.done( function( response ){ - self.deferred.notify({ curr: index, total: self.numToProcess, response: response }); + self.deferred.notify({ curr: fnIndex, total: self.numToProcess, response: response }); }); // (regardless of previous error or success) if not last ajax call, shift and call the next // if last fn, resolve deferred @@ -86,6 +87,8 @@ } else { this.deferred.resolve( this.responses ); } + this.numToProcess = 0; + this.deferred = jQuery.Deferred(); return this; }; @@ -137,6 +140,7 @@ /** add the obj.fn to the queue if obj.name hasn't been used before */ NamedAjaxQueue.prototype.add = function add( obj ){ + //console.debug( 'NamedAjaxQueue.adding:', obj ) //console.debug( 'NamedAjaxQueue.prototype.add:', obj ); if( !( obj.hasOwnProperty( 'name' ) && obj.hasOwnProperty( 'fn' ) ) ){ throw new Error( 'NamedAjaxQueue.add requires an object with both "name" and "fn": ' + JSON.stringify( obj ) ); @@ -146,7 +150,14 @@ return; } this.names[ obj.name ] = true; + //console.debug( '\t names: ', this.names ) AjaxQueue.prototype.add.call( this, obj.fn ); + //console.debug( '\t queue: ', this.queue.length ); +}; + +/** override to remove names */ +NamedAjaxQueue.prototype.clear = function clear(){ + this.names = {}; }; /** shortcut constructor / fire and forget diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -575,6 +575,26 @@ show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) @web.expose + def view_multiple( self, trans, include_deleted_histories=False, order='update' ): + """ + """ + #TODO: allow specifying user_id for admin? + include_deleted_histories = galaxy.util.string_as_bool( include_deleted_histories ) + order = order if order in ( 'update', 'name', 'size' ) else 'update' + + current_history = trans.get_history() + current_history_id = trans.security.encode_id( current_history.id ) if current_history else None + + history_dictionaries = [] + for history in self.get_user_histories( trans, user=trans.user, include_deleted=include_deleted_histories ): + history_dictionary = self.get_history_dict( trans, history ) + history_dictionaries.append( history_dictionary ) + + return trans.fill_template_mako( "history/view_multiple.mako", + current_history_id=current_history_id, histories=history_dictionaries, + include_deleted_histories=include_deleted_histories, order=order ) + + @web.expose def display_by_username_and_slug( self, trans, username, slug ): """ Display history based on a username and slug. diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -380,11 +380,6 @@ /** allow the view to be dragged, set up event handlers */ draggableOn : function(){ this.draggable = true; - //TODO: I have no idea why this doesn't work with the events hash or jq.on()... - //this.$el.find( '.title-bar' ) - // .attr( 'draggable', true ) - // .bind( 'dragstart', this.dragStartHandler, false ) - // .bind( 'dragend', this.dragEndHandler, false ); this.dragStartHandler = _.bind( this._dragStartHandler, this ); this.dragEndHandler = _.bind( this._dragEndHandler, this ); @@ -402,23 +397,22 @@ }, /** sets the dataTransfer data to the model's toJSON - * @fires dragstart (bbone event) which is passed this view + * @fires draggable:dragstart (bbone event) which is passed the event and this view */ _dragStartHandler : function( event ){ - //this.debug( 'dragStartHandler:', this, event, arguments ) - this.trigger( 'dragstart', this ); event.dataTransfer.effectAllowed = 'move'; + //ASSUMES: this.model //TODO: all except IE: should be 'application/json', IE: must be 'text' event.dataTransfer.setData( 'text', JSON.stringify( this.model.toJSON() ) ); + this.trigger( 'draggable:dragstart', event, this ); return false; }, /** handle the dragend - * @fires dragend (bbone event) which is passed this view + * @fires draggable:dragend (bbone event) which is passed the event and this view */ _dragEndHandler : function( event ){ - this.trigger( 'dragend', this ); - //this.debug( 'dragEndHandler:', event ) + this.trigger( 'draggable:dragend', event, this ); return false; } }; diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 static/scripts/mvc/dataset/dataset-li-edit.js --- a/static/scripts/mvc/dataset/dataset-li-edit.js +++ b/static/scripts/mvc/dataset/dataset-li-edit.js @@ -181,6 +181,8 @@ } var $visualizations = $( this.templates.visualizations( visualizations, this ) ); + //HACK: need to re-write those directed at galaxy_main with linkTarget + $visualizations.find( '[target="galaxy_main"]').attr( 'target', this.linkTarget ); // use addBack here to include the root $visualizations elem (for the case of 1 visualization) this._addScratchBookFn( $visualizations.find( '.visualization-link' ).addBack( '.visualization-link' ) ); return $visualizations; @@ -188,6 +190,7 @@ /** add scratchbook functionality to visualization links */ _addScratchBookFn : function( $links ){ + var li = this; $links.click( function( ev ){ if( Galaxy.frame && Galaxy.frame.active ){ Galaxy.frame.add({ diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 static/scripts/mvc/dataset/dataset-model.js --- a/static/scripts/mvc/dataset/dataset-model.js +++ b/static/scripts/mvc/dataset/dataset-model.js @@ -359,74 +359,11 @@ Backbone.Collection.prototype.set.call( this, models, options ); }, -// /** Convert this ad-hoc collection of hdas to a formal collection tracked -// by the server. -// **/ -// promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ -////TODO: seems like this would be better in mvc/collections -// options = options || {}; -// options.url = this.url(); -// options.type = "POST"; -// var full_collection_type = collection_type; -// var element_identifiers = [], -// name = null; -// -// // This mechanism is rough - no error handling, allows invalid selections, no way -// // for user to pick/override element identifiers. This is only really meant -// if( collection_type === "list" ) { -// this.chain().each( function( hda ) { -// // TODO: Handle duplicate names. -// var name = hda.attributes.name; -// var id = hda.get('id'); -// var content_type = hda.attributes.history_content_type; -// if( content_type === "dataset" ) { -// if( full_collection_type !== "list" ) { -// this.log( "Invalid collection type" ); -// } -// element_identifiers.push( { name: name, src: "hda", id: id } ); -// } else { -// if( full_collection_type === "list" ) { -// full_collection_type = "list:" + hda.attributes.collection_type; -// } else { -// if( full_collection_type !== "list:" + hda.attributes.collection_type ) { -// this.log( "Invalid collection type" ); -// } -// } -// element_identifiers.push( { name: name, src: "hdca", id: id } ); -// } -// }); -// name = "New Dataset List"; -// } else if( collection_type === "paired" ) { -// var ids = this.ids(); -// if( ids.length !== 2 ){ -// // TODO: Do something... -// } -// element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } ); -// element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } ); -// name = "New Dataset Pair"; -// } -// options.data = { -// type: "dataset_collection", -// name: name, -// collection_type: full_collection_type, -// element_identifiers: JSON.stringify( element_identifiers ) -// }; -// -// var xhr = jQuery.ajax( options ); -// xhr.done( function( message, status, responseObj ){ -// history.refresh( ); -// }); -// xhr.fail( function( xhr, status, message ){ -// if( xhr.responseJSON && xhr.responseJSON.error ){ -// error = xhr.responseJSON.error; -// } else { -// error = xhr.responseJSON; -// } -// xhr.responseText = error; -// // Do something? -// }); -// return xhr; -// }, + ///** Convert this ad-hoc collection of hdas to a formal collection tracked + // by the server. + //**/ + //promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ + //}, /** String representation. */ toString : function(){ diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -187,6 +187,7 @@ /** copy an existing, accessible hda into this collection */ copy : function( id ){ +//TODO: incorp collections var collection = this, xhr = jQuery.post( this.url(), { source : 'hda', diff -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 -r 633b4212806d850135a28966d9759da3157b22e8 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -117,7 +117,7 @@ return _.reduce( _.values( this.get( 'state_details' ) ), function( memo, num ){ return memo + num; }, 0 ); }, - // ........................................................................ ajax + // ........................................................................ updates /** does the contents collection indicate they're still running and need to be updated later? * delay + update if needed * @param {Function} onReadyCallback function to run when all contents are in the ready state @@ -187,6 +187,18 @@ return xhr; }, + // ........................................................................ ajax + /** save this history, _Mark_ing it as deleted (just a flag) */ + _delete : function( options ){ + if( this.get( 'deleted' ) ){ return jQuery.when(); } + return this.save( { deleted: true }, options ); + }, + /** save this history, _Mark_ing it as undeleted */ + undelete : function( options ){ + if( !this.get( 'deleted' ) ){ return jQuery.when(); } + return this.save( { deleted: false }, options ); + }, + /** Make a copy of this history on the server * @param {Boolean} current if true, set the copy as the new current history (default: true) * @param {String} name name of new history (default: none - server sets to: Copy of <current name>) @@ -210,9 +222,28 @@ //TODO:?? all datasets? var history = this, - xhr = jQuery.post( this.urlRoot, postData ); - xhr.done( function( newData ){ - history.trigger( 'copied', history, newData ); + copy = jQuery.post( this.urlRoot, postData ); + // if current - queue to setAsCurrent before firing 'copied' + if( current ){ + return copy.then( function( response ){ + var newHistory = new History( response ); + return newHistory.setAsCurrent() + .done( function(){ + history.trigger( 'copied', history, response ); + }); + }); + } + return copy.done( function( response ){ + history.trigger( 'copied', history, response ); + }); + }, + + setAsCurrent : function(){ + var history = this, + xhr = jQuery.getJSON( '/history/set_as_current?id=' + this.id ); + + xhr.done( function(){ + history.trigger( 'set-as-current', history ); }); return xhr; }, @@ -351,12 +382,15 @@ create : function create( data, hdas, historyOptions, xhrOptions ){ var collection = this, - history = new History( data || {}, hdas || [], historyOptions || {} ); - return history.save( xhrOptions ).done( function( newData ){ + xhr = jQuery.getJSON( galaxy_config.root + 'history/create_new_current' ); + return xhr.done( function( newData ){ + var history = new History( newData, [], historyOptions || {} ); // new histories go in the front //TODO: (implicit ordering by update time...) collection.unshift( history ); + collection.trigger( 'new-current' ); }); +//TODO: move back to using history.save (via Deferred.then w/ set_as_current) }, toString: function toString(){ This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History API: add 'size' and 'update_time' to history show
by commits-noreply＠bitbucket.org 29 Sep '14

29 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/349e558c8ef8/ Changeset: 349e558c8ef8 User: carlfeberhard Date: 2014-09-29 13:33:27+00:00 Summary: History API: add 'size' and 'update_time' to history show Affected #: 1 file diff -r 0ef7a9e6973794876c3aee484512fb6c23de517d -r 349e558c8ef8e4ed4393f403d31e16f3e7235319 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -877,7 +877,8 @@ class History( object, Dictifiable, UsesAnnotations, HasName ): dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' ) - dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged', 'importable', 'slug', 'empty' ) + dict_element_visible_keys = ( 'id', 'name', 'genome_build', 'deleted', 'purged', 'update_time', + 'published', 'importable', 'slug', 'empty' ) default_name = 'Unnamed history' def __init__( self, id=None, name=None, user=None ): @@ -1027,6 +1028,9 @@ tags_str_list.append( tag_str ) rval[ 'tags' ] = tags_str_list + if view == 'element': + rval[ 'size' ] = int( self.get_disk_size() ) + return rval def set_from_dict( self, new_data ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 27 Sep '14

27 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20ed0e6f5700/ Changeset: 20ed0e6f5700 User: jmchilton Date: 2014-09-28 00:50:09+00:00 Summary: Merge next-stable. Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/fe0cdf1166a8/ Changeset: fe0cdf1166a8 Branch: next-stable User: jmchilton Date: 2014-09-28 00:37:21+00:00 Summary: Fix tool migrations to respect GALAXY_CONFIG_* environment variables. Thanks to Bjoern for the bug report. Affected #: 1 file diff -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d -r fe0cdf1166a841eb4b06dae4b40f552d12d947c7 scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -19,6 +19,7 @@ from galaxy.model.orm.scripts import require_dialect_egg from galaxy.model.orm.scripts import read_config_file_arg +from galaxy.util.properties import load_app_properties log = logging.getLogger( __name__ ) @@ -28,18 +29,19 @@ sys.exit( 1 ) repo = 'lib/tool_shed/galaxy_install/migrate' +properties = load_app_properties( ini_file=config_file ) cp = SafeConfigParser() cp.read( config_file ) if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ: # Running functional tests. db_url = os.environ[ 'GALAXY_TEST_DBURI' ] -elif cp.has_option( "app:main", "install_database_connection" ): - db_url = cp.get( "app:main", "install_database_connection" ) -elif cp.has_option( "app:main", "database_connection" ): - db_url = cp.get( "app:main", "database_connection" ) -elif cp.has_option( "app:main", "database_file" ): - db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" ) +elif "install_database_connection" in properties: + db_url = properties[ "install_database_connection" ] +elif "database_connection" in properties: + db_url = properties[ "database_connection" ] +elif "database_file" in properties: + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % properties[ "database_file" ] else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" https://bitbucket.org/galaxy/galaxy-central/commits/0ef7a9e69737/ Changeset: 0ef7a9e69737 User: jmchilton Date: 2014-09-28 00:51:04+00:00 Summary: Merge next-stable. Affected #: 1 file diff -r 20ed0e6f5700dfee42cd0d82a2d5e4275fbe1829 -r 0ef7a9e6973794876c3aee484512fb6c23de517d scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -19,6 +19,7 @@ from galaxy.model.orm.scripts import require_dialect_egg from galaxy.model.orm.scripts import read_config_file_arg +from galaxy.util.properties import load_app_properties log = logging.getLogger( __name__ ) @@ -28,18 +29,19 @@ sys.exit( 1 ) repo = 'lib/tool_shed/galaxy_install/migrate' +properties = load_app_properties( ini_file=config_file ) cp = SafeConfigParser() cp.read( config_file ) if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ: # Running functional tests. db_url = os.environ[ 'GALAXY_TEST_DBURI' ] -elif cp.has_option( "app:main", "install_database_connection" ): - db_url = cp.get( "app:main", "install_database_connection" ) -elif cp.has_option( "app:main", "database_connection" ): - db_url = cp.get( "app:main", "database_connection" ) -elif cp.has_option( "app:main", "database_file" ): - db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" ) +elif "install_database_connection" in properties: + db_url = properties[ "install_database_connection" ] +elif "database_connection" in properties: + db_url = properties[ "database_connection" ] +elif "database_file" in properties: + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % properties[ "database_file" ] else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c29f651e4acc/ Changeset: c29f651e4acc User: martenson Date: 2014-09-26 19:17:35+00:00 Summary: select2 fixes and impl. of missing feature import from path Affected #: 12 files diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -54,7 +54,12 @@ 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.' + 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.' }, // genomes @@ -73,15 +78,12 @@ id: this.options.id, is_admin: false, is_anonym: true, - user_library_import_dir: Galaxy.config.user_library_import_dir, - allow_library_path_paste: Galaxy.config.allow_library_path_paste, - library_import_dir: Galaxy.config.library_import_dir, mutiple_add_dataset_options: false } if (Galaxy.currUser){ template_defaults.is_admin = Galaxy.currUser.isAdmin(); template_defaults.is_anonym = Galaxy.currUser.isAnonymous(); - if (template_defaults.user_library_import_dir !== null || template_defaults.allow_library_path_paste !== false || template_defaults.library_import_dir !== null ){ + if ( Galaxy.config.user_library_import_dir !== null || Galaxy.config.allow_library_path_paste !== false || Galaxy.config.library_import_dir !== null ){ template_defaults.mutiple_add_dataset_options = true; } } @@ -402,33 +404,38 @@ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy… var that = this; this.select_genome = new mod_select.View( { - css: 'genome', + css: 'library-genome-select', data: that.list_genomes, - container: Galaxy.modal.$el.find( '#genome' ), + container: Galaxy.modal.$el.find( '#library_genome_select' ), value: '?' } ); this.select_extension = new mod_select.View({ - css: 'extension', + css: 'library-extension-select', data: that.list_extensions, - container: Galaxy.modal.$el.find('#extension'), + container: Galaxy.modal.$el.find( '#library_extension_select' ), value: 'auto' }); }, + /** - * Create modal for importing form user's directory + * Create modal for importing from given directory * on Galaxy. Bind jQuery events. */ - importFilesFromUserdirModal: function(){ + importFilesFromGalaxyFolderModal: function( options ){ var that = this; + var template_modal = this.templateBrowserModal(); this.modal = Galaxy.modal; - var template_modal = this.templateBrowserModal(); this.modal.show({ closing_events : true, title : 'Please select folders or files', body : template_modal({}), buttons : { - 'Import' : function() {that.importFromUserdirClicked(that);}, - 'Close' : function() {Galaxy.modal.hide();} + 'Import' : function() { + that.importFromJstreePath( that, options ); + }, + 'Close' : function() { + Galaxy.modal.hide(); + } }, closing_callback: function(){ // TODO: should not trigger routes outside of the router @@ -437,21 +444,24 @@ }); this.renderSelectBoxes(); - this.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + this.renderJstree( options ); - $('input[type=radio]').change(function(event){ + $( 'input[type=radio]' ).change( function( event ){ if (event.target.value ==='jstree-disable-folders') { - that.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + that.renderJstree( options ); $('.jstree-folders-message').hide(); $('.jstree-preserve-structure').hide(); $('.jstree-link-files').hide(); $('.jstree-files-message').show(); - } else if (event.target.value ==='jstree-disable-files'){ + } else if ( event.target.value ==='jstree-disable-files' ){ $('.jstree-files-message').hide(); $('.jstree-folders-message').show(); $('.jstree-link-files').show(); $('.jstree-preserve-structure').show(); - that.renderJstree({disabled_jstree_element: 'files'}); + options.disabled_jstree_element = 'files'; + that.renderJstree( options ); } } ); @@ -463,12 +473,16 @@ * data. * @param {[type]} options [description] */ - renderJstree: function(options){ + renderJstree: function( options ){ var that = this; - this.options = _.extend(this.options, options); + this.options = _.extend( this.options, options ); + var target = options.source || 'userdir'; var disabled_jstree_element = this.options.disabled_jstree_element; this.jstree = new mod_library_model.Jstree(); - this.jstree.url = this.jstree.urlRoot + '?target=userdir&format=jstree&disable=' + disabled_jstree_element; + this.jstree.url = this.jstree.urlRoot + + '?target=' + target + + '&format=jstree' + + '&disable=' + disabled_jstree_element; this.jstree.fetch({ success: function(model, response){ // This is to prevent double jquery load. I think. Carl is magician. @@ -579,7 +593,7 @@ * jstree.js has to be loaded before * @see renderJstree */ - importFromUserdirClicked: function ( that ){ + importFromJstreePath: function ( that, options ){ var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true ); var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' ); var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' ); @@ -588,7 +602,7 @@ var selection_type = selected_nodes[0].type; var paths = []; if ( selected_nodes.length < 1 ){ - mod_toastr.info( 'You must select some items first.' ); + mod_toastr.info( 'Please select some items first.' ); } else { this.modal.disableButton( 'Import' ); for ( var i = selected_nodes.length - 1; i >= 0; i-- ){ @@ -598,17 +612,19 @@ } this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } ); if ( selection_type === 'folder' ){ - + var full_source = options.source + '_folder'; this.chainCallImportingFolders( { paths: paths, preserve_dirs: preserve_dirs, link_data: link_data, - source: 'userdir_folder', + source: full_source, file_type: file_type, dbkey: dbkey } ); } else if ( selection_type === 'file' ){ + var full_source = options.source + '_file'; this.chainCallImportingUserdirFiles( { paths : paths, file_type: file_type, - dbkey: dbkey } ); + dbkey: dbkey, + source: full_source } ); } } }, @@ -713,7 +729,7 @@ return true; } var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + - '&source=userdir_file' + + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + '&dbkey=' + options.dbkey ) ) @@ -760,22 +776,12 @@ '&dbkey=' + options.dbkey ) ) promise.done(function(response){ that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }) .fail(function(){ that.options.chain_call_control.failed_number += 1; that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }); }, @@ -952,12 +958,13 @@ this.addFilesFromHistoryModal(); break; case "importdir": + this.importFilesFromGalaxyFolderModal( { source: 'importdir' } ); break; case "path": this.importFilesFromPathModal(); break; case "userdir": - this.importFilesFromUserdirModal(); + this.importFilesFromGalaxyFolderModal( { source: 'userdir' } ); break; default: Galaxy.libraries.library_router.back(); @@ -984,17 +991,19 @@ tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>'); - tmpl_array.push('<% if(user_library_import_dir !== null) { %>'); + tmpl_array.push('<% if(Galaxy.config.user_library_import_dir !== null) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>'); tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); - // tmpl_array.push('<% if(allow_library_path_paste || library_import_dir !== null) { %>'); - tmpl_array.push(' <li class="divider"></li>'); - tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); - // tmpl_array.push('<% if(library_import_dir !== null) { %>'); - // tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); - // tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); + + tmpl_array.push(' <li class="divider"></li>'); + tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); + + tmpl_array.push('<% if(Galaxy.config.library_import_dir !== null) { %>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); + tmpl_array.push('<% } %>'); + + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>'); tmpl_array.push('<% } %>'); tmpl_array.push('<% } %>'); @@ -1154,8 +1163,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); @@ -1184,8 +1193,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb client/galaxy/scripts/mvc/ui/ui-select.js --- a/client/galaxy/scripts/mvc/ui/ui-select.js +++ b/client/galaxy/scripts/mvc/ui/ui-select.js @@ -155,7 +155,6 @@ data : this.select_data, containerCssClass : this.options.css, placeholder : this.options.placeholder, - width : 'resolve', dropdownAutoWidth : true }; this.$el.select2(select_opt); diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py @@ -49,7 +49,7 @@ userdir_jstree = self.__create_jstree( full_import_dir, disable ) response = userdir_jstree.jsonData() except Exception, exception: - log.debug(str(exception)) + log.debug( str( exception ) ) raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( full_import_dir ) ) elif format == 'ajax': raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) @@ -61,6 +61,26 @@ raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) else: raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) + elif target == 'importdir': + base_dir = trans.app.config.library_import_dir + if base_dir is None: + raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow usage of import directory.' ) + if format == 'jstree': + disable = kwd.get( 'disable', 'folders') + try: + importdir_jstree = self.__create_jstree( base_dir, disable ) + response = importdir_jstree.jsonData() + except Exception, exception: + log.debug( str( exception ) ) + raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( base_dir ) ) + elif format == 'ajax': + raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) + else: + try: + response = self.__load_all_filenames( base_dir ) + except Exception, exception: + log.error( 'Could not get user import files: %s', str( exception ), exc_info=True ) + raise exceptions.InternalServerError( 'Could not get the files from your import directory folder.' ) else: user_ftp_base_dir = trans.app.config.ftp_upload_dir if user_ftp_base_dir is None: diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -429,8 +429,15 @@ folder = self.folder_manager.get( trans, folder_id ) source = kwd.get( 'source', None ) - if source not in [ 'userdir_file', 'userdir_folder', 'admin_path' ]: - raise exceptions.RequestParameterMissingException( 'You have to specify "source" parameter. Possible values are "userdir_file", "userdir_folder" and "admin_path". ') + if source not in [ 'userdir_file', 'userdir_folder', 'importdir_file', 'importdir_folder', 'admin_path' ]: + raise exceptions.RequestParameterMissingException( 'You have to specify "source" parameter. Possible values are "userdir_file", "userdir_folder", "admin_path", "importdir_file" and "importdir_folder". ') + if source in [ 'importdir_file', 'importdir_folder' ]: + if not trans.user_is_admin: + raise exceptions.AdminRequiredException( 'Only admins can import from importdir.' ) + if not trans.app.config.library_import_dir: + raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow admins to import into library from importdir.' ) + user_base_dir = trans.app.config.library_import_dir + if source in [ 'userdir_file', 'userdir_folder' ]: user_login = trans.user.email @@ -505,6 +512,7 @@ return job_dict @web.expose + # TODO convert to expose_api def download( self, trans, format, **kwd ): """ download( self, trans, format, **kwd ) diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -54,7 +54,12 @@ 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.' + 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.' }, // genomes @@ -73,15 +78,12 @@ id: this.options.id, is_admin: false, is_anonym: true, - user_library_import_dir: Galaxy.config.user_library_import_dir, - allow_library_path_paste: Galaxy.config.allow_library_path_paste, - library_import_dir: Galaxy.config.library_import_dir, mutiple_add_dataset_options: false } if (Galaxy.currUser){ template_defaults.is_admin = Galaxy.currUser.isAdmin(); template_defaults.is_anonym = Galaxy.currUser.isAnonymous(); - if (template_defaults.user_library_import_dir !== null || template_defaults.allow_library_path_paste !== false || template_defaults.library_import_dir !== null ){ + if ( Galaxy.config.user_library_import_dir !== null || Galaxy.config.allow_library_path_paste !== false || Galaxy.config.library_import_dir !== null ){ template_defaults.mutiple_add_dataset_options = true; } } @@ -402,33 +404,38 @@ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy… var that = this; this.select_genome = new mod_select.View( { - css: 'genome', + css: 'library-genome-select', data: that.list_genomes, - container: Galaxy.modal.$el.find( '#genome' ), + container: Galaxy.modal.$el.find( '#library_genome_select' ), value: '?' } ); this.select_extension = new mod_select.View({ - css: 'extension', + css: 'library-extension-select', data: that.list_extensions, - container: Galaxy.modal.$el.find('#extension'), + container: Galaxy.modal.$el.find( '#library_extension_select' ), value: 'auto' }); }, + /** - * Create modal for importing form user's directory + * Create modal for importing from given directory * on Galaxy. Bind jQuery events. */ - importFilesFromUserdirModal: function(){ + importFilesFromGalaxyFolderModal: function( options ){ var that = this; + var template_modal = this.templateBrowserModal(); this.modal = Galaxy.modal; - var template_modal = this.templateBrowserModal(); this.modal.show({ closing_events : true, title : 'Please select folders or files', body : template_modal({}), buttons : { - 'Import' : function() {that.importFromUserdirClicked(that);}, - 'Close' : function() {Galaxy.modal.hide();} + 'Import' : function() { + that.importFromJstreePath( that, options ); + }, + 'Close' : function() { + Galaxy.modal.hide(); + } }, closing_callback: function(){ // TODO: should not trigger routes outside of the router @@ -437,21 +444,24 @@ }); this.renderSelectBoxes(); - this.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + this.renderJstree( options ); - $('input[type=radio]').change(function(event){ + $( 'input[type=radio]' ).change( function( event ){ if (event.target.value ==='jstree-disable-folders') { - that.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + that.renderJstree( options ); $('.jstree-folders-message').hide(); $('.jstree-preserve-structure').hide(); $('.jstree-link-files').hide(); $('.jstree-files-message').show(); - } else if (event.target.value ==='jstree-disable-files'){ + } else if ( event.target.value ==='jstree-disable-files' ){ $('.jstree-files-message').hide(); $('.jstree-folders-message').show(); $('.jstree-link-files').show(); $('.jstree-preserve-structure').show(); - that.renderJstree({disabled_jstree_element: 'files'}); + options.disabled_jstree_element = 'files'; + that.renderJstree( options ); } } ); @@ -463,12 +473,16 @@ * data. * @param {[type]} options [description] */ - renderJstree: function(options){ + renderJstree: function( options ){ var that = this; - this.options = _.extend(this.options, options); + this.options = _.extend( this.options, options ); + var target = options.source || 'userdir'; var disabled_jstree_element = this.options.disabled_jstree_element; this.jstree = new mod_library_model.Jstree(); - this.jstree.url = this.jstree.urlRoot + '?target=userdir&format=jstree&disable=' + disabled_jstree_element; + this.jstree.url = this.jstree.urlRoot + + '?target=' + target + + '&format=jstree' + + '&disable=' + disabled_jstree_element; this.jstree.fetch({ success: function(model, response){ // This is to prevent double jquery load. I think. Carl is magician. @@ -579,7 +593,7 @@ * jstree.js has to be loaded before * @see renderJstree */ - importFromUserdirClicked: function ( that ){ + importFromJstreePath: function ( that, options ){ var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true ); var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' ); var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' ); @@ -588,7 +602,7 @@ var selection_type = selected_nodes[0].type; var paths = []; if ( selected_nodes.length < 1 ){ - mod_toastr.info( 'You must select some items first.' ); + mod_toastr.info( 'Please select some items first.' ); } else { this.modal.disableButton( 'Import' ); for ( var i = selected_nodes.length - 1; i >= 0; i-- ){ @@ -598,17 +612,19 @@ } this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } ); if ( selection_type === 'folder' ){ - + var full_source = options.source + '_folder'; this.chainCallImportingFolders( { paths: paths, preserve_dirs: preserve_dirs, link_data: link_data, - source: 'userdir_folder', + source: full_source, file_type: file_type, dbkey: dbkey } ); } else if ( selection_type === 'file' ){ + var full_source = options.source + '_file'; this.chainCallImportingUserdirFiles( { paths : paths, file_type: file_type, - dbkey: dbkey } ); + dbkey: dbkey, + source: full_source } ); } } }, @@ -713,7 +729,7 @@ return true; } var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + - '&source=userdir_file' + + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + '&dbkey=' + options.dbkey ) ) @@ -760,22 +776,12 @@ '&dbkey=' + options.dbkey ) ) promise.done(function(response){ that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }) .fail(function(){ that.options.chain_call_control.failed_number += 1; that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }); }, @@ -952,12 +958,13 @@ this.addFilesFromHistoryModal(); break; case "importdir": + this.importFilesFromGalaxyFolderModal( { source: 'importdir' } ); break; case "path": this.importFilesFromPathModal(); break; case "userdir": - this.importFilesFromUserdirModal(); + this.importFilesFromGalaxyFolderModal( { source: 'userdir' } ); break; default: Galaxy.libraries.library_router.back(); @@ -984,17 +991,19 @@ tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>'); - tmpl_array.push('<% if(user_library_import_dir !== null) { %>'); + tmpl_array.push('<% if(Galaxy.config.user_library_import_dir !== null) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>'); tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); - // tmpl_array.push('<% if(allow_library_path_paste || library_import_dir !== null) { %>'); - tmpl_array.push(' <li class="divider"></li>'); - tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); - // tmpl_array.push('<% if(library_import_dir !== null) { %>'); - // tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); - // tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); + + tmpl_array.push(' <li class="divider"></li>'); + tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); + + tmpl_array.push('<% if(Galaxy.config.library_import_dir !== null) { %>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); + tmpl_array.push('<% } %>'); + + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>'); tmpl_array.push('<% } %>'); tmpl_array.push('<% } %>'); @@ -1154,8 +1163,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); @@ -1184,8 +1193,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/scripts/mvc/ui/ui-select.js --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -155,7 +155,6 @@ data : this.select_data, containerCssClass : this.options.css, placeholder : this.options.placeholder, - width : 'resolve', dropdownAutoWidth : true }; this.$el.select2(select_opt); diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=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"},defaults:{can_add_library_item:false,contains_file:false,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(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},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(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=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"},defaults:{can_add_library_item:false,contains_file:false,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(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},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(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.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();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/scripts/packed/mvc/ui/ui-select.js --- a/static/scripts/packed/mvc/ui/ui-select.js +++ b/static/scripts/packed/mvc/ui/ui-select.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,width:"resolve",dropdownAutoWidth:true};this.$el.select2(c);this._setValue(d)}else{var c={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.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:true};this.$el.select2(c);this._setValue(d)}else{var c={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}}); \ No newline at end of file diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1323,6 +1323,8 @@ li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} td.right-center{vertical-align:middle !important;text-align:right} +.library-genome-select{max-width:350px} +.library-extension-select{max-width:140px} .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} @@ -1574,6 +1576,7 @@ .jstree-default-large.jstree-rtl .jstree-node{background-image:url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAACAQMAAAAD0EyKAAAABlBMVEUAAAAdHRvEkCwcAAAAAXRSTlMAQObYZgAAAAxJREFUCNdjgIIGBgABCgCBvVLXcAAAAABJRU5ErkJggg==")} .jstree-default-large.jstree-rtl .jstree-last{background:transparent} @media (max-width:768px){#jstree-dnd.jstree-dnd-responsive{line-height:40px;font-weight:bold;font-size:1.1em;text-shadow:1px 1px white} #jstree-dnd.jstree-dnd-responsive>i{background:transparent;width:40px;height:40px} #jstree-dnd.jstree-dnd-responsive>.jstree-ok{background-image:url("../images/jstree/40px.png");background-position:0 -200px;background-size:120px 240px} #jstree-dnd.jstree-dnd-responsive>.jstree-er{background-image:url("../images/jstree/40px.png");background-position:-40px -200px;background-size:120px 240px} #jstree-marker.jstree-dnd-responsive{border-left-width:10px;border-top-width:10px;border-bottom-width:10px;margin-top:-10px}}@media (max-width:768px){.jstree-default-responsive{} .jstree-default-responsive .jstree-icon{background-image:url("../images/jstree/40px.png")} .jstree-default-responsive .jstree-node,.jstree-default-responsive .jstree-leaf>.jstree-ocl{background:transparent} .jstree-default-responsive .jstree-node{min-height:40px;line-height:40px;margin-left:40px;min-width:40px;white-space:nowrap} .jstree-default-responsive .jstree-anchor{line-height:40px;height:40px} .jstree-default-responsive .jstree-icon,.jstree-default-responsive .jstree-icon:empty{width:40px;height:40px;line-height:40px} .jstree-default-responsive>.jstree-container-ul>.jstree-node{margin-left:0} .jstree-default-responsive.jstree-rtl .jstree-node{margin-left:0;margin-right:40px} .jstree-default-responsive.jstree-rtl .jstree-container-ul>.jstree-node{margin-right:0} .jstree-default-responsive .jstree-ocl,.jstree-default-responsive .jstree-themeicon,.jstree-default-responsive .jstree-checkbox{background-size:120px 240px} .jstree-default-responsive .jstree-leaf>.jstree-ocl{background:transparent} .jstree-default-responsive .jstree-open>.jstree-ocl{background-position:0 0px !important} .jstree-default-responsive .jstree-closed>.jstree-ocl{background-position:0 -40px !important} .jstree-default-responsive.jstree-rtl .jstree-closed>.jstree-ocl{background-position:-40px 0 !important} .jstree-default-responsive .jstree-themeicon{background-position:-40px -40px} .jstree-default-responsive .jstree-checkbox,.jstree-default-responsive .jstree-checkbox:hover{background-position:-40px -80px} .jstree-default-responsive.jstree-checkbox-selection .jstree-clicked>.jstree-checkbox,.jstree-default-responsive.jstree-checkbox-selection .jstree-clicked>.jstree-checkbox:hover,.jstree-default-responsive .jstree-checked>.jstree-checkbox,.jstree-default-responsive .jstree-checked>.jstree-checkbox:hover{background-position:0 -80px} .jstree-default-responsive .jstree-anchor>.jstree-undetermined,.jstree-default-responsive .jstree-anchor>.jstree-undetermined:hover{background-position:0 -120px} .jstree-default-responsive .jstree-anchor{font-weight:bold;font-size:1.1em;text-shadow:1px 1px white} .jstree-default-responsive>.jstree-striped{background:transparent} .jstree-default-responsive .jstree-wholerow{border-top:1px solid rgba(255,255,255,0.7);border-bottom:1px solid rgba(64,64,64,0.2);background:#ebebeb;height:40px} .jstree-default-responsive .jstree-wholerow-hovered{background:#e7f4f9} .jstree-default-responsive .jstree-wholerow-clicked{background:#beebff} .jstree-default-responsive .jstree-children .jstree-last>.jstree-wholerow{box-shadow:inset 0 -6px 3px -5px #666} .jstree-default-responsive .jstree-children .jstree-open>.jstree-wholerow{box-shadow:inset 0 6px 3px -5px #666;border-top:0} .jstree-default-responsive .jstree-children .jstree-open+.jstree-open{box-shadow:none} .jstree-default-responsive .jstree-node,.jstree-default-responsive .jstree-icon,.jstree-default-responsive .jstree-node>.jstree-ocl,.jstree-default-responsive .jstree-themeicon,.jstree-default-responsive .jstree-checkbox{background-image:url("../images/jstree/40px.png");background-size:120px 240px} .jstree-default-responsive .jstree-node{background-position:-80px 0;background-repeat:repeat-y} .jstree-default-responsive .jstree-last{background:transparent} .jstree-default-responsive .jstree-leaf>.jstree-ocl{background-position:-40px -120px} .jstree-default-responsive .jstree-last>.jstree-ocl{background-position:-40px -160px} .jstree-default-responsive .jstree-themeicon-custom{background-color:transparent;background-image:none;background-position:0 0} .jstree-default-responsive .jstree-file{background:url("../images/jstree/40px.png") 0 -160px no-repeat;background-size:120px 240px} .jstree-default-responsive .jstree-folder{background:url("../images/jstree/40px.png") -40px -40px no-repeat;background-size:120px 240px}}.jstree-default>.jstree-container-ul>.jstree-node{margin-left:0;margin-right:0} +.select2-minwidth{min-width:256px} .unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%} .clear:before,.clear:after{content:" ";display:table;} diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -7,6 +7,8 @@ li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} td.right-center{vertical-align:middle !important;text-align:right} +.library-genome-select{max-width:350px} +.library-extension-select{max-width:140px} .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -31,6 +31,11 @@ // Mixins +/* fix for zero width select2 - remove when fixed there */ +.select2-minwidth { + min-width: 256px; +} + .unselectable { .user-select(none); } diff -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 -r c29f651e4accc25bb1ba5aba78cf4e84409c6fcb static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -29,13 +29,19 @@ background-color: @table-bg-accent; } -td.right-center{ +td.right-center { vertical-align: middle !important; text-align: right; - } -.library_table{ +.library-genome-select { + max-width: 350px; +} +.library-extension-select { + max-width: 140px; +} + +.library_table { td { border-top:1px solid #5f6990 !important; } https://bitbucket.org/galaxy/galaxy-central/commits/1af9145657c0/ Changeset: 1af9145657c0 Branch: next-stable User: martenson Date: 2014-09-26 19:17:35+00:00 Summary: select2 fixes and impl. of missing feature import from path Affected #: 12 files diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -54,7 +54,12 @@ 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.' + 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.' }, // genomes @@ -73,15 +78,12 @@ id: this.options.id, is_admin: false, is_anonym: true, - user_library_import_dir: Galaxy.config.user_library_import_dir, - allow_library_path_paste: Galaxy.config.allow_library_path_paste, - library_import_dir: Galaxy.config.library_import_dir, mutiple_add_dataset_options: false } if (Galaxy.currUser){ template_defaults.is_admin = Galaxy.currUser.isAdmin(); template_defaults.is_anonym = Galaxy.currUser.isAnonymous(); - if (template_defaults.user_library_import_dir !== null || template_defaults.allow_library_path_paste !== false || template_defaults.library_import_dir !== null ){ + if ( Galaxy.config.user_library_import_dir !== null || Galaxy.config.allow_library_path_paste !== false || Galaxy.config.library_import_dir !== null ){ template_defaults.mutiple_add_dataset_options = true; } } @@ -402,33 +404,38 @@ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy… var that = this; this.select_genome = new mod_select.View( { - css: 'genome', + css: 'library-genome-select', data: that.list_genomes, - container: Galaxy.modal.$el.find( '#genome' ), + container: Galaxy.modal.$el.find( '#library_genome_select' ), value: '?' } ); this.select_extension = new mod_select.View({ - css: 'extension', + css: 'library-extension-select', data: that.list_extensions, - container: Galaxy.modal.$el.find('#extension'), + container: Galaxy.modal.$el.find( '#library_extension_select' ), value: 'auto' }); }, + /** - * Create modal for importing form user's directory + * Create modal for importing from given directory * on Galaxy. Bind jQuery events. */ - importFilesFromUserdirModal: function(){ + importFilesFromGalaxyFolderModal: function( options ){ var that = this; + var template_modal = this.templateBrowserModal(); this.modal = Galaxy.modal; - var template_modal = this.templateBrowserModal(); this.modal.show({ closing_events : true, title : 'Please select folders or files', body : template_modal({}), buttons : { - 'Import' : function() {that.importFromUserdirClicked(that);}, - 'Close' : function() {Galaxy.modal.hide();} + 'Import' : function() { + that.importFromJstreePath( that, options ); + }, + 'Close' : function() { + Galaxy.modal.hide(); + } }, closing_callback: function(){ // TODO: should not trigger routes outside of the router @@ -437,21 +444,24 @@ }); this.renderSelectBoxes(); - this.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + this.renderJstree( options ); - $('input[type=radio]').change(function(event){ + $( 'input[type=radio]' ).change( function( event ){ if (event.target.value ==='jstree-disable-folders') { - that.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + that.renderJstree( options ); $('.jstree-folders-message').hide(); $('.jstree-preserve-structure').hide(); $('.jstree-link-files').hide(); $('.jstree-files-message').show(); - } else if (event.target.value ==='jstree-disable-files'){ + } else if ( event.target.value ==='jstree-disable-files' ){ $('.jstree-files-message').hide(); $('.jstree-folders-message').show(); $('.jstree-link-files').show(); $('.jstree-preserve-structure').show(); - that.renderJstree({disabled_jstree_element: 'files'}); + options.disabled_jstree_element = 'files'; + that.renderJstree( options ); } } ); @@ -463,12 +473,16 @@ * data. * @param {[type]} options [description] */ - renderJstree: function(options){ + renderJstree: function( options ){ var that = this; - this.options = _.extend(this.options, options); + this.options = _.extend( this.options, options ); + var target = options.source || 'userdir'; var disabled_jstree_element = this.options.disabled_jstree_element; this.jstree = new mod_library_model.Jstree(); - this.jstree.url = this.jstree.urlRoot + '?target=userdir&format=jstree&disable=' + disabled_jstree_element; + this.jstree.url = this.jstree.urlRoot + + '?target=' + target + + '&format=jstree' + + '&disable=' + disabled_jstree_element; this.jstree.fetch({ success: function(model, response){ // This is to prevent double jquery load. I think. Carl is magician. @@ -579,7 +593,7 @@ * jstree.js has to be loaded before * @see renderJstree */ - importFromUserdirClicked: function ( that ){ + importFromJstreePath: function ( that, options ){ var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true ); var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' ); var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' ); @@ -588,7 +602,7 @@ var selection_type = selected_nodes[0].type; var paths = []; if ( selected_nodes.length < 1 ){ - mod_toastr.info( 'You must select some items first.' ); + mod_toastr.info( 'Please select some items first.' ); } else { this.modal.disableButton( 'Import' ); for ( var i = selected_nodes.length - 1; i >= 0; i-- ){ @@ -598,17 +612,19 @@ } this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } ); if ( selection_type === 'folder' ){ - + var full_source = options.source + '_folder'; this.chainCallImportingFolders( { paths: paths, preserve_dirs: preserve_dirs, link_data: link_data, - source: 'userdir_folder', + source: full_source, file_type: file_type, dbkey: dbkey } ); } else if ( selection_type === 'file' ){ + var full_source = options.source + '_file'; this.chainCallImportingUserdirFiles( { paths : paths, file_type: file_type, - dbkey: dbkey } ); + dbkey: dbkey, + source: full_source } ); } } }, @@ -713,7 +729,7 @@ return true; } var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + - '&source=userdir_file' + + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + '&dbkey=' + options.dbkey ) ) @@ -760,22 +776,12 @@ '&dbkey=' + options.dbkey ) ) promise.done(function(response){ that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }) .fail(function(){ that.options.chain_call_control.failed_number += 1; that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }); }, @@ -952,12 +958,13 @@ this.addFilesFromHistoryModal(); break; case "importdir": + this.importFilesFromGalaxyFolderModal( { source: 'importdir' } ); break; case "path": this.importFilesFromPathModal(); break; case "userdir": - this.importFilesFromUserdirModal(); + this.importFilesFromGalaxyFolderModal( { source: 'userdir' } ); break; default: Galaxy.libraries.library_router.back(); @@ -984,17 +991,19 @@ tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>'); - tmpl_array.push('<% if(user_library_import_dir !== null) { %>'); + tmpl_array.push('<% if(Galaxy.config.user_library_import_dir !== null) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>'); tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); - // tmpl_array.push('<% if(allow_library_path_paste || library_import_dir !== null) { %>'); - tmpl_array.push(' <li class="divider"></li>'); - tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); - // tmpl_array.push('<% if(library_import_dir !== null) { %>'); - // tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); - // tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); + + tmpl_array.push(' <li class="divider"></li>'); + tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); + + tmpl_array.push('<% if(Galaxy.config.library_import_dir !== null) { %>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); + tmpl_array.push('<% } %>'); + + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>'); tmpl_array.push('<% } %>'); tmpl_array.push('<% } %>'); @@ -1154,8 +1163,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); @@ -1184,8 +1193,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d client/galaxy/scripts/mvc/ui/ui-select.js --- a/client/galaxy/scripts/mvc/ui/ui-select.js +++ b/client/galaxy/scripts/mvc/ui/ui-select.js @@ -155,7 +155,6 @@ data : this.select_data, containerCssClass : this.options.css, placeholder : this.options.placeholder, - width : 'resolve', dropdownAutoWidth : true }; this.$el.select2(select_opt); diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ b/lib/galaxy/webapps/galaxy/api/ftp_files.py @@ -49,7 +49,7 @@ userdir_jstree = self.__create_jstree( full_import_dir, disable ) response = userdir_jstree.jsonData() except Exception, exception: - log.debug(str(exception)) + log.debug( str( exception ) ) raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( full_import_dir ) ) elif format == 'ajax': raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) @@ -61,6 +61,26 @@ raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) else: raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) + elif target == 'importdir': + base_dir = trans.app.config.library_import_dir + if base_dir is None: + raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow usage of import directory.' ) + if format == 'jstree': + disable = kwd.get( 'disable', 'folders') + try: + importdir_jstree = self.__create_jstree( base_dir, disable ) + response = importdir_jstree.jsonData() + except Exception, exception: + log.debug( str( exception ) ) + raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( base_dir ) ) + elif format == 'ajax': + raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) + else: + try: + response = self.__load_all_filenames( base_dir ) + except Exception, exception: + log.error( 'Could not get user import files: %s', str( exception ), exc_info=True ) + raise exceptions.InternalServerError( 'Could not get the files from your import directory folder.' ) else: user_ftp_base_dir = trans.app.config.ftp_upload_dir if user_ftp_base_dir is None: diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -429,8 +429,15 @@ folder = self.folder_manager.get( trans, folder_id ) source = kwd.get( 'source', None ) - if source not in [ 'userdir_file', 'userdir_folder', 'admin_path' ]: - raise exceptions.RequestParameterMissingException( 'You have to specify "source" parameter. Possible values are "userdir_file", "userdir_folder" and "admin_path". ') + if source not in [ 'userdir_file', 'userdir_folder', 'importdir_file', 'importdir_folder', 'admin_path' ]: + raise exceptions.RequestParameterMissingException( 'You have to specify "source" parameter. Possible values are "userdir_file", "userdir_folder", "admin_path", "importdir_file" and "importdir_folder". ') + if source in [ 'importdir_file', 'importdir_folder' ]: + if not trans.user_is_admin: + raise exceptions.AdminRequiredException( 'Only admins can import from importdir.' ) + if not trans.app.config.library_import_dir: + raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow admins to import into library from importdir.' ) + user_base_dir = trans.app.config.library_import_dir + if source in [ 'userdir_file', 'userdir_folder' ]: user_login = trans.user.email @@ -505,6 +512,7 @@ return job_dict @web.expose + # TODO convert to expose_api def download( self, trans, format, **kwd ): """ download( self, trans, format, **kwd ) diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -54,7 +54,12 @@ 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.' + 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.' }, // genomes @@ -73,15 +78,12 @@ id: this.options.id, is_admin: false, is_anonym: true, - user_library_import_dir: Galaxy.config.user_library_import_dir, - allow_library_path_paste: Galaxy.config.allow_library_path_paste, - library_import_dir: Galaxy.config.library_import_dir, mutiple_add_dataset_options: false } if (Galaxy.currUser){ template_defaults.is_admin = Galaxy.currUser.isAdmin(); template_defaults.is_anonym = Galaxy.currUser.isAnonymous(); - if (template_defaults.user_library_import_dir !== null || template_defaults.allow_library_path_paste !== false || template_defaults.library_import_dir !== null ){ + if ( Galaxy.config.user_library_import_dir !== null || Galaxy.config.allow_library_path_paste !== false || Galaxy.config.library_import_dir !== null ){ template_defaults.mutiple_add_dataset_options = true; } } @@ -402,33 +404,38 @@ // https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy… var that = this; this.select_genome = new mod_select.View( { - css: 'genome', + css: 'library-genome-select', data: that.list_genomes, - container: Galaxy.modal.$el.find( '#genome' ), + container: Galaxy.modal.$el.find( '#library_genome_select' ), value: '?' } ); this.select_extension = new mod_select.View({ - css: 'extension', + css: 'library-extension-select', data: that.list_extensions, - container: Galaxy.modal.$el.find('#extension'), + container: Galaxy.modal.$el.find( '#library_extension_select' ), value: 'auto' }); }, + /** - * Create modal for importing form user's directory + * Create modal for importing from given directory * on Galaxy. Bind jQuery events. */ - importFilesFromUserdirModal: function(){ + importFilesFromGalaxyFolderModal: function( options ){ var that = this; + var template_modal = this.templateBrowserModal(); this.modal = Galaxy.modal; - var template_modal = this.templateBrowserModal(); this.modal.show({ closing_events : true, title : 'Please select folders or files', body : template_modal({}), buttons : { - 'Import' : function() {that.importFromUserdirClicked(that);}, - 'Close' : function() {Galaxy.modal.hide();} + 'Import' : function() { + that.importFromJstreePath( that, options ); + }, + 'Close' : function() { + Galaxy.modal.hide(); + } }, closing_callback: function(){ // TODO: should not trigger routes outside of the router @@ -437,21 +444,24 @@ }); this.renderSelectBoxes(); - this.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + this.renderJstree( options ); - $('input[type=radio]').change(function(event){ + $( 'input[type=radio]' ).change( function( event ){ if (event.target.value ==='jstree-disable-folders') { - that.renderJstree({disabled_jstree_element: 'folders'}); + options.disabled_jstree_element = 'folders'; + that.renderJstree( options ); $('.jstree-folders-message').hide(); $('.jstree-preserve-structure').hide(); $('.jstree-link-files').hide(); $('.jstree-files-message').show(); - } else if (event.target.value ==='jstree-disable-files'){ + } else if ( event.target.value ==='jstree-disable-files' ){ $('.jstree-files-message').hide(); $('.jstree-folders-message').show(); $('.jstree-link-files').show(); $('.jstree-preserve-structure').show(); - that.renderJstree({disabled_jstree_element: 'files'}); + options.disabled_jstree_element = 'files'; + that.renderJstree( options ); } } ); @@ -463,12 +473,16 @@ * data. * @param {[type]} options [description] */ - renderJstree: function(options){ + renderJstree: function( options ){ var that = this; - this.options = _.extend(this.options, options); + this.options = _.extend( this.options, options ); + var target = options.source || 'userdir'; var disabled_jstree_element = this.options.disabled_jstree_element; this.jstree = new mod_library_model.Jstree(); - this.jstree.url = this.jstree.urlRoot + '?target=userdir&format=jstree&disable=' + disabled_jstree_element; + this.jstree.url = this.jstree.urlRoot + + '?target=' + target + + '&format=jstree' + + '&disable=' + disabled_jstree_element; this.jstree.fetch({ success: function(model, response){ // This is to prevent double jquery load. I think. Carl is magician. @@ -579,7 +593,7 @@ * jstree.js has to be loaded before * @see renderJstree */ - importFromUserdirClicked: function ( that ){ + importFromJstreePath: function ( that, options ){ var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true ); var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' ); var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' ); @@ -588,7 +602,7 @@ var selection_type = selected_nodes[0].type; var paths = []; if ( selected_nodes.length < 1 ){ - mod_toastr.info( 'You must select some items first.' ); + mod_toastr.info( 'Please select some items first.' ); } else { this.modal.disableButton( 'Import' ); for ( var i = selected_nodes.length - 1; i >= 0; i-- ){ @@ -598,17 +612,19 @@ } this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } ); if ( selection_type === 'folder' ){ - + var full_source = options.source + '_folder'; this.chainCallImportingFolders( { paths: paths, preserve_dirs: preserve_dirs, link_data: link_data, - source: 'userdir_folder', + source: full_source, file_type: file_type, dbkey: dbkey } ); } else if ( selection_type === 'file' ){ + var full_source = options.source + '_file'; this.chainCallImportingUserdirFiles( { paths : paths, file_type: file_type, - dbkey: dbkey } ); + dbkey: dbkey, + source: full_source } ); } } }, @@ -713,7 +729,7 @@ return true; } var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + - '&source=userdir_file' + + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + '&dbkey=' + options.dbkey ) ) @@ -760,22 +776,12 @@ '&dbkey=' + options.dbkey ) ) promise.done(function(response){ that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }) .fail(function(){ that.options.chain_call_control.failed_number += 1; that.updateProgress(); - that.chainCallImportingFolders( { paths: options.paths, - preserve_dirs: options.preserve_dirs, - link_data: options.link_data, - source: options.source, - file_type: options.file_type, - dbkey: options.dbkey } ); + that.chainCallImportingFolders( options ); }); }, @@ -952,12 +958,13 @@ this.addFilesFromHistoryModal(); break; case "importdir": + this.importFilesFromGalaxyFolderModal( { source: 'importdir' } ); break; case "path": this.importFilesFromPathModal(); break; case "userdir": - this.importFilesFromUserdirModal(); + this.importFilesFromGalaxyFolderModal( { source: 'userdir' } ); break; default: Galaxy.libraries.library_router.back(); @@ -984,17 +991,19 @@ tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>'); - tmpl_array.push('<% if(user_library_import_dir !== null) { %>'); + tmpl_array.push('<% if(Galaxy.config.user_library_import_dir !== null) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>'); tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); - // tmpl_array.push('<% if(allow_library_path_paste || library_import_dir !== null) { %>'); - tmpl_array.push(' <li class="divider"></li>'); - tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); - // tmpl_array.push('<% if(library_import_dir !== null) { %>'); - // tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); - // tmpl_array.push('<% } %>'); - tmpl_array.push('<% if(allow_library_path_paste) { %>'); + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); + + tmpl_array.push(' <li class="divider"></li>'); + tmpl_array.push(' <li class="dropdown-header">Admins only</li>'); + + tmpl_array.push('<% if(Galaxy.config.library_import_dir !== null) { %>'); + tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>'); + tmpl_array.push('<% } %>'); + + tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>'); tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>'); tmpl_array.push('<% } %>'); tmpl_array.push('<% } %>'); @@ -1154,8 +1163,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); @@ -1184,8 +1193,8 @@ tmpl_array.push('<hr />'); tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>'); tmpl_array.push('<div>'); - tmpl_array.push('Type: <span id="extension" class="extension" />'); - tmpl_array.push(' Genome: <span id="genome" class="genome" />'); + tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />'); + tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />'); tmpl_array.push('</div>'); tmpl_array.push('</div>'); diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/scripts/mvc/ui/ui-select.js --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -155,7 +155,6 @@ data : this.select_data, containerCssClass : this.options.css, placeholder : this.options.placeholder, - width : 'resolve', dropdownAutoWidth : true }; this.$el.select2(select_opt); diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=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"},defaults:{can_add_library_item:false,contains_file:false,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(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},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(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=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"},defaults:{can_add_library_item:false,contains_file:false,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(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},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(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.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();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/scripts/packed/mvc/ui/ui-select.js --- a/static/scripts/packed/mvc/ui/ui-select.js +++ b/static/scripts/packed/mvc/ui/ui-select.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,width:"resolve",dropdownAutoWidth:true};this.$el.select2(c);this._setValue(d)}else{var c={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.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:true};this.$el.select2(c);this._setValue(d)}else{var c={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}}); \ No newline at end of file diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1322,6 +1322,8 @@ li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} td.right-center{vertical-align:middle !important;text-align:right} +.library-genome-select{max-width:350px} +.library-extension-select{max-width:140px} .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} @@ -1573,6 +1575,7 @@ .jstree-default-large.jstree-rtl .jstree-node{background-image:url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAACAQMAAAAD0EyKAAAABlBMVEUAAAAdHRvEkCwcAAAAAXRSTlMAQObYZgAAAAxJREFUCNdjgIIGBgABCgCBvVLXcAAAAABJRU5ErkJggg==")} .jstree-default-large.jstree-rtl .jstree-last{background:transparent} @media (max-width:768px){#jstree-dnd.jstree-dnd-responsive{line-height:40px;font-weight:bold;font-size:1.1em;text-shadow:1px 1px white} #jstree-dnd.jstree-dnd-responsive>i{background:transparent;width:40px;height:40px} #jstree-dnd.jstree-dnd-responsive>.jstree-ok{background-image:url("../images/jstree/40px.png");background-position:0 -200px;background-size:120px 240px} #jstree-dnd.jstree-dnd-responsive>.jstree-er{background-image:url("../images/jstree/40px.png");background-position:-40px -200px;background-size:120px 240px} #jstree-marker.jstree-dnd-responsive{border-left-width:10px;border-top-width:10px;border-bottom-width:10px;margin-top:-10px}}@media (max-width:768px){.jstree-default-responsive{} .jstree-default-responsive .jstree-icon{background-image:url("../images/jstree/40px.png")} .jstree-default-responsive .jstree-node,.jstree-default-responsive .jstree-leaf>.jstree-ocl{background:transparent} .jstree-default-responsive .jstree-node{min-height:40px;line-height:40px;margin-left:40px;min-width:40px;white-space:nowrap} .jstree-default-responsive .jstree-anchor{line-height:40px;height:40px} .jstree-default-responsive .jstree-icon,.jstree-default-responsive .jstree-icon:empty{width:40px;height:40px;line-height:40px} .jstree-default-responsive>.jstree-container-ul>.jstree-node{margin-left:0} .jstree-default-responsive.jstree-rtl .jstree-node{margin-left:0;margin-right:40px} .jstree-default-responsive.jstree-rtl .jstree-container-ul>.jstree-node{margin-right:0} .jstree-default-responsive .jstree-ocl,.jstree-default-responsive .jstree-themeicon,.jstree-default-responsive .jstree-checkbox{background-size:120px 240px} .jstree-default-responsive .jstree-leaf>.jstree-ocl{background:transparent} .jstree-default-responsive .jstree-open>.jstree-ocl{background-position:0 0px !important} .jstree-default-responsive .jstree-closed>.jstree-ocl{background-position:0 -40px !important} .jstree-default-responsive.jstree-rtl .jstree-closed>.jstree-ocl{background-position:-40px 0 !important} .jstree-default-responsive .jstree-themeicon{background-position:-40px -40px} .jstree-default-responsive .jstree-checkbox,.jstree-default-responsive .jstree-checkbox:hover{background-position:-40px -80px} .jstree-default-responsive.jstree-checkbox-selection .jstree-clicked>.jstree-checkbox,.jstree-default-responsive.jstree-checkbox-selection .jstree-clicked>.jstree-checkbox:hover,.jstree-default-responsive .jstree-checked>.jstree-checkbox,.jstree-default-responsive .jstree-checked>.jstree-checkbox:hover{background-position:0 -80px} .jstree-default-responsive .jstree-anchor>.jstree-undetermined,.jstree-default-responsive .jstree-anchor>.jstree-undetermined:hover{background-position:0 -120px} .jstree-default-responsive .jstree-anchor{font-weight:bold;font-size:1.1em;text-shadow:1px 1px white} .jstree-default-responsive>.jstree-striped{background:transparent} .jstree-default-responsive .jstree-wholerow{border-top:1px solid rgba(255,255,255,0.7);border-bottom:1px solid rgba(64,64,64,0.2);background:#ebebeb;height:40px} .jstree-default-responsive .jstree-wholerow-hovered{background:#e7f4f9} .jstree-default-responsive .jstree-wholerow-clicked{background:#beebff} .jstree-default-responsive .jstree-children .jstree-last>.jstree-wholerow{box-shadow:inset 0 -6px 3px -5px #666} .jstree-default-responsive .jstree-children .jstree-open>.jstree-wholerow{box-shadow:inset 0 6px 3px -5px #666;border-top:0} .jstree-default-responsive .jstree-children .jstree-open+.jstree-open{box-shadow:none} .jstree-default-responsive .jstree-node,.jstree-default-responsive .jstree-icon,.jstree-default-responsive .jstree-node>.jstree-ocl,.jstree-default-responsive .jstree-themeicon,.jstree-default-responsive .jstree-checkbox{background-image:url("../images/jstree/40px.png");background-size:120px 240px} .jstree-default-responsive .jstree-node{background-position:-80px 0;background-repeat:repeat-y} .jstree-default-responsive .jstree-last{background:transparent} .jstree-default-responsive .jstree-leaf>.jstree-ocl{background-position:-40px -120px} .jstree-default-responsive .jstree-last>.jstree-ocl{background-position:-40px -160px} .jstree-default-responsive .jstree-themeicon-custom{background-color:transparent;background-image:none;background-position:0 0} .jstree-default-responsive .jstree-file{background:url("../images/jstree/40px.png") 0 -160px no-repeat;background-size:120px 240px} .jstree-default-responsive .jstree-folder{background:url("../images/jstree/40px.png") -40px -40px no-repeat;background-size:120px 240px}}.jstree-default>.jstree-container-ul>.jstree-node{margin-left:0;margin-right:0} +.select2-minwidth{min-width:256px} .unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%} .clear:before,.clear:after{content:" ";display:table;} diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -7,6 +7,8 @@ li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} td.right-center{vertical-align:middle !important;text-align:right} +.library-genome-select{max-width:350px} +.library-extension-select{max-width:140px} .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -31,6 +31,11 @@ // Mixins +/* fix for zero width select2 - remove when fixed there */ +.select2-minwidth { + min-width: 256px; +} + .unselectable { .user-select(none); } diff -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -29,13 +29,19 @@ background-color: @table-bg-accent; } -td.right-center{ +td.right-center { vertical-align: middle !important; text-align: right; - } -.library_table{ +.library-genome-select { + max-width: 350px; +} +.library-extension-select { + max-width: 140px; +} + +.library_table { td { border-top:1px solid #5f6990 !important; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Add wait modal and error modal
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/10bf4bbcc3fa/ Changeset: 10bf4bbcc3fa User: guerler Date: 2014-09-26 15:39:32+00:00 Summary: ToolForm: Add wait modal and error modal Affected #: 12 files diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -24,6 +24,13 @@ // link this var self = this; + // link galaxy modal or create one + if (parent.Galaxy && parent.Galaxy.modal) { + this.modal = parent.Galaxy.modal; + } else { + this.modal = new Ui.Modal.View(); + } + // link options this.options = options; diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -32,23 +32,41 @@ console.debug('tools-jobs::submit - Submission canceled. Validation failed.'); return; } - console.log(job_def); + + // debug + console.debug(job_def); + + // show progress modal + this.app.modal.show({title: 'Please wait...', body: 'progress'}); // post job Utils.request('POST', galaxy_config.root + 'api/tools', job_def, // success handler function(response) { + self.app.modal.hide(); self.app.message(ToolTemplate.success(response)); self._refreshHdas(); }, // error handler - function(response) { - console.debug(response); + function(response, response_full) { + self.app.modal.hide(); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); } + } else { + // show modal with error message + self.app.modal.show({ + title: response_full.statusText, + body: ToolTemplate.error(job_def), + closing_events: true, + buttons: { + 'Close': function() { + self.app.modal.hide(); + } + } + }); } } ); diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -40,6 +40,17 @@ return tmpl; }, + error: function(job_def) { + return '<div>' + + '<p>' + + 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + '</p>' + + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + + JSON.stringify(job_def, undefined, 4) + + '</textarea>' + + '</div>'; + }, + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 client/galaxy/scripts/utils/utils.js --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -13,6 +13,12 @@ // generic function to send json to url function request (method, url, data, success, error) { + // configure + var ajaxConfig = { + url : url, + type : method, + 'contentType' : 'application/json' + } // encode data into url if (method == 'GET' || method == 'DELETE') { @@ -22,40 +28,25 @@ url += '&'; } url += $.param(data) + } else { + ajaxConfig['data'] = JSON.stringify(data); + ajaxConfig['dataType'] = 'json'; } - // prepare request - var xhr = new XMLHttpRequest(); - xhr.open(method, url, true); - xhr.setRequestHeader('Accept', 'application/json'); - xhr.setRequestHeader('Cache-Control', 'no-cache'); - xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); - xhr.setRequestHeader('Content-Type', 'application/json'); - xhr.onloadend = function() { - // get status - var status = xhr.status; - - // read response + // make request + $.ajax(ajaxConfig) + .done(function(response) { + success && success(response); + }) + .fail(function(response) { + var response_text = null; try { - response = jQuery.parseJSON(xhr.responseText); + response_text = jQuery.parseJSON(response.responseText); } catch (e) { - response = xhr.responseText; + response_text = response.responseText; } - - // parse response - if (status == 200) { - success && success(response); - } else { - error && error(response); - } - }; - - // make request - if (method == 'GET' || method == 'DELETE') { - xhr.send(); - } else { - xhr.send(JSON.stringify(data)); - } + error && error(response_text, response); + }); }; // get css value diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -24,6 +24,13 @@ // link this var self = this; + // link galaxy modal or create one + if (parent.Galaxy && parent.Galaxy.modal) { + this.modal = parent.Galaxy.modal; + } else { + this.modal = new Ui.Modal.View(); + } + // link options this.options = options; diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -32,23 +32,41 @@ console.debug('tools-jobs::submit - Submission canceled. Validation failed.'); return; } - console.log(job_def); + + // debug + console.debug(job_def); + + // show progress modal + this.app.modal.show({title: 'Please wait...', body: 'progress'}); // post job Utils.request('POST', galaxy_config.root + 'api/tools', job_def, // success handler function(response) { + self.app.modal.hide(); self.app.message(ToolTemplate.success(response)); self._refreshHdas(); }, // error handler - function(response) { - console.debug(response); + function(response, response_full) { + self.app.modal.hide(); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); for (var input_id in error_messages) { self._foundError(input_id, error_messages[input_id]); } + } else { + // show modal with error message + self.app.modal.show({ + title: response_full.statusText, + body: ToolTemplate.error(job_def), + closing_events: true, + buttons: { + 'Close': function() { + self.app.modal.hide(); + } + } + }); } } ); diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -40,6 +40,17 @@ return tmpl; }, + error: function(job_def) { + return '<div>' + + '<p>' + + 'Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.' + + '</p>' + + '<textarea class="ui-textarea" disabled style="color: black;" rows="6">' + + JSON.stringify(job_def, undefined, 4) + + '</textarea>' + + '</div>'; + }, + batchMode: function() { return '<div class="ui-table-form-info">' + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.log(d);b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var g=c.app.tree.matchResponse(e.message.data);for(var f in g){c._foundError(f,g[f])}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress"});b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{c.app.modal.show({title:g.statusText,body:a.error(d),closing_events:true,buttons:{Close:function(){c.app.modal.hide()}}})}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>Sorry, the server could not complete the request. Please contact the Galaxy Team if this error is persistent.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,l,m,o,k){if(p=="GET"||p=="DELETE"){if(l.indexOf("?")==-1){l+="?"}else{l+="&"}l+=$.param(m)}var n=new XMLHttpRequest();n.open(p,l,true);n.setRequestHeader("Accept","application/json");n.setRequestHeader("Cache-Control","no-cache");n.setRequestHeader("X-Requested-With","XMLHttpRequest");n.setRequestHeader("Content-Type","application/json");n.onloadend=function(){var q=n.status;try{response=jQuery.parseJSON(n.responseText)}catch(r){response=n.responseText}if(q==200){o&&o(response)}else{k&&k(response)}};if(p=="GET"||p=="DELETE"){n.send()}else{n.send(JSON.stringify(m))}}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file +define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,m,n,o,l){var k={url:m,type:p,contentType:"application/json"};if(p=="GET"||p=="DELETE"){if(m.indexOf("?")==-1){m+="?"}else{m+="&"}m+=$.param(n)}else{k.data=JSON.stringify(n);k.dataType="json"}$.ajax(k).done(function(q){o&&o(q)}).fail(function(r){var q=null;try{q=jQuery.parseJSON(r.responseText)}catch(s){q=r.responseText}l&&l(q,r)})}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file diff -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f -r 10bf4bbcc3fa0ade8b325aa814b21655c3b33ba1 static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -13,6 +13,12 @@ // generic function to send json to url function request (method, url, data, success, error) { + // configure + var ajaxConfig = { + url : url, + type : method, + 'contentType' : 'application/json' + } // encode data into url if (method == 'GET' || method == 'DELETE') { @@ -22,40 +28,25 @@ url += '&'; } url += $.param(data) + } else { + ajaxConfig['data'] = JSON.stringify(data); + ajaxConfig['dataType'] = 'json'; } - // prepare request - var xhr = new XMLHttpRequest(); - xhr.open(method, url, true); - xhr.setRequestHeader('Accept', 'application/json'); - xhr.setRequestHeader('Cache-Control', 'no-cache'); - xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); - xhr.setRequestHeader('Content-Type', 'application/json'); - xhr.onloadend = function() { - // get status - var status = xhr.status; - - // read response + // make request + $.ajax(ajaxConfig) + .done(function(response) { + success && success(response); + }) + .fail(function(response) { + var response_text = null; try { - response = jQuery.parseJSON(xhr.responseText); + response_text = jQuery.parseJSON(response.responseText); } catch (e) { - response = xhr.responseText; + response_text = response.responseText; } - - // parse response - if (status == 200) { - success && success(response); - } else { - error && error(response); - } - }; - - // make request - if (method == 'GET' || method == 'DELETE') { - xhr.send(); - } else { - xhr.send(JSON.stringify(data)); - } + error && error(response_text, response); + }); }; // get css value Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix data column parameters pointed at multiple data parameters.
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95bcb99ad2b4/ Changeset: 95bcb99ad2b4 User: jmchilton Date: 2014-09-26 14:49:43+00:00 Summary: Fix data column parameters pointed at multiple data parameters. Before it would just die with an unhelpful server side exception - now it attempts to build, validate, and use a useful set of columns. Affected #: 4 files diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1170,34 +1170,47 @@ Generate a select list containing the columns of the associated dataset (if found). """ - column_list = [] # No value indicates a configuration error, the named DataToolParameter # must preceed this parameter in the config assert self.data_ref in other_values, "Value for associated DataToolParameter not found" # Get the value of the associated DataToolParameter (a dataset) dataset = other_values[ self.data_ref ] # Check if a dataset is selected - if dataset is None or dataset == '': + if dataset is None or dataset == '' or dataset == []: # NOTE: Both of these values indicate that no dataset is selected. # However, 'None' indicates that the dataset is optional # while '' indicates that it is not. Currently column # parameters do not work well with optional datasets - return column_list - # Generate options - if not dataset.metadata.columns: - if self.accept_default: - column_list.append( self.default_value or '1' ) - return column_list - if not self.force_select: + return [] + column_list = None + for dataset in util.listify( dataset ): + # Handle columns not available. + if not dataset.metadata.columns: + default_column_list = [] + if self.accept_default: + default_column_list.append( self.default_value or '1' ) + return default_column_list + + # Build up possible columns for this dataset + this_column_list = [] + if self.numerical: + # If numerical was requested, filter columns based on metadata + for i, col in enumerate( dataset.metadata.column_types ): + if col == 'int' or col == 'float': + this_column_list.append( str( i + 1 ) ) + else: + for i in range(0, dataset.metadata.columns): + this_column_list.append( str( i + 1 ) ) + + # Take the intersection of these columns with the other columns. + if column_list is None: + column_list = this_column_list + else: + column_list = filter(lambda c: c in this_column_list, column_list) + + if not self.force_select and 'None' not in column_list: column_list.append( 'None' ) - if self.numerical: - # If numerical was requested, filter columns based on metadata - for i, col in enumerate( dataset.metadata.column_types ): - if col == 'int' or col == 'float': - column_list.append( str( i + 1 ) ) - else: - for i in range(0, dataset.metadata.columns): - column_list.append( str( i + 1 ) ) + return column_list def get_options( self, trans, other_values ): @@ -1249,14 +1262,15 @@ if self.data_ref not in context: return False # Get the selected dataset if selected - dataset = context[ self.data_ref ] - if dataset: - # Check if the dataset does not have the expected metadata for columns - if not dataset.metadata.columns: - # Only allow late validation if the dataset is not yet ready - # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending or not dataset.datatype.matches_any( self.ref_input.formats ): - return True + datasets = util.listify( context[ self.data_ref ] ) + for dataset in datasets: + if dataset: + # Check if the dataset does not have the expected metadata for columns + if not dataset.metadata.columns: + # Only allow late validation if the dataset is not yet ready + # (since we have reason to expect the metadata to be ready eventually) + if dataset.is_pending or not dataset.datatype.matches_any( self.ref_input.formats ): + return True # No late validation return False diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f test/functional/tools/column_multi_param.xml --- /dev/null +++ b/test/functional/tools/column_multi_param.xml @@ -0,0 +1,25 @@ +<tool id="column_multi_param" name="Column Param Multi"> + <command> + #for $input in $input1# + cut -f '$col' '$input' >> 'col_output'; + #end for# + </command> + <inputs> + <param type="data" format="tabular" name="input1" label="Input 1" multiple="true" /> + <param name="col" type="data_column" data_ref="input1" label="Column to Use" /> + </inputs> + <outputs> + <data name="output1" type="tabular" from_work_dir="col_output" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.tabular,2.tabular" /> + <param name="col" value="2" /> + <output name="outpu1"> + <assert_contents> + <has_line line="68" /> + </assert_contents> + </output> + </test> + </tests> +</tool> diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f test/functional/tools/column_param.xml --- /dev/null +++ b/test/functional/tools/column_param.xml @@ -0,0 +1,23 @@ +<tool id="column_param" name="Column Param"> + <command> + cut -f '$col' '$input1' > 'col_output' + </command> + <inputs> + <param type="data" format="tabular" name="input1" label="Input 1" /> + <param name="col" type="data_column" data_ref="input1" label="Column to Use" /> + </inputs> + <outputs> + <data name="output1" type="tabular" from_work_dir="col_output" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.tabular" /> + <param name="col" value="2" /> + <output name="output1"> + <assert_contents> + <has_line line="68" /> + </assert_contents> + </output> + </test> + </tests> +</tool> diff -r d27e8692adadf069e30d454cdb7a634526a6ba45 -r 95bcb99ad2b467ca0176a1e5e747bb18cd3cc61f test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -20,6 +20,8 @@ <tool file="parallelism_optional.xml" /><tool file="implicit_default_conds.xml" /><tool file="multi_data_param.xml" /> + <tool file="column_param.xml" /> + <tool file="column_multi_param.xml" /><tool file="special_params.xml" /><tool file="validation_default.xml" /><tool file="validation_sanitizer.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Fix boolean handling
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d27e8692adad/ Changeset: d27e8692adad User: guerler Date: 2014-09-26 13:52:32+00:00 Summary: ToolForm: Fix boolean handling Affected #: 3 files diff -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 -r d27e8692adadf069e30d454cdb7a634526a6ba45 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -109,16 +109,6 @@ } } break; - // handle boolean input - case 'boolean': - var value = self.app.field_list[input.id].value(); - if (value === 'true') { - value = input.truevalue; - } else { - value = input.falsevalue; - } - add (job_input_id, input.id, value); - break; default: // handle default value add (job_input_id, input.id, self.app.field_list[input.id].value()); diff -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 -r d27e8692adadf069e30d454cdb7a634526a6ba45 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -109,16 +109,6 @@ } } break; - // handle boolean input - case 'boolean': - var value = self.app.field_list[input.id].value(); - if (value === 'true') { - value = input.truevalue; - } else { - value = input.falsevalue; - } - add (job_input_id, input.id, value); - break; default: // handle default value add (job_input_id, input.id, self.app.field_list[input.id].value()); diff -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 -r d27e8692adadf069e30d454cdb7a634526a6ba45 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var n=e.input;var h=j;if(j!=""){h+="|"}h+=n.name;switch(n.type){case"repeat":var d="section-";var q=[];var l=null;for(var p in e){var k=p.indexOf(d);if(k!=-1){k+=d.length;q.push(parseInt(p.substr(k)));if(!l){l=p.substr(0,k)}}}q.sort(function(r,i){return r-i});var g=0;for(var f in q){b(h+"_"+g++,e[l+q[f]])}break;case"conditional":var o=a.app.field_list[n.id].value();c(h+"|"+n.test_param.name,n.id,o);for(var f in n.cases){if(n.cases[f].value==o){b(h,m[n.id+"-section-"+f]);break}}break;case"boolean":var o=a.app.field_list[n.id].value();if(o==="true"){o=n.truevalue}else{o=n.falsevalue}c(h,n.id,o);break;default:c(h,n.id,a.app.field_list[n.id].value())}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var n=e.input;var h=j;if(j!=""){h+="|"}h+=n.name;switch(n.type){case"repeat":var d="section-";var q=[];var l=null;for(var p in e){var k=p.indexOf(d);if(k!=-1){k+=d.length;q.push(parseInt(p.substr(k)));if(!l){l=p.substr(0,k)}}}q.sort(function(r,i){return r-i});var g=0;for(var f in q){b(h+"_"+g++,e[l+q[f]])}break;case"conditional":var o=a.app.field_list[n.id].value();c(h+"|"+n.test_param.name,n.id,o);for(var f in n.cases){if(n.cases[f].value==o){b(h,m[n.id+"-section-"+f]);break}}break;default:c(h,n.id,a.app.field_list[n.id].value())}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Tool test case demonstrating wrapping multiple data params in new meta-parameter wrapper.
by commits-noreply＠bitbucket.org 26 Sep '14

26 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/38f6cf2629ef/ Changeset: 38f6cf2629ef User: jmchilton Date: 2014-09-26 13:29:53+00:00 Summary: Tool test case demonstrating wrapping multiple data params in new meta-parameter wrapper. ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_multidata_param It was what was requested, but I am not sure I love this behavior - seems like for consistency that should maybe be a list of lists? I can see the other side of the argument though. Affected #: 1 file diff -r f52d7d6d64a671039a85959e1c720445f0ee672e -r 38f6cf2629efd071b4e7cc3e420a4e5081ad51e0 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -106,6 +106,23 @@ output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output ) assert output1_content == "--ex1,ex2" + @skip_without_tool( "multi_data_param" ) + def test_multidata_param( self ): + history_id = self.dataset_populator.new_history() + hda1 = dataset_to_param( self.dataset_populator.new_dataset( history_id, content='1\t2\t3' ) ) + hda2 = dataset_to_param( self.dataset_populator.new_dataset( history_id, content='4\t5\t6' ) ) + inputs = { + "f1": { 'batch': False, 'values': [ hda1, hda2 ] }, + "f2": { 'batch': False, 'values': [ hda2, hda1 ] }, + } + response = self._run( "multi_data_param", history_id, inputs, assert_ok=True ) + output1 = response[ "outputs" ][ 0 ] + output2 = response[ "outputs" ][ 1 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output1 ) + output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output2 ) + assert output1_content == "1\t2\t3\n4\t5\t6\n", output1_content + assert output2_content == "4\t5\t6\n1\t2\t3\n", output2_content + @skip_without_tool( "cat1" ) def test_run_cat1( self ): # Run simple non-upload tool with an input data parameter. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1a87b74d4f42/ Changeset: 1a87b74d4f42 Branch: next-stable User: natefoo Date: 2014-09-25 20:23:06+00:00 Summary: Fix bug in finding relocated tool_data_table_conf.xml Affected #: 1 file diff -r fdcefd1c3661ea71661584e7bcc03f33022641d1 -r 1a87b74d4f428ac25dfe5517506ec16bfa9a1bc4 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -394,7 +394,7 @@ ) listify_defaults = dict( - tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], # rationale: # [0]: user has explicitly created config/tool_conf.xml but did not # move their existing shed_tool_conf.xml, don't use https://bitbucket.org/galaxy/galaxy-central/commits/f52d7d6d64a6/ Changeset: f52d7d6d64a6 User: natefoo Date: 2014-09-25 20:23:31+00:00 Summary: Merge next-stable. Affected #: 1 file diff -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 -r f52d7d6d64a671039a85959e1c720445f0ee672e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -394,7 +394,7 @@ ) listify_defaults = dict( - tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], + tool_data_table_config_path = [ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ], # rationale: # [0]: user has explicitly created config/tool_conf.xml but did not # move their existing shed_tool_conf.xml, don't use Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Improve validation, minor fixes
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f02fcf8a931c/ Changeset: f02fcf8a931c User: guerler Date: 2014-09-25 20:14:56+00:00 Summary: ToolForm: Improve validation, minor fixes Affected #: 12 files diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -46,18 +46,35 @@ console.debug(response); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); - for (var id in error_messages) { - var error_text = error_messages[id]; - if (!error_text) { - error_text = 'Please verify this parameter.'; - } - self.app.element_list[id].error(error_text); + for (var input_id in error_messages) { + self._foundError(input_id, error_messages[input_id]); } } } ); }, + /** Highlight and scroll to error + */ + _foundError: function (input_id, message) { + // get input field + var input_element = this.app.element_list[input_id]; + + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // set flag + if (this.valid) { + // scroll to first input element + $(this.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // set error flag + this.valid = false; + } + }, + /** Validate job definition */ _validation: function(job_def) { @@ -65,30 +82,7 @@ var job_inputs = job_def.inputs; // validation flag - var valid = true; - - // link this - var self = this; - - /** Highlight and scroll to error */ - function foundError (input_id, message) { - // get input field - var input_element = self.app.element_list[input_id]; - - // mark error - input_element.error(message || 'Please verify this parameter.'); - - // set flag - if (valid) { - // scroll to first input element - $(self.app.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - - // set error flag - valid = false; - } - } + this.valid = true; // counter for values declared in batch mode var n_values = -1; @@ -105,7 +99,7 @@ // check basic field validation if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { - foundError(input_id); + this._foundError(input_id); } // check if input field is in batch mode @@ -115,15 +109,15 @@ n_values = n; } else { if (n_values !== n) { - foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); } } } } - // return result - return valid; + // return validation result + return this.valid; }, /** Refreshes the history panel diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -540,6 +540,10 @@ /** Slider field */ _field_slider: function(input_def) { + // set min/max + input_def.min = input_def.min || 0; + input_def.max = input_def.max || 100000; + // calculate step size var step = 1; if (input_def.type == 'float') { @@ -549,8 +553,8 @@ // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, - min : input_def.min || 0, - max : input_def.max || 1000, + min : input_def.min, + max : input_def.max, step : step }); }, diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -114,7 +114,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } @@ -149,7 +149,7 @@ // get selected values var selected = this.$el.find(':checked'); if (selected.length == 0) { - return null; + return 'null'; } // return multiple or single value diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -91,7 +91,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -46,18 +46,35 @@ console.debug(response); if (response && response.message && response.message.data) { var error_messages = self.app.tree.matchResponse(response.message.data); - for (var id in error_messages) { - var error_text = error_messages[id]; - if (!error_text) { - error_text = 'Please verify this parameter.'; - } - self.app.element_list[id].error(error_text); + for (var input_id in error_messages) { + self._foundError(input_id, error_messages[input_id]); } } } ); }, + /** Highlight and scroll to error + */ + _foundError: function (input_id, message) { + // get input field + var input_element = this.app.element_list[input_id]; + + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // set flag + if (this.valid) { + // scroll to first input element + $(this.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // set error flag + this.valid = false; + } + }, + /** Validate job definition */ _validation: function(job_def) { @@ -65,30 +82,7 @@ var job_inputs = job_def.inputs; // validation flag - var valid = true; - - // link this - var self = this; - - /** Highlight and scroll to error */ - function foundError (input_id, message) { - // get input field - var input_element = self.app.element_list[input_id]; - - // mark error - input_element.error(message || 'Please verify this parameter.'); - - // set flag - if (valid) { - // scroll to first input element - $(self.app.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - - // set error flag - valid = false; - } - } + this.valid = true; // counter for values declared in batch mode var n_values = -1; @@ -105,7 +99,7 @@ // check basic field validation if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { - foundError(input_id); + this._foundError(input_id); } // check if input field is in batch mode @@ -115,15 +109,15 @@ n_values = n; } else { if (n_values !== n) { - foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + this._foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); } } } } - // return result - return valid; + // return validation result + return this.valid; }, /** Refreshes the history panel diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -540,6 +540,10 @@ /** Slider field */ _field_slider: function(input_def) { + // set min/max + input_def.min = input_def.min || 0; + input_def.max = input_def.max || 100000; + // calculate step size var step = 1; if (input_def.type == 'float') { @@ -549,8 +553,8 @@ // create slider return new Ui.Slider.View({ id : 'field-' + input_def.id, - min : input_def.min || 0, - max : input_def.max || 1000, + min : input_def.min, + max : input_def.max, step : step }); }, diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -114,7 +114,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } @@ -149,7 +149,7 @@ // get selected values var selected = this.$el.find(':checked'); if (selected.length == 0) { - return null; + return 'null'; } // return multiple or single value diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -91,7 +91,7 @@ current = [current]; } for (var i in current) { - if (current[i] === 'null' || !current[i]) { + if (current[i] === 'null') { return false; } } diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.log(d);b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var g in h){var f=h[g];if(!f){f="Please verify this parameter."}c.app.element_list[g].error(f)}}})},_validation:function(h){var e=h.inputs;var c=true;var o=this;function m(n,p){var q=o.app.element_list[n];q.error(p||"Please verify this parameter.");if(c){$(o.app.container).animate({scrollTop:q.$el.offset().top-20},500);c=false}}var l=-1;for(var k in e){var f=e[k];var j=this.app.tree.match(k);var d=this.app.field_list[j];var i=this.app.input_list[j];if(i&&!i.optional&&d&&d.validate&&!d.validate()){m(j)}if(f.batch){var g=f.values.length;if(l===-1){l=g}else{if(l!==g){m(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+l+"</b>.")}}}}return c},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.log(d);b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var g=c.app.tree.matchResponse(e.message.data);for(var f in g){c._foundError(f,g[f])}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");if(this.valid){$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500);this.valid=false}},_validation:function(g){var c=g.inputs;this.valid=true;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j)}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.")}}}}return this.valid},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new a.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new b.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(l){var v=l.values[0].id;var t=i.app.tree.references(j,"data_column");if(t.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}var o=i.app.datasets.filter(v);var x=null;if(o){console.debug("tool-form::field_data() - Selected dataset "+v+".");x=o.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+v+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+v+".")}for(var p in t){var r=i.app.input_list[t[p]];var s=i.app.field_list[t[p]];if(!r||!s){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=r.numerical;var m=[];for(var w in x){var u=x[w];var k=(parseInt(w)+1);var q="Text";if(u=="int"||u=="float"){q="Number"}if(u=="int"||u=="float"||!n){m.push({label:"Column: "+k+" ["+q+"]",value:k})}}if(s){s.update(m);if(!s.exists(s.value())){s.value(s.first())}}}}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min||0,max:h.max||1000,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-dataset"],function(d,a,g,c,b){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new a.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._field_text(h);break;case"select":i=this._field_select(h);break;case"data":i=this._field_data(h);break;case"data_column":i=this._field_select(h);break;case"conditional":i=this._field_conditional(h);break;case"hidden":i=this._field_hidden(h);break;case"integer":i=this._field_slider(h);break;case"float":i=this._field_slider(h);break;case"boolean":i=this._field_boolean(h);break}if(!i){if(h.options){i=this._field_select(h)}else{i=this._field_text(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_field_conditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_field_data:function(h){var i=this;var j=h.id;return new b.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(l){var v=l.values[0].id;var t=i.app.tree.references(j,"data_column");if(t.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}var o=i.app.datasets.filter(v);var x=null;if(o){console.debug("tool-form::field_data() - Selected dataset "+v+".");x=o.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+v+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+v+".")}for(var p in t){var r=i.app.input_list[t[p]];var s=i.app.field_list[t[p]];if(!r||!s){console.debug("tool-form::field_data() - FAILED: Column not found.")}var n=r.numerical;var m=[];for(var w in x){var u=x[w];var k=(parseInt(w)+1);var q="Text";if(u=="int"||u=="float"){q="Number"}if(u=="int"||u=="float"||!n){m.push({label:"Column: "+k+" ["+q+"]",value:k})}}if(s){s.update(m);if(!s.exists(s.value())){s.value(s.first())}}}}})},_field_select:function(h){var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_field_text:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_field_slider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_field_hidden:function(h){return new g.Hidden({id:"field-"+h.id})},_field_boolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if(g[f]==="null"||!g[f]){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return null}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={value:[],visible:true,data:[],id:b.uuid(),empty:"No data available"};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$error=$(this._templateError(g));this.$options=$(this._template(g));this.$el.append(this.$error);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$el.find(".ui-option").remove();for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},exists:function(g){if(typeof g==="string"){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if(g[f]==="null"){return false}}return true},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){var f=this.$el.find(".ui-option").length;if(f==0){this.$error.show();this.$options.hide()}else{this.$error.hide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_templateError:function(f){return'<div class="ui-error" style="display: none;">'+f.empty+"</div>"}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(typeof f==="string"){f=[f]}if(f!==undefined){this.$el.find("input").prop("checked",false);for(var g in f){this.$el.find("input[value="+f[g]+"]").prop("checked",true)}}return this._getValue()},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"},_template:function(){return'<div class="ui-options"/>'}});var c={};c.View=d.View.extend({initialize:function(f){f.multiple=true;d.View.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 -r f02fcf8a931c4862cfb6698da0e097d68c8025c6 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if(d[c]==="null"||!d[c]){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if(d[c]==="null"){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down");this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin");this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b737af143fce/ Changeset: b737af143fce Branch: next-stable User: jmchilton Date: 2014-09-25 17:49:04+00:00 Summary: Fix various BibTex styling problems. Need to get out of the BibTeX formatting game as quickly as possible this is a loosing battle, but until then plugging holes in the ship. Affected #: 2 files diff -r f3284eb7ec210d50a3e9f2c0d393cffcb24894da -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 client/galaxy/scripts/libs/bibtex.js --- a/client/galaxy/scripts/libs/bibtex.js +++ b/client/galaxy/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r f3284eb7ec210d50a3e9f2c0d393cffcb24894da -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 client/galaxy/scripts/mvc/citation/citation-view.js --- a/client/galaxy/scripts/mvc/citation/citation-view.js +++ b/client/galaxy/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } https://bitbucket.org/galaxy/galaxy-central/commits/fdcefd1c3661/ Changeset: fdcefd1c3661 Branch: next-stable User: jmchilton Date: 2014-09-25 17:49:04+00:00 Summary: Grunting at the scripts. Affected #: 4 files diff -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 -r fdcefd1c3661ea71661584e7bcc03f33022641d1 static/scripts/libs/bibtex.js --- a/static/scripts/libs/bibtex.js +++ b/static/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 -r fdcefd1c3661ea71661584e7bcc03f33022641d1 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } diff -r b737af143fcecafb89b187a2bd1b05d5cab6c3b5 -r fdcefd1c3661ea71661584e7bcc03f33022641d1 static/scripts/packed/libs/bibtex.js --- a/static/scripts/packed/libs/bibtex.js +++ b/static/scripts/packed/libs/bibtex.js @@ -1,1 +1,1 @@ -function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,data:999};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no value.');this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(l=="="){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_VALUE;this.PARSETMP_.Value="";this.VALBRACES_={'"':[],"{":[]}}break;case this.STATES_.KV_VALUE:var k=this.VALBRACES_;var j=this.PARSETMP_.Value;var h=false;if(l=='"'||l=="{"||l=="}"||l==","){if(l==","){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}h=true}}if(l=='"'){if(0===k['"'].length+k["{"].length){k['"'].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false;break}if(k['"'].length==1&&k["{"].length==0&&(j.length==0||j[j.length-1]!="\\")){h=true}else{}}if(l=="{"){if(j.length==0||j[j.length-1]!="\\"){k["{"].push(this.CHAR_);this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{}}if(l=="}"){if(0===k['"'].length+k["{"].length){var g=this.PARSETMP_.Value.trim();if(g in this.MACROS_){this.PARSETMP_.Value=this.MACROS_[g]}else{this.error_("Reference to an undefined macro: "+g)}f=true;h=true}else{if(j.length==0||j[j.length-1]!="\\"){if(k["{"].length>0){k["{"].splice(k["{"].length-1,1);if(0==k["{"].length+k['"'].length){h=true}else{}}}else{}}}}if(h){this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.KV_KEY;this.DATA_.Fields[this.PARSETMP_.Key]=this.PARSETMP_.Value;this.PARSETMP_={Key:""};this.VALBRACES_=null}else{this.PARSETMP_.Value+=l}break}}};this.CHARCONV_=[[/\\space /g,"\u0020"],[/\\textdollar /g,"\u0024"],[/\\textquotesingle /g,"\u0027"],[/\\ast /g,"\u002A"],[/\\textbackslash /g,"\u005C"],[/\\\^\{\}/g,"\u005E"],[/\\textasciigrave /g,"\u0060"],[/\\lbrace /g,"\u007B"],[/\\vert /g,"\u007C"],[/\\rbrace /g,"\u007D"],[/\\textasciitilde /g,"\u007E"],[/\\textexclamdown /g,"\u00A1"],[/\\textcent /g,"\u00A2"],[/\\textsterling /g,"\u00A3"],[/\\textcurrency /g,"\u00A4"],[/\\textyen 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/g,"\u27F5"],[/\\longrightarrow /g,"\u27F6"],[/\\longleftrightarrow /g,"\u27F7"],[/\\Longleftarrow /g,"\u27F8"],[/\\Longrightarrow /g,"\u27F9"],[/\\Longleftrightarrow /g,"\u27FA"],[/\\longmapsto /g,"\u27FC"],[/\\sim\\joinrel\\leadsto/g,"\u27FF"],[/\\ElsevierGlyph\{E212\}/g,"\u2905"],[/\\UpArrowBar /g,"\u2912"],[/\\DownArrowBar /g,"\u2913"],[/\\ElsevierGlyph\{E20C\}/g,"\u2923"],[/\\ElsevierGlyph\{E20D\}/g,"\u2924"],[/\\ElsevierGlyph\{E20B\}/g,"\u2925"],[/\\ElsevierGlyph\{E20A\}/g,"\u2926"],[/\\ElsevierGlyph\{E211\}/g,"\u2927"],[/\\ElsevierGlyph\{E20E\}/g,"\u2928"],[/\\ElsevierGlyph\{E20F\}/g,"\u2929"],[/\\ElsevierGlyph\{E210\}/g,"\u292A"],[/\\ElsevierGlyph\{E21C\}/g,"\u2933"],[/\\ElsevierGlyph\{E21D\}/g,"\u2933-00338"],[/\\ElsevierGlyph\{E21A\}/g,"\u2936"],[/\\ElsevierGlyph\{E219\}/g,"\u2937"],[/\\Elolarr /g,"\u2940"],[/\\Elorarr /g,"\u2941"],[/\\ElzRlarr /g,"\u2942"],[/\\ElzrLarr /g,"\u2944"],[/\\Elzrarrx /g,"\u2947"],[/\\LeftRightVector /g,"\u294E"],[/\\RightUpDownVector /g,"\u294F"],[/\\DownLeftRightVector /g,"\u2950"],[/\\LeftUpDownVector /g,"\u2951"],[/\\LeftVectorBar /g,"\u2952"],[/\\RightVectorBar /g,"\u2953"],[/\\RightUpVectorBar /g,"\u2954"],[/\\RightDownVectorBar /g,"\u2955"],[/\\DownLeftVectorBar /g,"\u2956"],[/\\DownRightVectorBar /g,"\u2957"],[/\\LeftUpVectorBar /g,"\u2958"],[/\\LeftDownVectorBar /g,"\u2959"],[/\\LeftTeeVector /g,"\u295A"],[/\\RightTeeVector /g,"\u295B"],[/\\RightUpTeeVector /g,"\u295C"],[/\\RightDownTeeVector /g,"\u295D"],[/\\DownLeftTeeVector /g,"\u295E"],[/\\DownRightTeeVector /g,"\u295F"],[/\\LeftUpTeeVector /g,"\u2960"],[/\\LeftDownTeeVector /g,"\u2961"],[/\\UpEquilibrium /g,"\u296E"],[/\\ReverseUpEquilibrium /g,"\u296F"],[/\\RoundImplies /g,"\u2970"],[/\\ElsevierGlyph\{E214\}/g,"\u297C"],[/\\ElsevierGlyph\{E215\}/g,"\u297D"],[/\\Elztfnc /g,"\u2980"],[/\\ElsevierGlyph\{3018\}/g,"\u2985"],[/\\Elroang /g,"\u2986"],[/\\ElsevierGlyph\{E291\}/g,"\u2994"],[/\\Elzddfnc /g,"\u2999"],[/\\Angle /g,"\u299C"],[/\\Elzlpargt /g,"\u29A0"],[/\\ElsevierGlyph\{E260\}/g,"\u29B5"],[/\\ElsevierGlyph\{E61B\}/g,"\u29B6"],[/\\ElzLap /g,"\u29CA"],[/\\Elzdefas /g,"\u29CB"],[/\\LeftTriangleBar /g,"\u29CF"],[/\\NotLeftTriangleBar /g,"\u29CF-00338"],[/\\RightTriangleBar /g,"\u29D0"],[/\\NotRightTriangleBar /g,"\u29D0-00338"],[/\\ElsevierGlyph\{E372\}/g,"\u29DC"],[/\\blacklozenge /g,"\u29EB"],[/\\RuleDelayed /g,"\u29F4"],[/\\Elxuplus /g,"\u2A04"],[/\\ElzThr /g,"\u2A05"],[/\\Elxsqcup /g,"\u2A06"],[/\\ElzInf /g,"\u2A07"],[/\\ElzSup /g,"\u2A08"],[/\\ElzCint /g,"\u2A0D"],[/\\clockoint /g,"\u2A0F"],[/\\ElsevierGlyph\{E395\}/g,"\u2A10"],[/\\sqrint /g,"\u2A16"],[/\\ElsevierGlyph\{E25A\}/g,"\u2A25"],[/\\ElsevierGlyph\{E25B\}/g,"\u2A2A"],[/\\ElsevierGlyph\{E25C\}/g,"\u2A2D"],[/\\ElsevierGlyph\{E25D\}/g,"\u2A2E"],[/\\ElzTimes /g,"\u2A2F"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A34"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A35"],[/\\ElsevierGlyph\{E259\}/g,"\u2A3C"],[/\\amalg /g,"\u2A3F"],[/\\ElzAnd /g,"\u2A53"],[/\\ElzOr /g,"\u2A54"],[/\\ElsevierGlyph\{E36E\}/g,"\u2A55"],[/\\ElOr /g,"\u2A56"],[/\\perspcorrespond /g,"\u2A5E"],[/\\Elzminhat /g,"\u2A5F"],[/\\ElsevierGlyph\{225A\}/g,"\u2A63"],[/\\stackrel\{*\}\{=\}/g,"\u2A6E"],[/\\Equal /g,"\u2A75"],[/\\leqslant /g,"\u2A7D"],[/\\nleqslant /g,"\u2A7D-00338"],[/\\geqslant /g,"\u2A7E"],[/\\ngeqslant /g,"\u2A7E-00338"],[/\\lessapprox /g,"\u2A85"],[/\\gtrapprox /g,"\u2A86"],[/\\lneq /g,"\u2A87"],[/\\gneq /g,"\u2A88"],[/\\lnapprox /g,"\u2A89"],[/\\gnapprox /g,"\u2A8A"],[/\\lesseqqgtr /g,"\u2A8B"],[/\\gtreqqless /g,"\u2A8C"],[/\\eqslantless /g,"\u2A95"],[/\\eqslantgtr /g,"\u2A96"],[/\\Pisymbol\{ppi020\}\{117\}/g,"\u2A9D"],[/\\Pisymbol\{ppi020\}\{105\}/g,"\u2A9E"],[/\\NestedLessLess /g,"\u2AA1"],[/\\NotNestedLessLess /g,"\u2AA1-00338"],[/\\NestedGreaterGreater /g,"\u2AA2"],[/\\NotNestedGreaterGreater /g,"\u2AA2-00338"],[/\\preceq /g,"\u2AAF"],[/\\not\\preceq /g,"\u2AAF-00338"],[/\\succeq /g,"\u2AB0"],[/\\not\\succeq /g,"\u2AB0-00338"],[/\\precneqq /g,"\u2AB5"],[/\\succneqq /g,"\u2AB6"],[/\\precapprox /g,"\u2AB7"],[/\\succapprox /g,"\u2AB8"],[/\\precnapprox /g,"\u2AB9"],[/\\succnapprox /g,"\u2ABA"],[/\\subseteqq /g,"\u2AC5"],[/\\nsubseteqq /g,"\u2AC5-00338"],[/\\supseteqq /g,"\u2AC6"],[/\\nsupseteqq/g,"\u2AC6-00338"],[/\\subsetneqq /g,"\u2ACB"],[/\\supsetneqq /g,"\u2ACC"],[/\\ElsevierGlyph\{E30D\}/g,"\u2AEB"],[/\\Elztdcol /g,"\u2AF6"],[/\\ElsevierGlyph\{300A\}/g,"\u300A"],[/\\ElsevierGlyph\{300B\}/g,"\u300B"],[/\\ElsevierGlyph\{3018\}/g,"\u3018"],[/\\ElsevierGlyph\{3019\}/g,"\u3019"],[/\\openbracketleft /g,"\u301A"],[/\\openbracketright /g,"\u301B"]];return this}if(typeof module!=="undefined"&&module.exports){module.exports=BibtexParser}; \ No newline at end of file +function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,online:998,data:999};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no 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":"")+(l.note?l.note+".":"")}else{if(i=="techreport"){g=o+this._asSentence(n)+this._asSentence(l.institution)+this._asSentence(l.number)+this._asSentence(l.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=o+" "+this._formatBookInfo(l)}else{g=o+" "+this._asSentence(n)+this._asSentence(l.howpublished)+this._asSentence(l.note)}}}}}var m="";if(l.doi){m="http://dx.doi.org/"+l.doi;g+='[<a href="'+m+'">doi:'+l.doi+"</a>]"}var f=l.url||m;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/82f8d68414f5/ Changeset: 82f8d68414f5 User: jmchilton Date: 2014-09-25 17:49:29+00:00 Summary: Merge latest next-stable. Affected #: 6 files diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 client/galaxy/scripts/libs/bibtex.js --- a/client/galaxy/scripts/libs/bibtex.js +++ b/client/galaxy/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 client/galaxy/scripts/mvc/citation/citation-view.js --- a/client/galaxy/scripts/mvc/citation/citation-view.js +++ b/client/galaxy/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 static/scripts/libs/bibtex.js --- a/static/scripts/libs/bibtex.js +++ b/static/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'online' : 998 // Galaxy MOD: Handle @online entries for preprints. ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -24,11 +24,12 @@ var pages = fields.pages ? ("pp. " + fields.pages) : ""; var address = fields.address; if( entryType == "article" ) { + var volume = (fields.volume ? fields.volume : "") + + (fields.number ? ( " (" + fields.number + ")" ) : "") + + (pages ? ", " + pages : ""); ref = authorsAndYear + this._asSentence(title) + (fields.journal ? ("In <em>" + fields.journal + ", ") : "") + - (fields.volume ? fields.volume : "") + - (fields.number ? ( "(" + fields.number + "), " ) : ", " ) + - this._asSentence(pages) + + this._asSentence(volume) + this._asSentence(fields.address) + "<\/em>"; } else if( entryType == "inproceedings" || entryType == "proceedings" ) { @@ -43,14 +44,14 @@ (fields.howpublished ? fields.howpublished + ". " : "") + (fields.note ? fields.note + "." : ""); } else if( entryType == "techreport" ) { - ref = authorsAndYear + ". " + this._asSentence(title) + + ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type); } else if( entryType == "book" || entryType == "inbook" || entryType == "incollection" ) { - ref = this._asSentence(authorsAndYear) + " " + this._formatBookInfo(fields); + ref = authorsAndYear + " " + this._formatBookInfo(fields); } else { - ref = this._asSentence(authorsAndYear) + " " + this._asSentence(title) + + ref = authorsAndYear + " " + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note); } diff -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 -r 82f8d68414f5c9a0e5aeaaabca85cf7044e06183 static/scripts/packed/libs/bibtex.js --- a/static/scripts/packed/libs/bibtex.js +++ b/static/scripts/packed/libs/bibtex.js @@ -1,1 +1,1 @@ -function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser 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/g,"\u27F5"],[/\\longrightarrow /g,"\u27F6"],[/\\longleftrightarrow /g,"\u27F7"],[/\\Longleftarrow /g,"\u27F8"],[/\\Longrightarrow /g,"\u27F9"],[/\\Longleftrightarrow /g,"\u27FA"],[/\\longmapsto /g,"\u27FC"],[/\\sim\\joinrel\\leadsto/g,"\u27FF"],[/\\ElsevierGlyph\{E212\}/g,"\u2905"],[/\\UpArrowBar /g,"\u2912"],[/\\DownArrowBar /g,"\u2913"],[/\\ElsevierGlyph\{E20C\}/g,"\u2923"],[/\\ElsevierGlyph\{E20D\}/g,"\u2924"],[/\\ElsevierGlyph\{E20B\}/g,"\u2925"],[/\\ElsevierGlyph\{E20A\}/g,"\u2926"],[/\\ElsevierGlyph\{E211\}/g,"\u2927"],[/\\ElsevierGlyph\{E20E\}/g,"\u2928"],[/\\ElsevierGlyph\{E20F\}/g,"\u2929"],[/\\ElsevierGlyph\{E210\}/g,"\u292A"],[/\\ElsevierGlyph\{E21C\}/g,"\u2933"],[/\\ElsevierGlyph\{E21D\}/g,"\u2933-00338"],[/\\ElsevierGlyph\{E21A\}/g,"\u2936"],[/\\ElsevierGlyph\{E219\}/g,"\u2937"],[/\\Elolarr /g,"\u2940"],[/\\Elorarr /g,"\u2941"],[/\\ElzRlarr /g,"\u2942"],[/\\ElzrLarr /g,"\u2944"],[/\\Elzrarrx /g,"\u2947"],[/\\LeftRightVector /g,"\u294E"],[/\\RightUpDownVector /g,"\u294F"],[/\\DownLeftRightVector /g,"\u2950"],[/\\LeftUpDownVector /g,"\u2951"],[/\\LeftVectorBar /g,"\u2952"],[/\\RightVectorBar /g,"\u2953"],[/\\RightUpVectorBar /g,"\u2954"],[/\\RightDownVectorBar /g,"\u2955"],[/\\DownLeftVectorBar /g,"\u2956"],[/\\DownRightVectorBar /g,"\u2957"],[/\\LeftUpVectorBar /g,"\u2958"],[/\\LeftDownVectorBar /g,"\u2959"],[/\\LeftTeeVector /g,"\u295A"],[/\\RightTeeVector /g,"\u295B"],[/\\RightUpTeeVector /g,"\u295C"],[/\\RightDownTeeVector /g,"\u295D"],[/\\DownLeftTeeVector /g,"\u295E"],[/\\DownRightTeeVector /g,"\u295F"],[/\\LeftUpTeeVector /g,"\u2960"],[/\\LeftDownTeeVector /g,"\u2961"],[/\\UpEquilibrium /g,"\u296E"],[/\\ReverseUpEquilibrium /g,"\u296F"],[/\\RoundImplies /g,"\u2970"],[/\\ElsevierGlyph\{E214\}/g,"\u297C"],[/\\ElsevierGlyph\{E215\}/g,"\u297D"],[/\\Elztfnc /g,"\u2980"],[/\\ElsevierGlyph\{3018\}/g,"\u2985"],[/\\Elroang /g,"\u2986"],[/\\ElsevierGlyph\{E291\}/g,"\u2994"],[/\\Elzddfnc /g,"\u2999"],[/\\Angle /g,"\u299C"],[/\\Elzlpargt /g,"\u29A0"],[/\\ElsevierGlyph\{E260\}/g,"\u29B5"],[/\\ElsevierGlyph\{E61B\}/g,"\u29B6"],[/\\ElzLap /g,"\u29CA"],[/\\Elzdefas /g,"\u29CB"],[/\\LeftTriangleBar /g,"\u29CF"],[/\\NotLeftTriangleBar /g,"\u29CF-00338"],[/\\RightTriangleBar /g,"\u29D0"],[/\\NotRightTriangleBar /g,"\u29D0-00338"],[/\\ElsevierGlyph\{E372\}/g,"\u29DC"],[/\\blacklozenge /g,"\u29EB"],[/\\RuleDelayed /g,"\u29F4"],[/\\Elxuplus /g,"\u2A04"],[/\\ElzThr /g,"\u2A05"],[/\\Elxsqcup /g,"\u2A06"],[/\\ElzInf /g,"\u2A07"],[/\\ElzSup /g,"\u2A08"],[/\\ElzCint /g,"\u2A0D"],[/\\clockoint /g,"\u2A0F"],[/\\ElsevierGlyph\{E395\}/g,"\u2A10"],[/\\sqrint /g,"\u2A16"],[/\\ElsevierGlyph\{E25A\}/g,"\u2A25"],[/\\ElsevierGlyph\{E25B\}/g,"\u2A2A"],[/\\ElsevierGlyph\{E25C\}/g,"\u2A2D"],[/\\ElsevierGlyph\{E25D\}/g,"\u2A2E"],[/\\ElzTimes /g,"\u2A2F"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A34"],[/\\ElsevierGlyph\{E25E\}/g,"\u2A35"],[/\\ElsevierGlyph\{E259\}/g,"\u2A3C"],[/\\amalg /g,"\u2A3F"],[/\\ElzAnd /g,"\u2A53"],[/\\ElzOr /g,"\u2A54"],[/\\ElsevierGlyph\{E36E\}/g,"\u2A55"],[/\\ElOr /g,"\u2A56"],[/\\perspcorrespond /g,"\u2A5E"],[/\\Elzminhat /g,"\u2A5F"],[/\\ElsevierGlyph\{225A\}/g,"\u2A63"],[/\\stackrel\{*\}\{=\}/g,"\u2A6E"],[/\\Equal /g,"\u2A75"],[/\\leqslant /g,"\u2A7D"],[/\\nleqslant /g,"\u2A7D-00338"],[/\\geqslant /g,"\u2A7E"],[/\\ngeqslant /g,"\u2A7E-00338"],[/\\lessapprox /g,"\u2A85"],[/\\gtrapprox /g,"\u2A86"],[/\\lneq /g,"\u2A87"],[/\\gneq /g,"\u2A88"],[/\\lnapprox /g,"\u2A89"],[/\\gnapprox /g,"\u2A8A"],[/\\lesseqqgtr /g,"\u2A8B"],[/\\gtreqqless /g,"\u2A8C"],[/\\eqslantless /g,"\u2A95"],[/\\eqslantgtr /g,"\u2A96"],[/\\Pisymbol\{ppi020\}\{117\}/g,"\u2A9D"],[/\\Pisymbol\{ppi020\}\{105\}/g,"\u2A9E"],[/\\NestedLessLess /g,"\u2AA1"],[/\\NotNestedLessLess /g,"\u2AA1-00338"],[/\\NestedGreaterGreater /g,"\u2AA2"],[/\\NotNestedGreaterGreater /g,"\u2AA2-00338"],[/\\preceq /g,"\u2AAF"],[/\\not\\preceq /g,"\u2AAF-00338"],[/\\succeq /g,"\u2AB0"],[/\\not\\succeq /g,"\u2AB0-00338"],[/\\precneqq /g,"\u2AB5"],[/\\succneqq /g,"\u2AB6"],[/\\precapprox /g,"\u2AB7"],[/\\succapprox /g,"\u2AB8"],[/\\precnapprox /g,"\u2AB9"],[/\\succnapprox /g,"\u2ABA"],[/\\subseteqq /g,"\u2AC5"],[/\\nsubseteqq /g,"\u2AC5-00338"],[/\\supseteqq /g,"\u2AC6"],[/\\nsupseteqq/g,"\u2AC6-00338"],[/\\subsetneqq /g,"\u2ACB"],[/\\supsetneqq /g,"\u2ACC"],[/\\ElsevierGlyph\{E30D\}/g,"\u2AEB"],[/\\Elztdcol /g,"\u2AF6"],[/\\ElsevierGlyph\{300A\}/g,"\u300A"],[/\\ElsevierGlyph\{300B\}/g,"\u300B"],[/\\ElsevierGlyph\{3018\}/g,"\u3018"],[/\\ElsevierGlyph\{3019\}/g,"\u3019"],[/\\openbracketleft /g,"\u301A"],[/\\openbracketright /g,"\u301B"]];return this}if(typeof module!=="undefined"&&module.exports){module.exports=BibtexParser}; \ No newline at end of file +function BibtexParser(c){if(typeof c=="string"){var d={};var a=[];function b(f){a.push(f)}var e=BibtexParser.call(d,b);e.parse(c);return{entries:a,errors:e.getErrors()}}if(typeof c!="function"){throw"Invalid parser construction."}this.STATES_={ENTRY_OR_JUNK:0,OBJECT_TYPE:1,ENTRY_KEY:2,KV_KEY:3,EQUALS:4,KV_VALUE:5};this.DATA_={};this.CALLBACK_=c;this.CHAR_=0;this.LINE_=1;this.CHAR_IN_LINE_=0;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={};this.SKIPTILLEOL_=false;this.VALBRACES_=null;this.BRACETYPE_=null;this.BRACECOUNT_=0;this.STATE_=this.STATES_.ENTRY_OR_JUNK;this.ERRORS_=[];this.ENTRY_TYPES_={inproceedings:1,proceedings:2,article:3,techreport:4,misc:5,mastersthesis:6,book:7,phdthesis:8,incollection:9,unpublished:10,inbook:11,manual:12,periodical:13,booklet:14,masterthesis:15,conference:16,online:998,data:999};this.MACROS_={jan:"January",feb:"February",mar:"March",apr:"April",may:"May",jun:"June",jul:"July",aug:"August",sep:"September",oct:"October",nov:"November",dec:"December",Jan:"January",Feb:"February",Mar:"March",Apr:"April",May:"May",Jun:"June",Jul:"July",Aug:"August",Sep:"September",Oct:"October",Nov:"November",Dec:"December"};this.getErrors=function(){return this.ERRORS_};this.parse=function(f){for(var g=0;g<f.length;g++){this.processCharacter_(f[g])}};this.error_=function(f){this.ERRORS_.push([this.LINE_,this.CHAR_IN_LINE_,this.CHAR_,f])};this.processEntry_=function(){var h=this.DATA_;if(h.Fields){for(var k in h.Fields){var p=h.Fields[k];for(var j=0;j<this.CHARCONV_.length;j++){var q=this.CHARCONV_[j][0];var n=this.CHARCONV_[j][1];p=p.replace(q,n)}p=p.replace(/[\n\r\t]/g," ").replace(/\s\s+/g," ").replace(/^\s+|\s+$/g,"");var l=p.length;var g="";for(var j=0;j<l;j++){var m=p[j];var o=false;if(m=="\\"&&j<l-1){m=p[++j]}else{if(m=="{"||m=="}"){o=true}}if(!o){g+=m}}h.Fields[k]=g}}if(h.ObjectType=="string"){for(var k in h.Fields){this.MACROS_[k]=h.Fields[k]}}else{this.CALLBACK_(h)}};this.processCharacter_=function(l){this.CHAR_++;this.CHAR_IN_LINE_++;if(l=="\n"){this.LINE_++;this.CHAR_IN_LINE_=1}if(this.SKIPTILLEOL_){if(l=="\n"){this.SKIPTILLEOL_=false}return}if(this.SKIPCOMMENT_&&l=="%"){this.SKIPTILLEOL_=true;return}if(this.SKIPWS_&&/\s/.test(l)){return}this.SKIPWS_=false;this.SKIPCOMMENT_=false;this.SKIPTILLEOL_=false;var f=true;while(f){f=false;switch(this.STATE_){case this.STATES_.ENTRY_OR_JUNK:if(l=="@"){this.STATE_=this.STATES_.OBJECT_TYPE;this.DATA_={ObjectType:""}}this.BRACETYPE_=null;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break;case this.STATES_.OBJECT_TYPE:if(/[A-Za-z]/.test(l)){this.DATA_.ObjectType+=l.toLowerCase();this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{var i=this.DATA_.ObjectType;if(i=="comment"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i=="string"){this.DATA_.ObjectType=i;this.DATA_.Fields={};this.BRACETYPE_=l;this.BRACECOUNT_=1;this.STATE_=this.STATES_.KV_KEY;this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.PARSETMP_={Key:""}}else{if(i=="preamble"){this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{if(i in this.ENTRY_TYPES_){this.DATA_.ObjectType="entry";this.DATA_.EntryType=i;this.DATA_.EntryKey="";this.STATE_=this.STATES_.ENTRY_KEY;f=true}else{this.error_('Unrecognized object type: "'+this.DATA_.ObjectType+'"');this.STATE_=this.STATES_.ENTRY_OR_JUNK}}}}}break;case this.STATES_.ENTRY_KEY:if((l==="{"||l==="(")&&this.BRACETYPE_==null){this.BRACETYPE_=l;this.BRACECOUNT_=1;this.SKIPWS_=true;this.SKIPCOMMENT_=true;break}if(/[,%\s]/.test(l)){if(this.DATA_.EntryKey.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{if(this.BRACETYPE_==null){this.error_("No opening brace for object.");this.STATE_=this.STATES_.ENTRY_OR_JUNK}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;f=true;this.STATE_=this.STATES_.KV_KEY;this.PARSETMP_.Key="";this.DATA_.Fields={}}}}else{this.DATA_.EntryKey+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}break;case this.STATES_.KV_KEY:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.processEntry_();this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.ENTRY_OR_JUNK;break}if(/[\-A-Za-z:]/.test(l)){this.PARSETMP_.Key+=l;this.SKIPWS_=false;this.SKIPCOMMENT_=false}else{if(this.PARSETMP_.Key.length<1){this.SKIPWS_=true;this.SKIPCOMMENT_=true}else{this.SKIPWS_=true;this.SKIPCOMMENT_=true;this.STATE_=this.STATES_.EQUALS;f=true}}break;case this.STATES_.EQUALS:if((l=="}"&&this.BRACETYPE_=="{")||(l==")"&&this.BRACETYPE_=="(")){this.error_('Key-value pair has key "'+this.PARSETMP_.Key+'", but no 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When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var k=this.model;var i=k.entryType();var l=k.fields();var g="";var o=this._asSentence((l.author?l.author:"")+(l.year?(" ("+l.year+")"):""))+" ";var n=l.title||"";var h=l.pages?("pp. "+l.pages):"";var p=l.address;if(i=="article"){var j=(l.volume?l.volume:"")+(l.number?(" ("+l.number+")"):"")+(h?", "+h:"");g=o+this._asSentence(n)+(l.journal?("In <em>"+l.journal+", "):"")+this._asSentence(j)+this._asSentence(l.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=o+this._asSentence(n)+(l.booktitle?("In <em>"+l.booktitle+", "):"")+(h?h:"")+(p?", "+p:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=o+this._asSentence(n)+(l.howpublished?l.howpublished+". ":"")+(l.note?l.note+".":"")}else{if(i=="techreport"){g=o+this._asSentence(n)+this._asSentence(l.institution)+this._asSentence(l.number)+this._asSentence(l.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=o+" "+this._formatBookInfo(l)}else{g=o+" "+this._asSentence(n)+this._asSentence(l.howpublished)+this._asSentence(l.note)}}}}}var m="";if(l.doi){m="http://dx.doi.org/"+l.doi;g+='[<a href="'+m+'">doi:'+l.doi+"</a>]"}var f=l.url||m;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0880211749b/ Changeset: a0880211749b Branch: next-stable User: saketkc Date: 2014-09-25 06:10:51+00:00 Summary: Update tool_list to reflect recent change in use of envirnoment variables tool_list.py now makese use of GALAXY_TEST_TOOL_CONF and exits throwing an appropriate error Affected #: 1 file diff -r 5296d69134bddeb11246c70347d83c6073da646f -r a0880211749b1f65c4fa78f9c121fa2234decc67 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -1,9 +1,15 @@ -import os,sys +import os +import sys #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml", "r"): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) +if not os.path.isfile(tool_conf_file): + sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) + sys.exit(1) + +for line in open(tool_conf_file, "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: https://bitbucket.org/galaxy/galaxy-central/commits/f3284eb7ec21/ Changeset: f3284eb7ec21 Branch: next-stable User: jmchilton Date: 2014-09-25 13:00:38+00:00 Summary: Fixes to tool_list.py for legacy configurations and modified tool confs. Now uses roughly the same order of precedence as Galaxy proper's config. Affected #: 1 file diff -r a0880211749b1f65c4fa78f9c121fa2234decc67 -r f3284eb7ec210d50a3e9f2c0d393cffcb24894da tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -4,8 +4,15 @@ #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) -if not os.path.isfile(tool_conf_file): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', None ) + +if tool_conf_file is None: + for possible_tool_file in [ 'config/tool_conf.xml', 'tool_conf.xml', 'config/tool_conf.xml.sample' ]: + tool_conf_file = possible_tool_file + if os.path.isfile( possible_tool_file ): + break + +if tool_conf_file is None or not os.path.isfile(tool_conf_file): sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) sys.exit(1) https://bitbucket.org/galaxy/galaxy-central/commits/1db1d66229db/ Changeset: 1db1d66229db User: jmchilton Date: 2014-09-25 13:03:21+00:00 Summary: Merge latest next-stable. Affected #: 1 file diff -r bcd98385d0af97c1dd5d4ba7944da49ff28158e1 -r 1db1d66229db79f633f70b6f5b52d339cdb2dbb4 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -4,8 +4,15 @@ #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) -if not os.path.isfile(tool_conf_file): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', None ) + +if tool_conf_file is None: + for possible_tool_file in [ 'config/tool_conf.xml', 'tool_conf.xml', 'config/tool_conf.xml.sample' ]: + tool_conf_file = possible_tool_file + if os.path.isfile( possible_tool_file ): + break + +if tool_conf_file is None or not os.path.isfile(tool_conf_file): sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) sys.exit(1) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: saketkc: Update tool_list to reflect recent change in use of envirnoment variables
by commits-noreply＠bitbucket.org 25 Sep '14

25 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bcd98385d0af/ Changeset: bcd98385d0af User: saketkc Date: 2014-09-25 06:10:51+00:00 Summary: Update tool_list to reflect recent change in use of envirnoment variables tool_list.py now makese use of GALAXY_TEST_TOOL_CONF and exits throwing an appropriate error Affected #: 1 file diff -r a3d10d4db962d762d045bf3e46163508d3572e95 -r bcd98385d0af97c1dd5d4ba7944da49ff28158e1 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -1,9 +1,15 @@ -import os,sys +import os +import sys #--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml", "r"): +tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'config/tool_conf.xml' ) +if not os.path.isfile(tool_conf_file): + sys.stderr.write( "Tool config file not found: {}\n".format(tool_conf_file) ) + sys.exit(1) + +for line in open(tool_conf_file, "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Fix datatype mapping, provide data mapping through api
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3d10d4db962/ Changeset: a3d10d4db962 User: guerler Date: 2014-09-25 01:13:45+00:00 Summary: ToolForm: Fix datatype mapping, provide data mapping through api Affected #: 7 files diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 client/galaxy/scripts/mvc/tools/tools-datasets.js --- a/client/galaxy/scripts/mvc/tools/tools-datasets.js +++ b/client/galaxy/scripts/mvc/tools/tools-datasets.js @@ -1,38 +1,58 @@ -define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){ +define([ 'mvc/history/history-contents', 'utils/utils' ], function( HistoryContents, Utils ){ return Backbone.Model.extend({ // initialize initialize: function(options) { // create history contents container - this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({}); + this.currHistoryContents = new HistoryContents.HistoryContents({}); // identify current history id this.currHistoryContents.historyId = options.history_id; - // make request + // prepare datatype structure + this.typedict = {}; + + // link this var self = this; - var xhr = this.currHistoryContents.fetchAllDetails() - .done( function(){ - // log request success - console.debug('tools-datasets::initialize() - Completed.'); + + // request datatypes + Utils.get(galaxy_config.root + 'api/datatypes/mapping', + // success + function(typedict) { + // backup datatype dictionary + self.typedict = typedict; - // callback - options.success && options.success(); - }) - .fail( function(){ + // make request + var xhr = self.currHistoryContents.fetchAllDetails() + .done( function(){ + // log request success + console.debug('tools-datasets::initialize() - Completed.'); + + // callback + options.success && options.success(); + }) + .fail( function(){ + // log request failure + console.debug('tools-datasets::initialize() - Ajax request for history datasets failed.'); + }); + }, + // error + function(response) { // log request failure - console.debug('tools-datasets::initialize() - Ajax request failed.'); - }); + console.debug('tools-datasets::initialize() - Ajax request for datatype dictionary failed.'); + } + ); }, /** Filters datasets by data type. */ filterType: function(options) { options = options || {}; + var self = this; return this.currHistoryContents.filter(function(content){ // match datatypes var found = false; for (var i in options.data_types) { - if (content.get('data_type').indexOf(options.data_types[i]) != -1) { + if (self._matchType(content.get('data_type'), options.data_types[i])) { found = true; break; } @@ -48,6 +68,26 @@ */ filter: function(filter_id) { return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); + }, + + /** Check if datatypes match + */ + _matchType: function(reference, target) { + // check if target class is available + var target_class = this.typedict.ext_to_class_name[target]; + if (!target_class) { + console.debug('tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.'); + return true; + } + + // check reference group + var reference_group = this.typedict.class_to_classes[reference]; + if (reference_group[target_class]) { + return true; + } + + // classes do not match + return false; } }); }); \ No newline at end of file diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 lib/galaxy/webapps/galaxy/api/datatypes.py --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -5,6 +5,7 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController from galaxy.util import asbool +from galaxy.datatypes.data import Data import logging log = logging.getLogger( __name__ ) @@ -43,6 +44,37 @@ return { 'error': str( exception ) } @web.expose_api_anonymous + def mapping( self, trans ): + ''' + GET /api/datatypes/mapping + Return a dictionary of class to class mappings. + ''' + try: + ext_to_class_name = dict() + classes = [] + for k, v in trans.app.datatypes_registry.datatypes_by_extension.iteritems(): + c = v.__class__ + ext_to_class_name[k] = c.__module__ + "." + c.__name__ + classes.append( c ) + class_to_classes = dict() + + def visit_bases( types, cls ): + for base in cls.__bases__: + if issubclass( base, Data ): + types.add( base.__module__ + "." + base.__name__ ) + visit_bases( types, base ) + for c in classes: + n = c.__module__ + "." + c.__name__ + types = set( [ n ] ) + visit_bases( types, c ) + class_to_classes[ n ] = dict( ( t, True ) for t in types ) + return dict( ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes ) + except Exception, exception: + log.error( 'could not get datatype mapping: %s', str( exception ), exc_info=True ) + trans.response.status = 500 + return { 'error': str( exception ) } + + @web.expose_api_anonymous def sniffers( self, trans, **kwd ): ''' GET /api/datatypes/sniffers diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -192,7 +192,7 @@ webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api', - collection={ 'sniffers': 'GET' }, + collection={ 'sniffers': 'GET', 'mapping' : 'GET' }, parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1179,28 +1179,6 @@ use_panels=True, myexperiment_target_url=myexperiment_target_url ) - @web.json - def get_datatypes( self, trans ): - ext_to_class_name = dict() - classes = [] - for k, v in trans.app.datatypes_registry.datatypes_by_extension.iteritems(): - c = v.__class__ - ext_to_class_name[k] = c.__module__ + "." + c.__name__ - classes.append( c ) - class_to_classes = dict() - - def visit_bases( types, cls ): - for base in cls.__bases__: - if issubclass( base, Data ): - types.add( base.__module__ + "." + base.__name__ ) - visit_bases( types, base ) - for c in classes: - n = c.__module__ + "." + c.__name__ - types = set( [ n ] ) - visit_bases( types, c ) - class_to_classes[ n ] = dict( ( t, True ) for t in types ) - return dict( ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes ) - @web.expose def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None ): user = trans.get_user() diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 static/scripts/mvc/tools/tools-datasets.js --- a/static/scripts/mvc/tools/tools-datasets.js +++ b/static/scripts/mvc/tools/tools-datasets.js @@ -1,38 +1,58 @@ -define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){ +define([ 'mvc/history/history-contents', 'utils/utils' ], function( HistoryContents, Utils ){ return Backbone.Model.extend({ // initialize initialize: function(options) { // create history contents container - this.currHistoryContents = new HISTORY_CONTENTS.HistoryContents({}); + this.currHistoryContents = new HistoryContents.HistoryContents({}); // identify current history id this.currHistoryContents.historyId = options.history_id; - // make request + // prepare datatype structure + this.typedict = {}; + + // link this var self = this; - var xhr = this.currHistoryContents.fetchAllDetails() - .done( function(){ - // log request success - console.debug('tools-datasets::initialize() - Completed.'); + + // request datatypes + Utils.get(galaxy_config.root + 'api/datatypes/mapping', + // success + function(typedict) { + // backup datatype dictionary + self.typedict = typedict; - // callback - options.success && options.success(); - }) - .fail( function(){ + // make request + var xhr = self.currHistoryContents.fetchAllDetails() + .done( function(){ + // log request success + console.debug('tools-datasets::initialize() - Completed.'); + + // callback + options.success && options.success(); + }) + .fail( function(){ + // log request failure + console.debug('tools-datasets::initialize() - Ajax request for history datasets failed.'); + }); + }, + // error + function(response) { // log request failure - console.debug('tools-datasets::initialize() - Ajax request failed.'); - }); + console.debug('tools-datasets::initialize() - Ajax request for datatype dictionary failed.'); + } + ); }, /** Filters datasets by data type. */ filterType: function(options) { options = options || {}; + var self = this; return this.currHistoryContents.filter(function(content){ // match datatypes var found = false; for (var i in options.data_types) { - if (content.get('data_type').indexOf(options.data_types[i]) != -1) { + if (self._matchType(content.get('data_type'), options.data_types[i])) { found = true; break; } @@ -48,6 +68,26 @@ */ filter: function(filter_id) { return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); + }, + + /** Check if datatypes match + */ + _matchType: function(reference, target) { + // check if target class is available + var target_class = this.typedict.ext_to_class_name[target]; + if (!target_class) { + console.debug('tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.'); + return true; + } + + // check reference group + var reference_group = this.typedict.class_to_classes[reference]; + if (reference_group[target_class]) { + return true; + } + + // classes do not match + return false; } }); }); \ No newline at end of file diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 static/scripts/packed/mvc/tools/tools-datasets.js --- a/static/scripts/packed/mvc/tools/tools-datasets.js +++ b/static/scripts/packed/mvc/tools/tools-datasets.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents"],function(a){return Backbone.Model.extend({initialize:function(c){this.currHistoryContents=new a.HistoryContents({});this.currHistoryContents.historyId=c.history_id;var b=this;var d=this.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");c.success&&c.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request failed.")})},filterType:function(b){b=b||{};return this.currHistoryContents.filter(function(d){var e=false;for(var c in b.data_types){if(d.get("data_type").indexOf(b.data_types[c])!=-1){e=true;break}}return(d.get("history_content_type")===b.content_type||!b.content_type)&&(e||!b.data_types)&&!d.get("deleted")})},filter:function(b){return _.first(this.currHistoryContents.filter(function(c){return c.get("id")===b}))}})}); \ No newline at end of file +define(["mvc/history/history-contents","utils/utils"],function(b,a){return Backbone.Model.extend({initialize:function(d){this.currHistoryContents=new b.HistoryContents({});this.currHistoryContents.historyId=d.history_id;this.typedict={};var c=this;a.get(galaxy_config.root+"api/datatypes/mapping",function(e){c.typedict=e;var f=c.currHistoryContents.fetchAllDetails().done(function(){console.debug("tools-datasets::initialize() - Completed.");d.success&&d.success()}).fail(function(){console.debug("tools-datasets::initialize() - Ajax request for history datasets failed.")})},function(e){console.debug("tools-datasets::initialize() - Ajax request for datatype dictionary failed.")})},filterType:function(d){d=d||{};var c=this;return this.currHistoryContents.filter(function(f){var g=false;for(var e in d.data_types){if(c._matchType(f.get("data_type"),d.data_types[e])){g=true;break}}return(f.get("history_content_type")===d.content_type||!d.content_type)&&(g||!d.data_types)&&!f.get("deleted")})},filter:function(c){return _.first(this.currHistoryContents.filter(function(d){return d.get("id")===c}))},_matchType:function(c,f){var d=this.typedict.ext_to_class_name[f];if(!d){console.debug("tools-datasets::_matchType() - Specific target class unavailable. Accepting all formats.");return true}var e=this.typedict.class_to_classes[c];if(e[d]){return true}return false}})}); \ No newline at end of file diff -r 09aa10faa300c54071abff167f301dade9b76b95 -r a3d10d4db962d762d045bf3e46163508d3572e95 templates/webapps/galaxy/workflow/editor.mako --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -41,7 +41,7 @@ // URLs used by galaxy.workflows.js var tool_search_url = "${h.url_for( controller='root', action='tool_search' )}", - get_datatypes_url = "${h.url_for( controller='workflow', action='get_datatypes' )}", + get_datatypes_url = "${h.url_for( '/api/datatypes/mapping' )}", load_workflow_url = "${h.url_for( controller='workflow', action='load_workflow' )}", run_workflow_url = "${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(stored.id))}", rename_async_url = "${h.url_for( controller='workflow', action='rename_async', id=trans.security.encode_id(stored.id) )}", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Tool API test submitting multiple select checkboxes as a list of values.
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/09aa10faa300/ Changeset: 09aa10faa300 User: jmchilton Date: 2014-09-25 00:08:03+00:00 Summary: Tool API test submitting multiple select checkboxes as a list of values. Run with: ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_multi_select_as_list Affected #: 1 file diff -r 85c30938943db094cd54c3848b8402efb0ffd590 -r 09aa10faa300c54071abff167f301dade9b76b95 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -95,6 +95,17 @@ result_content = self._upload_and_get_content( table ) self.assertEquals( result_content, table ) + @skip_without_tool( "multi_select" ) + def test_multi_select_as_list( self ): + history_id = self.dataset_populator.new_history() + inputs = { + "select_ex": ["--ex1", "ex2"], + } + response = self._run( "multi_select", history_id, inputs, assert_ok=True ) + output = response[ "outputs" ][ 0 ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output ) + assert output1_content == "--ex1,ex2" + @skip_without_tool( "cat1" ) def test_run_cat1( self ): # Run simple non-upload tool with an input data parameter. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: scripts/common_startup.sh executes fetch_eggs.py correctly.
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/85c30938943d/ Changeset: 85c30938943d User: davebgx Date: 2014-09-24 20:54:53+00:00 Summary: scripts/common_startup.sh executes fetch_eggs.py correctly. Affected #: 1 file diff -r 583d9ba9c4f9673c42f4378829b741845e95f1c0 -r 85c30938943db094cd54c3848b8402efb0ffd590 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -126,5 +126,3 @@ echo "Appending tool-data/shared/ucsc/builds.txt.buildbot to tool-data/shared/ucsc/builds.txt" cat tool-data/shared/ucsc/builds.txt.buildbot >> tool-data/shared/ucsc/builds.txt - -python ./scripts/fetch_eggs.py all Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/usegalaxy-playbook] b313e0: Update Pulsar's Galaxy clone at the same time as G...
by GitHub 24 Sep '14

24 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b313e093118a58233c2b15eaab5b3aa8fff36d26 https://github.com/galaxyproject/usegalaxy-playbook/commit/b313e093118a5823… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M galaxy.yml Log Message: ----------- Update Pulsar's Galaxy clone at the same time as Galaxy so I stop forgetting to do it as a second step.

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[galaxyproject/usegalaxy-playbook] 716cc2: Update Main.
by GitHub 24 Sep '14

24 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 716cc2b4d668f6c24bf75790c8681705441156e2 https://github.com/galaxyproject/usegalaxy-playbook/commit/716cc2b4d668f6c2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main.

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