January 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: carlfeberhard: History panel: fix positioning of title when both editing title and having search bar open; UI: add dropDownSelect and FilterControl components
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef98f48690fc/ Changeset: ef98f48690fc User: carlfeberhard Date: 2014-01-07 19:45:24 Summary: History panel: fix positioning of title when both editing title and having search bar open; UI: add dropDownSelect and FilterControl components Affected #: 13 files diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -980,8 +980,9 @@ * clicking the clear button will clear the search * uses searchInput in ui.js */ - renderSearchControls : function( $where ){ - var panel = this; + setUpSearchInput : function( $where ){ + var panel = this, + inputSelector = '.history-search-input'; function onSearch( searchFor ){ //console.debug( 'onSearch', searchFor, panel ); @@ -996,10 +997,10 @@ onSearch( searchFor ); return; } - panel.$el.find( '.history-search-controls' ).searchInput( 'toggle-loading' ); + panel.$el.find( inputSelector ).searchInput( 'toggle-loading' ); panel.model.hdas.fetchAllDetails({ silent: true }) .always( function(){ - panel.$el.find( '.history-search-controls' ).searchInput( 'toggle-loading' ); + panel.$el.find( inputSelector ).searchInput( 'toggle-loading' ); }) .done( function(){ onSearch( searchFor ); @@ -1012,7 +1013,7 @@ panel.trigger( 'search:clear', panel ); panel.renderHdas(); } - return $where.searchInput({ + $where.searchInput({ initialVal : panel.searchFor, name : 'history-search', placeholder : 'search datasets', @@ -1021,18 +1022,25 @@ onsearch : onSearch, onclear : onSearchClear }); + return $where; }, //TODO: to hidden/shown plugin showSearchControls : function( speed ){ speed = ( speed === undefined )?( this.fxSpeed ):( speed ); var panel = this, - $searchControls = this.$el.find( '.history-search-controls' ); + $searchControls = this.$el.find( '.history-search-controls' ), + $input = $searchControls.find( '.history-search-input' ); // if it hasn't been rendered - do it now - if( !$searchControls.children().size() ){ - $searchControls = this.renderSearchControls( $searchControls ).hide(); + if( !$input.children().size() ){ + this.setUpSearchInput( $input ); + //$searchControls.append( faIconButton({ + // title : _l( 'More search options' ), + // classes : 'history-search-advanced', + // faIcon : 'fa-ellipsis-horizontal' + //}) ); } // then slide open, focusing on the input, and persisting the setting when it's done - $searchControls.show( speed, function(){ + $searchControls.slideDown( speed, function(){ $( this ).find( 'input' ).focus(); panel.preferences.set( 'searching', true ); }); @@ -1040,7 +1048,7 @@ hideSearchControls : function(){ speed = ( speed === undefined )?( this.fxSpeed ):( speed ); var panel = this; - this.$el.find( '.history-search-controls' ).hide( speed, function(){ + this.$el.find( '.history-search-controls' ).slideUp( speed, function(){ panel.preferences.set( 'searching', false ); }); }, diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -637,7 +637,7 @@ // initial render if( jQuery.type( options ) === 'object' ){ - options = jQuery.extend( true, defaults, options ); + options = jQuery.extend( true, {}, defaults, options ); } //NOTE: prepended return $parentNode.addClass( 'search-input' ).prepend([ $input(), $clearBtn(), $loadingIndicator() ]); @@ -881,3 +881,200 @@ }; return self; } + + +//============================================================================== +/** + * Template function that produces a bootstrap dropdown to replace the + * vanilla HTML select input. Pass in an array of options and an initial selection: + * $( '.my-div' ).append( dropDownSelect( [ 'option1', 'option2' ], 'option2' ); + * + * When the user changes the selected option a 'change.dropdown-select' event will + * fire with both the jq event and the new selection text as arguments. + * + * Get the currently selected choice using: + * var userChoice = $( '.my-div .dropdown-select .dropdown-select-selected' ).text(); + * + */ +function dropDownSelect( options, selected ){ + // replacement for vanilla select element using bootstrap dropdowns instead + selected = selected || (( !_.isEmpty( options ) )?( options[0] ):( '' )); + var $select = $([ + '<div class="dropdown-select btn-group">', + '<button type="button" class="btn btn-default">', + '<span class="dropdown-select-selected">' + selected + '</span>', + '</button>', + '</div>' + ].join( '\n' )); + + // if there's only one option, do not style/create as buttons, dropdown - use simple span + // otherwise, a dropdown displaying the current selection + if( options && options.length > 1 ){ + $select.find( 'button' ) + .addClass( 'dropdown-toggle' ).attr( 'data-toggle', 'dropdown' ) + .append( ' <span class="caret"></span>' ); + $select.append([ + '<ul class="dropdown-menu" role="menu">', + _.map( options, function( option ){ + return [ + '<li><a href="javascript:void(0)">', option, '</a></li>' + ].join( '' ); + }).join( '\n' ), + '</ul>' + ].join( '\n' )); + } + + // trigger 'change.dropdown-select' when a new selection is made using the dropdown + function selectThis( event ){ + var $this = $( this ), + $select = $this.parents( '.dropdown-select' ), + newSelection = $this.text(); + $select.find( '.dropdown-select-selected' ).text( newSelection ); + $select.trigger( 'change.dropdown-select', newSelection ); + } + + $select.find( 'a' ).click( selectThis ); + return $select; +} + + +//============================================================================== +(function(){ + /** + * Creates a three part bootstrap button group (key, op, value) meant to + * allow the user control of filters (e.g. { key: 'name', op: 'contains', value: 'my_history' }) + * + * Each field uses a dropDownSelect (from ui.js) to allow selection + * (with the 'value' field appearing as an input when set to do so). + * + * Any change or update in any of the fields will trigger a 'change.filter-control' + * event which will be passed an object containing those fields (as the example above). + * + * Pass in an array of possible filter objects to control what the user can select. + * Each filter object should have: + * key : generally the attribute name on which to filter something + * ops : an array of 1 or more filter operations (e.g. [ 'is', '<', 'contains', '!=' ]) + * values (optional) : an array of possible values for the filter (e.g. [ 'true', 'false' ]) + * @example: + * $( '.my-div' ).filterControl({ + * filters : [ + * { key: 'name', ops: [ 'is exactly', 'contains' ] } + * { key: 'deleted', ops: [ 'is' ], values: [ 'true', 'false' ] } + * ] + * }); + * // after initialization, you can prog. get the current value using: + * $( '.my-div' ).filterControl( 'val' ) + * + */ + function FilterControl( element, options ){ + return this.init( element, options ); + } + /** the data key that this object will be stored under in the DOM element */ + FilterControl.prototype.DATA_KEY = 'filter-control'; + + /** parses options, sets up instance vars, and does initial render */ + FilterControl.prototype.init = function _init( element, options ){ + options = options || { filters: [] }; + this.$element = $( element ).addClass( 'filter-control btn-group' ); + this.options = jQuery.extend( true, {}, this.defaults, options ); + + this.currFilter = this.options.filters[0]; + return this.render(); + }; + + /** render (or re-render) the controls on the element */ + FilterControl.prototype.render = function _render(){ + this.$element.empty() + .append([ this._renderKeySelect(), this._renderOpSelect(), this._renderValueInput() ]); + return this; + }; + + /** render the key dropDownSelect, bind a change event to it, and return it */ + FilterControl.prototype._renderKeySelect = function __renderKeySelect(){ + var filterControl = this; + var keys = this.options.filters.map( function( filter ){ + return filter.key; + }); + this.$keySelect = dropDownSelect( keys, this.currFilter.key ) + .addClass( 'filter-control-key' ) + .on( 'change.dropdown-select', function( event, selection ){ + filterControl.currFilter = _.findWhere( filterControl.options.filters, { key: selection }); + // when the filter/key changes, re-render the control entirely + filterControl.render()._triggerChange(); + }); + return this.$keySelect; + }; + + /** render the op dropDownSelect, bind a change event to it, and return it */ + FilterControl.prototype._renderOpSelect = function __renderOpSelect(){ + var filterControl = this, + ops = this.currFilter.ops; + //TODO: search for currOp in avail. ops: use that for selected if there; otherwise: first op + this.$opSelect = dropDownSelect( ops, ops[0] ) + .addClass( 'filter-control-op' ) + .on( 'change.dropdown-select', function( event, selection ){ + filterControl._triggerChange(); + }); + return this.$opSelect; + }; + + /** render the value control, bind a change event to it, and return it */ + FilterControl.prototype._renderValueInput = function __renderValueInput(){ + var filterControl = this; + // if a values attribute is prov. on the filter - make this a dropdown; otherwise, use an input + if( this.currFilter.values ){ + this.$valueSelect = dropDownSelect( this.currFilter.values, this.currFilter.values[0] ) + .on( 'change.dropdown-select', function( event, selection ){ + filterControl._triggerChange(); + }); + } else { + //TODO: allow setting a value type (mainly for which html5 input to use: range, number, etc.) + this.$valueSelect = $( '<input/>' ).addClass( 'form-control' ) + .on( 'change', function( event, value ){ + filterControl._triggerChange(); + }); + } + this.$valueSelect.addClass( 'filter-control-value' ); + return this.$valueSelect; + }; + + /** return the current state/setting for the filter as a three key object: key, op, value */ + FilterControl.prototype.val = function _val(){ + var key = this.$element.find( '.filter-control-key .dropdown-select-selected' ).text(), + op = this.$element.find( '.filter-control-op .dropdown-select-selected' ).text(), + // handle either a dropdown or plain input + $value = this.$element.find( '.filter-control-value' ), + value = ( $value.hasClass( 'dropdown-select' ) )?( $value.find( '.dropdown-select-selected' ).text() ) + :( $value.val() ); + return { key: key, op: op, value: value }; + }; + + // single point of change for change event + FilterControl.prototype._triggerChange = function __triggerChange(){ + this.$element.trigger( 'change.filter-control', this.val() ); + }; + + + // as jq plugin + jQuery.fn.extend({ + filterControl : function $filterControl( options ){ + var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); + return this.map( function(){ + var $this = $( this ), + data = $this.data( FilterControl.prototype.DATA_KEY ); + + if( jQuery.type( options ) === 'object' ){ + data = new FilterControl( $this, options ); + $this.data( FilterControl.prototype.DATA_KEY, data ); + } + if( data && jQuery.type( options ) === 'string' ){ + var fn = data[ options ]; + if( jQuery.type( fn ) === 'function' ){ + return fn.apply( data, nonOptionsArgs ); + } + } + return this; + }); + } + }); +}()); diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(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",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){var m=k.model.get("name");if(l&&l!==m){k.$el.find(".history-name").text(l);k.model.save({name:l}).fail(function(){k.$el.find(".history-name").text(k.model.previous("name"))})}else{k.$el.find(".history-name").text(m)}}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(k){var l=this;function n(o){l.searchFor=o;l.filters=[function(p){return p.matchesAll(l.searchFor)}];l.trigger("search:searching",o,l);l.renderHdas()}function j(o){if(l.model.hdas.haveDetails()){n(o);return}l.$el.find(".history-search-controls").searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){n(o)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}return k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m})},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls");if(!k.children().size()){k=this.renderSearchControls(k).hide()}k.show(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").hide(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},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(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(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",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){var m=k.model.get("name");if(l&&l!==m){k.$el.find(".history-name").text(l);k.model.save({name:l}).fail(function(){k.$el.find(".history-name").text(k.model.previous("name"))})}else{k.$el.find(".history-name").text(m)}}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},setUpSearchInput:function(k){var l=this,o=".history-search-input";function n(p){l.searchFor=p;l.filters=[function(q){return q.matchesAll(l.searchFor)}];l.trigger("search:searching",p,l);l.renderHdas()}function j(p){if(l.model.hdas.haveDetails()){n(p);return}l.$el.find(o).searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(o).searchInput("toggle-loading")}).done(function(){n(p)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m});return k},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls"),m=k.find(".history-search-input");if(!m.children().size()){this.setUpSearchInput(m)}k.slideDown(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").slideUp(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},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(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d 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.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=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};(function(){function a(j,p){var d=27,m=13,c=$(j),e=true,g={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(q){},minSearchLen:0,escWillClear:true,oninit:function(){}};function i(q){var r=$(this).parent().children("input");r.val("");r.trigger("clear:searchInput");p.onclear()}function o(r,q){$(this).trigger("search:searchInput",q);if(typeof p.onfirstsearch==="function"&&e){e=false;p.onfirstsearch(q)}else{p.onsearch(q)}}function f(){return['<input type="text" name="',p.name,'" placeholder="',p.placeholder,'" ','class="search-query ',p.classes,'" ',"/>"].join("")}function l(){return $(f()).focus(function(q){$(this).select()}).keyup(function(r){if(r.which===d&&p.escWillClear){i.call(this,r)}else{var q=$(this).val();if((r.which===m)||(p.minSearchLen&&q.length>=p.minSearchLen)){o.call(this,r,q)}else{if(!q.length){i.call(this,r)}}}}).val(p.initialVal)}function k(){return $(['<span class="search-clear fa fa-times-circle" ','title="',_l("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(q){i.call(this,q)})}function n(){return $(['<span class="search-loading fa fa-spinner fa-spin" ','title="',_l("loading..."),'"></span>'].join("")).hide().tooltip({placement:"bottom"})}function h(){c.find(".search-loading").toggle();c.find(".search-clear").toggle()}if(jQuery.type(p)==="string"){if(p==="toggle-loading"){h()}return c}if(jQuery.type(p)==="object"){p=jQuery.extend(true,g,p)}return c.addClass("search-input").prepend([l(),k(),n()])}jQuery.fn.extend({searchInput:function b(c){return this.each(function(){return a(this,c)})}})}());(function(){function b(m,l){this.currModeIndex=0;return this.init(m,l)}b.prototype.DATA_KEY="mode-button";b.prototype.defaults={modes:[{mode:"default"}]};b.prototype.init=function f(m,l){l=l||{};this.$element=$(m);this.options=jQuery.extend(true,{},this.defaults,l);var o=this;this.$element.click(function n(p){o.callModeFn();o._incModeIndex();$(this).html(o.options.modes[o.currModeIndex].html)});this.currModeIndex=0;if(this.options.initialMode){this.currModeIndex=this._getModeIndex(this.options.initialMode)}return this};b.prototype._getModeIndex=function j(l){for(var m=0;m<this.options.modes.length;m+=1){if(this.options.modes[m].mode===l){return m}}throw new Error("mode not found: "+l)};b.prototype.getCurrMode=function a(){return this.options.modes[this.currModeIndex]};b.prototype.getMode=function g(l){if(!l){return this.getCurrMode()}return this.options.modes[(this._getModeIndex(l))]};b.prototype.hasMode=function k(l){return !!this.getMode(l)};b.prototype.currentMode=function e(){return this.options.modes[this.currModeIndex]};b.prototype.setMode=function c(m){var l=this.getMode(m);this.$element.html(l.html||null);return this};b.prototype._incModeIndex=function d(){this.currModeIndex+=1;if(this.currModeIndex>=this.options.modes.length){this.currModeIndex=0}return this};b.prototype.callModeFn=function h(l){var m=this.getMode(l).onclick;if(m&&jQuery.type(m==="function")){return m.call(this)}return undefined};jQuery.fn.extend({modeButton:function i(m){var l=jQuery.makeArray(arguments).slice(1);return this.map(function(){var p=$(this),o=p.data("mode-button");if(jQuery.type(m)==="object"){o=new b(p,m);p.data("mode-button",o)}else{if(o&&jQuery.type(m)==="string"){var n=o[m];if(jQuery.type(n)==="function"){return n.apply(o,l)}}else{if(o){return o}}}return this})}})}());function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(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";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.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$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 $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<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.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 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Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n \n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,t),data:t});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(3,m,t),data:t});if(i||i===0){q+=i}q+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(5,k,t),data:t});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(7,j,t),data:t};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(9,g,t),data:t};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(11,s,t),data:t};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})(); \ No newline at end of file diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(g,r,p,l,x){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);x=x||{};var q="",i,f,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(B,A){var y="",z;y+='\n <div class="history-name">\n ';if(z=p.name){z=z.call(B,{hash:{},data:A})}else{z=B.name;z=typeof z===e?z.apply(B):z}y+=d(z)+"\n </div>\n ";return y}function m(B,A){var y="",z;y+='\n <div class="history-size">';if(z=p.nice_size){z=z.call(B,{hash:{},data:A})}else{z=B.nice_size;z=typeof z===e?z.apply(B):z}y+=d(z)+"</div>\n ";return y}function k(C,B){var y="",A,z;y+='\n <div class="warningmessagesmall"><strong>\n ';z={hash:{},inverse:o.noop,fn:o.program(6,j,B),data:B};if(A=p.local){A=A.call(C,z)}else{A=C.local;A=typeof A===e?A.apply(C):A}if(!p.local){A=c.call(C,A,z)}if(A||A===0){y+=A}y+="\n </strong></div>\n ";return y}function j(z,y){return"You are currently viewing a deleted history!"}function h(B,A){var y="",z;y+='\n \n <div class="';if(z=p.status){z=z.call(B,{hash:{},data:A})}else{z=B.status;z=typeof z===e?z.apply(B):z}y+=d(z)+'message">';if(z=p.message){z=z.call(B,{hash:{},data:A})}else{z=B.message;z=typeof z===e?z.apply(B):z}y+=d(z)+"</div>\n ";return y}function w(z,y){return"You are over your disk quota"}function v(z,y){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function u(z,y){return"Select all"}function t(z,y){return"For all selected"}function s(z,y){return"Your history is empty. Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n <div class="history-search-controls"></div>\n\n <div class="history-title">\n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,x),data:x});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(3,m,x),data:x});if(i||i===0){q+=i}q+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n ';i=p["if"].call(r,r.deleted,{hash:{},inverse:o.noop,fn:o.program(5,k,x),data:x});if(i||i===0){q+=i}q+='\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(8,h,x),data:x});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(10,w,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(12,v,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="history-dataset-actions">\n <button class="history-select-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:o.noop,fn:o.program(14,u,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='</button>\n <button class="history-dataset-action-popup-btn btn btn-default"\n >';f={hash:{},inverse:o.noop,fn:o.program(16,t,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='...</button>\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(18,s,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(g,r,p,l,x){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);x=x||{};var q="",i,f,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(B,A){var y="",z;y+='\n <div class="history-name">\n ';if(z=p.name){z=z.call(B,{hash:{},data:A})}else{z=B.name;z=typeof z===e?z.apply(B):z}y+=d(z)+"\n </div>\n ";return y}function m(B,A){var y="",z;y+='\n <div class="history-size">';if(z=p.nice_size){z=z.call(B,{hash:{},data:A})}else{z=B.nice_size;z=typeof z===e?z.apply(B):z}y+=d(z)+"</div>\n ";return y}function k(C,B){var y="",A,z;y+='\n <div class="warningmessagesmall"><strong>\n ';z={hash:{},inverse:o.noop,fn:o.program(6,j,B),data:B};if(A=p.local){A=A.call(C,z)}else{A=C.local;A=typeof A===e?A.apply(C):A}if(!p.local){A=c.call(C,A,z)}if(A||A===0){y+=A}y+="\n </strong></div>\n ";return y}function j(z,y){return"You are currently viewing a deleted history!"}function h(B,A){var y="",z;y+='\n \n <div class="';if(z=p.status){z=z.call(B,{hash:{},data:A})}else{z=B.status;z=typeof z===e?z.apply(B):z}y+=d(z)+'message">';if(z=p.message){z=z.call(B,{hash:{},data:A})}else{z=B.message;z=typeof z===e?z.apply(B):z}y+=d(z)+"</div>\n ";return y}function w(z,y){return"You are over your disk quota"}function v(z,y){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function u(z,y){return"Select all"}function t(z,y){return"For all selected"}function s(z,y){return"Your history is empty. Click 'Get Data' on the left pane to start"}q+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n ';i=p["if"].call(r,r.name,{hash:{},inverse:o.noop,fn:o.program(1,n,x),data:x});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=p["if"].call(r,r.nice_size,{hash:{},inverse:o.noop,fn:o.program(3,m,x),data:x});if(i||i===0){q+=i}q+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n ';i=p["if"].call(r,r.deleted,{hash:{},inverse:o.noop,fn:o.program(5,k,x),data:x});if(i||i===0){q+=i}q+='\n\n <div class="message-container">\n ';i=p["if"].call(r,r.message,{hash:{},inverse:o.noop,fn:o.program(8,h,x),data:x});if(i||i===0){q+=i}q+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:o.noop,fn:o.program(10,w,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+=".\n ";f={hash:{},inverse:o.noop,fn:o.program(12,v,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="history-dataset-actions">\n <button class="history-select-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:o.noop,fn:o.program(14,u,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='</button>\n <button class="history-dataset-action-popup-btn btn btn-default"\n >';f={hash:{},inverse:o.noop,fn:o.program(16,t,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+='...</button>\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:o.noop,fn:o.program(18,s,x),data:x};if(i=p.local){i=i.call(r,f)}else{i=r.local;i=typeof i===e?i.apply(r):i}if(!p.local){i=c.call(r,i,f)}if(i||i===0){q+=i}q+="\n </div>";return q})})(); \ No newline at end of file diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -363,7 +363,103 @@ return "Your history is empty. Click 'Get Data' on the left pane to start"; } - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\"></div>\n\n <div class=\"history-title\">\n " + buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " + + "\n "; + stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; + stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n <div class=\"message-container\">\n "; + stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; + options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ".\n "; + options = {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ".\n </div>\n\n </div>" + + "\n\n " + + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; + options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>"; + return buffer; + }); +})();(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-historyPanel-anon'] = template(function (Handlebars,depth0,helpers,partials,data) { + this.compilerInfo = [4,'>= 1.0.0']; +helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; + var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + +function program1(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <div class=\"history-name\">\n "; + if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "\n </div>\n "; + return buffer; + } + +function program3(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <div class=\"history-size\">"; + if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</div>\n "; + return buffer; + } + +function program5(depth0,data) { + + var buffer = "", stack1; + buffer += "\n " + + "\n <div class=\""; + if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "message\">"; + if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</div>\n "; + return buffer; + } + +function program7(depth0,data) { + + + return "You are over your disk quota"; + } + +function program9(depth0,data) { + + + return "Tool execution is on hold until your disk usage drops below your allocated quota"; + } + +function program11(depth0,data) { + + + return "Your history is empty. Click 'Get Data' on the left pane to start"; + } + + buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " + "\n "; stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } @@ -489,7 +585,147 @@ return "Your history is empty. Click 'Get Data' on the left pane to start"; } - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\"></div>\n\n <div class=\"history-title\">\n "; + buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n "; + stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; + stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; + stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n <div class=\"message-container\">\n "; + stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; + options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ".\n "; + options = {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; + options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</button>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; + options = {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "...</button>\n </div>\n\n </div>" + + "\n\n " + + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; + options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>"; + return buffer; + }); +})();(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { + this.compilerInfo = [4,'>= 1.0.0']; +helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; + var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + +function program1(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <div class=\"history-name\">\n "; + if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "\n </div>\n "; + return buffer; + } + +function program3(depth0,data) { + + var buffer = "", stack1; + buffer += "\n <div class=\"history-size\">"; + if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</div>\n "; + return buffer; + } + +function program5(depth0,data) { + + var buffer = "", stack1, options; + buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; + options = {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}; + if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </strong></div>\n "; + return buffer; + } +function program6(depth0,data) { + + + return "You are currently viewing a deleted history!"; + } + +function program8(depth0,data) { + + var buffer = "", stack1; + buffer += "\n " + + "\n <div class=\""; + if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "message\">"; + if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } + else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } + buffer += escapeExpression(stack1) + + "</div>\n "; + return buffer; + } + +function program10(depth0,data) { + + + return "You are over your disk quota"; + } + +function program12(depth0,data) { + + + return "Tool execution is on hold until your disk usage drops below your allocated quota"; + } + +function program14(depth0,data) { + + + return "Select all"; + } + +function program16(depth0,data) { + + + return "For all selected"; + } + +function program18(depth0,data) { + + + return "Your history is empty. Click 'Get Data' on the left pane to start"; + } + + buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n "; stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/templates/compiled/template-history-historyPanel-anon.js --- a/static/scripts/templates/compiled/template-history-historyPanel-anon.js +++ b/static/scripts/templates/compiled/template-history-historyPanel-anon.js @@ -61,7 +61,7 @@ return "Your history is empty. Click 'Get Data' on the left pane to start"; } - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\"></div>\n\n <div class=\"history-title\">\n " + buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " + "\n "; stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -91,7 +91,7 @@ return "Your history is empty. Click 'Get Data' on the left pane to start"; } - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\"></div>\n\n <div class=\"history-title\">\n "; + buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n "; stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -2,7 +2,9 @@ <script type="text/template" class="template-history" id="template-history-historyPanel"><div class="history-controls"> - <div class="history-search-controls"></div> + <div class="history-search-controls"> + <div class="history-search-input"></div> + </div><div class="history-title"> {{#if name }} @@ -63,7 +65,9 @@ <script type="text/template" class="template-history" id="template-history-historyPanel-anon"><div class="history-controls"> - <div class="history-search-controls"></div> + <div class="history-search-controls"> + <div class="history-search-input"></div> + </div><div class="history-title"> {{! wouldn't this always be 'unnamed history'? }} diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1564,7 +1564,7 @@ .icon-btn:hover{background-color:white;color:maroon} .icon-btn.disabled{background-color:transparent;color:rgba(0,0,0,0.05)} .search-input .search-query{width:100%;padding-right:24px} -.search-input .search-clear,.search-input .search-loading{position:relative;float:right;left:-4px;top:-23px;font-size:1.4em;line-height:23px;color:grey} +.search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} .search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:20px;width:20px;text-align:center;line-height:17px;font-size:1.2em;padding:0px} .history-panel [class$="messagesmall"]{margin:0px} diff -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f -r ef98f48690fc9ce5d1b8f662a2e91f384514013d static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -69,9 +69,12 @@ .search-loading { // it places the icons on the right of the bar (and puts the lotion on its skin) position : relative; + display : inline-block; + float : right; - left : -4px; - top : -23px; + margin-top : -23px; + margin-right : 4px; + font-size : 1.4em; line-height : 23px; color : grey; @@ -123,6 +126,13 @@ padding: 0px; .history-search-controls { + .history-search-input { + //margin-right: 22px; + } + //.history-search-advanced { + // margin-top : -21px; + // float : right; + //} display: none; padding: 0px 0px 8px 0px; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Restrict population of repository dependency installation containers during the tool shed's install and test run if they were last populated 12 hours previously or less.
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4c6b4cc9e060/ Changeset: 4c6b4cc9e060 User: greg Date: 2014-01-07 19:15:46 Summary: Restrict population of repository dependency installation containers during the tool shed's install and test run if they were last populated 12 hours previously or less. Affected #: 1 file diff -r 5fbd5656e3dde2ba871f39f01a0841cea656a669 -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -24,6 +24,9 @@ import tool_shed.util.shed_util_common as suc import urllib +from datetime import datetime +from datetime import timedelta + from common import update from galaxy.util import asbool @@ -312,7 +315,7 @@ dependency tree will be inspected. """ log.debug( 'Checking revision %s of repository %s owned by %s for missing repository dependencies.' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.changeset_revision ) ) ) + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) missing_repository_dependencies = repository.missing_repository_dependencies for missing_required_repository in missing_repository_dependencies: log.debug( 'Revision %s of required repository %s owned by %s has status %s.' % \ @@ -331,7 +334,7 @@ dependency tree will be inspected. """ log.debug( 'Checking revision %s of repository %s owned by %s for missing tool dependencies.' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.changeset_revision ) ) ) + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) missing_tool_dependencies = repository.missing_tool_dependencies for missing_tool_dependency in missing_tool_dependencies: log.debug( 'Tool dependency %s version %s has status %s.' % \ @@ -517,6 +520,26 @@ static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), static_robots_txt = os.path.join( static_dir, 'robots.txt' ) ) +def get_time_last_tested( tool_shed_url, encoded_repository_metadata_id ): + """ + Return the datetime value stored in the Tool Shed's repository_metadata.time_last_tested column + via the Tool Shed API. + """ + error_message = '' + parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] + api_url = get_api_url( base=tool_shed_url, parts=parts ) + repository_metadata_dict, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + if isinstance( repository_metadata_dict, dict ): + # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently + # return a list. + time_last_tested = repository_metadata_dict.get( 'time_last_tested', None ) + return time_last_tested, error_message + else: + error_message = 'The url %s returned the invalid repository_metadata_dict %s' % ( str( api_url ), str( repository_metadata_dict ) ) + return None, error_message + def get_tool_test_results_dict( tool_test_results_dicts ): if tool_test_results_dicts: # Inspect the tool_test_results_dict for the last test run to make sure it contains only a test_environment @@ -862,7 +885,7 @@ name = str( repository_dependencies_dict[ 'name' ] ) owner = str( repository_dependencies_dict[ 'owner' ] ) changeset_revision = str( repository_dependencies_dict[ 'changeset_revision' ] ) - log.debug( 'Checking installation containers for revision %s of required repository %s owned by %s' % \ + log.debug( 'Checking installation containers for revision %s of repository dependency %s owned by %s' % \ ( changeset_revision, name, owner ) ) required_repository_metadata_id = repository_dependencies_dict[ 'id' ] # Get the current list of tool_test_results dictionaries associated with the repository_metadata @@ -870,78 +893,92 @@ tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, required_repository_metadata_id ) if error_message: - log.debug( 'Cannot check install container for version %s of repository %s owned by %s ' % \ + log.debug( 'Cannot check install container for version %s of repository dependency %s owned by %s ' % \ ( changeset_revision, name, owner ) ) log.debug( 'due to the following error getting tool_test_results:\n%s' % str( error_message ) ) else: - # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated + # Check the required repository's time_last_tested value to see if its tool_test_results column + # has been updated within the past 12 hours. + twelve_hours_ago = datetime.utcnow() - timedelta( hours=12 ) + time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, repository_metadata_id ) + if time_last_tested is not None and time_last_tested < twelve_hours_ago: + log.debug( 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ + ( changeset_revision, name, owner ) ) + log.debug( 'populated within the past 12 hours (likely in this test run), so skipping this check.' ) + continue + if time_last_tested is None: + log.debug( 'The time_last_tested column value is None for version %s of repository dependency %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + elif time_last_tested < twelve_hours_ago: + log.debug( 'Version %s of repository dependency %s owned by %s was last tested less than 12 hours ago.' % \ + ( changeset_revision, name, owner ) ) + else: + log.debug( 'Version %s of repository dependency %s owned by %s was last tested more than 12 hours ago.' % \ + ( changeset_revision, name, owner ) ) + # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated. if len( tool_test_results_dicts ) == 0: - populated = False tool_test_results_dict = {} else: tool_test_results_dict = tool_test_results_dicts[ 0 ] if len( tool_test_results_dict ) <= 1: - populated = False tool_test_results_dict = tool_test_results_dicts.pop( 0 ) elif len( tool_test_results_dict ) == 2 and \ 'test_environment' in tool_test_results_dict and \ 'missing_test_components' in tool_test_results_dict: - populated = False tool_test_results_dict = tool_test_results_dicts.pop( 0 ) else: - populated = True - if not populated: - # Make sure all expected entries are available in the tool_test_results_dict. - tool_test_results_dict = initialize_tool_tests_results_dict( app, tool_test_results_dict ) - # Get the installed repository record from the Galaxy database. - cleaned_tool_shed_url = clean_tool_shed_url( galaxy_tool_shed_url ) - required_repository = \ - suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, - cleaned_tool_shed_url, - name, - owner, - changeset_revision ) - if required_repository is not None: - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - if required_repository.is_installed: - # The required_repository was successfully installed, so populate the installation - # containers (success and error) for the repository's immediate dependencies. - params, install_and_test_statistics_dict, tool_test_results_dict = \ - populate_dependency_install_containers( app, - required_repository, - repository_identifier_dict, - install_and_test_statistics_dict, - tool_test_results_dict ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('\n=============================================================\n' ) - else: - # The required repository's installation failed. - tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) - params = dict( test_install_error=True, - do_not_test=False ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('\n=============================================================\n' ) + tool_test_results_dict = {} + # Make sure all expected entries are available in the tool_test_results_dict. + tool_test_results_dict = initialize_tool_tests_results_dict( app, tool_test_results_dict ) + # Get the installed repository record from the Galaxy database. + cleaned_tool_shed_url = clean_tool_shed_url( galaxy_tool_shed_url ) + required_repository = \ + suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, + cleaned_tool_shed_url, + name, + owner, + changeset_revision ) + if required_repository is not None: + repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + if required_repository.is_installed: + # The required_repository was successfully installed, so populate the installation + # containers (success and error) for the repository's immediate dependencies. + params, install_and_test_statistics_dict, tool_test_results_dict = \ + populate_dependency_install_containers( app, + required_repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) else: - log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ - ( changeset_revision, name, owner ) ) - log.debug( 'so tool_test_results cannot be saved.' ) - log.debug( 'The attributes used to retrieve the record are:' ) - log.debug( '\ntool_shed: %s name: %s owner: %s changeset_revision: %s' % \ - ( cleaned_tool_shed_url, name, owner, changeset_revision ) ) + # The required repository's installation failed. + tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) + params = dict( test_install_error=True, + do_not_test=False ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) + else: + log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ + ( changeset_revision, name, owner ) ) + log.debug( 'so tool_test_results cannot be saved.' ) + log.debug( 'The attributes used to retrieve the record are:\n' ) + log.debug( 'tool_shed: %s name: %s owner: %s changeset_revision: %s' % \ + ( cleaned_tool_shed_url, name, owner, changeset_revision ) ) def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5fbd5656e3dd/ Changeset: 5fbd5656e3dd User: dannon Date: 2014-01-07 15:47:37 Summary: Update cloudlaunch default AMI Affected #: 2 files diff -r 2f1c111663308e0d8f081c2b443aa39808641046 -r 5fbd5656e3dde2ba871f39f01a0841cea656a669 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -313,7 +313,7 @@ self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Cloud configuration options self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) ) - self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-118bfc78' ) + self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-a7dbf6ce' ) # Galaxy messaging (AMQP) configuration options self.amqp = {} try: diff -r 2f1c111663308e0d8f081c2b443aa39808641046 -r 5fbd5656e3dde2ba871f39f01a0841cea656a669 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -426,7 +426,7 @@ # Cloud Launch #enable_cloud_launch = False -#cloudlaunch_default_ami = ami-118bfc78 +#cloudlaunch_default_ami = ami-a7dbf6ce # -- Advanced proxy features https://bitbucket.org/galaxy/galaxy-central/commits/a0f7e0e5f05a/ Changeset: a0f7e0e5f05a Branch: stable User: dannon Date: 2014-01-07 15:47:37 Summary: Update cloudlaunch default AMI Affected #: 2 files diff -r 27350e3fc09bd36fea964c703b5ea787e2215de4 -r a0f7e0e5f05af4112ded852cf61c138582c99c04 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -299,7 +299,7 @@ self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Cloud configuration options self.enable_cloud_launch = string_as_bool( kwargs.get( 'enable_cloud_launch', False ) ) - self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-118bfc78' ) + self.cloudlaunch_default_ami = kwargs.get( 'cloudlaunch_default_ami', 'ami-a7dbf6ce' ) # Galaxy messaging (AMQP) configuration options self.amqp = {} try: diff -r 27350e3fc09bd36fea964c703b5ea787e2215de4 -r a0f7e0e5f05af4112ded852cf61c138582c99c04 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -419,7 +419,7 @@ # Cloud Launch #enable_cloud_launch = False -#cloudlaunch_default_ami = ami-118bfc78 +#cloudlaunch_default_ami = ami-a7dbf6ce # -- Advanced proxy features 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: greg: Fix for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f1c11166330/ Changeset: 2f1c11166330 User: greg Date: 2014-01-07 15:23:01 Summary: Fix for the tool shed's install and test framework. Affected #: 1 file diff -r 22fb2b5a46ac2fd1a97b6dd50124b29962e2103b -r 2f1c111663308e0d8f081c2b443aa39808641046 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -207,6 +207,23 @@ def shutdown( self ): pass +def clean_tool_shed_url( base_url ): + """Eliminate the protocol from the received base_url and return the possibly altered url.""" + # The tool_shed value stored in the tool_shed_repository record does not include the protocol, but does + # include the port if one exists. + if base_url: + if base_url.find( '://' ) > -1: + try: + protocol, base = base_url.split( '://' ) + except ValueError, e: + # The received base_url must be an invalid url. + log.debug( "Returning unchanged invalid base_url from clean_tool_shed_url: %s" % str( base_url ) ) + return base_url + return base.rstrip( '/' ) + return base_url.rstrip( '/' ) + log.debug( "Returning base_url from clean_tool_shed_url: %s" % str( base_url ) ) + return base_url + def display_repositories_by_owner( repository_dicts ): # Group summary display by repository owner. repository_dicts_by_owner = {} @@ -877,9 +894,10 @@ # Make sure all expected entries are available in the tool_test_results_dict. tool_test_results_dict = initialize_tool_tests_results_dict( app, tool_test_results_dict ) # Get the installed repository record from the Galaxy database. + cleaned_tool_shed_url = clean_tool_shed_url( galaxy_tool_shed_url ) required_repository = \ suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, - galaxy_tool_shed_url, + cleaned_tool_shed_url, name, owner, changeset_revision ) @@ -919,8 +937,11 @@ log.debug('\n=============================================================\n' ) else: log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ - ( changeset_revision, name, owner, str( response_dict ) ) ) + ( changeset_revision, name, owner ) ) log.debug( 'so tool_test_results cannot be saved.' ) + log.debug( 'The attributes used to retrieve the record are:' ) + log.debug( '\ntool_shed: %s name: %s owner: %s changeset_revision: %s' % \ + ( cleaned_tool_shed_url, name, owner, changeset_revision ) ) def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) 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: greg: Handle case where a repository dependency has not yet been created during the current test run in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 07 Jan '14

07 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/22fb2b5a46ac/ Changeset: 22fb2b5a46ac User: greg Date: 2014-01-07 12:56:19 Summary: Handle case where a repository dependency has not yet been created during the current test run in the tool shed's install and test framework. Affected #: 1 file diff -r 19391092ba1b49999eca9ced0ae9864015ea3199 -r 22fb2b5a46ac2fd1a97b6dd50124b29962e2103b test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -883,39 +883,44 @@ name, owner, changeset_revision ) - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - if required_repository.is_installed: - # The required_repository was successfully installed, so populate the installation - # containers (success and error) for the repository's immediate dependencies. - params, install_and_test_statistics_dict, tool_test_results_dict = \ - populate_dependency_install_containers( app, - required_repository, - repository_identifier_dict, - install_and_test_statistics_dict, - tool_test_results_dict ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + if required_repository is not None: + repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + if required_repository.is_installed: + # The required_repository was successfully installed, so populate the installation + # containers (success and error) for the repository's immediate dependencies. + params, install_and_test_statistics_dict, tool_test_results_dict = \ + populate_dependency_install_containers( app, + required_repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) + else: + # The required repository's installation failed. + tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) + params = dict( test_install_error=True, + do_not_test=False ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) + else: + log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('\n=============================================================\n' ) - else: - # The required repository's installation failed. - tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) - params = dict( test_install_error=True, - do_not_test=False ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('\n=============================================================\n' ) + log.debug( 'so tool_test_results cannot be saved.' ) def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) 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: greg: Handle exceptions attempting to retrieve the tool_test_results column from the repository_metadata table in the tool shed.
by commits-noreply＠bitbucket.org 06 Jan '14

06 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/19391092ba1b/ Changeset: 19391092ba1b User: greg Date: 2014-01-07 03:35:57 Summary: Handle exceptions attempting to retrieve the tool_test_results column from the repository_metadata table in the tool shed. Affected #: 1 file diff -r 47e869a73907381c094b691185c88d620a13fa97 -r 19391092ba1b49999eca9ced0ae9864015ea3199 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -532,13 +532,17 @@ error_message = '' parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] api_url = get_api_url( base=tool_shed_url, parts=parts ) - repository_metadata, error_message = json_from_url( api_url ) + repository_metadata_dict, error_message = json_from_url( api_url ) if error_message: return None, error_message - # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently - # return a list. - tool_test_results = listify( repository_metadata.get( 'tool_test_results', [] ) ) - return tool_test_results, error_message + if isinstance( repository_metadata_dict, dict ): + # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently + # return a list. + tool_test_results = listify( repository_metadata_dict.get( 'tool_test_results', [] ) ) + return tool_test_results, error_message + else: + error_message = 'The url %s returned the invalid repository_metadata_dict %s' % ( str( api_url ), str( repository_metadata_dict ) ) + return None, error_message def get_webapp_global_conf(): """Return the global_conf dictionary sent as the first argument to app_factory.""" 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: greg: Always initialize the tool shed install and tes framework's tool_test_results_dict.
by commits-noreply＠bitbucket.org 06 Jan '14

06 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47e869a73907/ Changeset: 47e869a73907 User: greg Date: 2014-01-07 03:13:25 Summary: Always initialize the tool shed install and tes framework's tool_test_results_dict. Affected #: 1 file diff -r 9df289e311209975ab34c288d8229096683af0e0 -r 47e869a73907381c094b691185c88d620a13fa97 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -856,7 +856,7 @@ # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated if len( tool_test_results_dicts ) == 0: populated = False - tool_test_results_dict = initialize_tool_tests_results_dict( app, {} ) + tool_test_results_dict = {} else: tool_test_results_dict = tool_test_results_dicts[ 0 ] if len( tool_test_results_dict ) <= 1: @@ -870,6 +870,8 @@ else: populated = True if not populated: + # Make sure all expected entries are available in the tool_test_results_dict. + tool_test_results_dict = initialize_tool_tests_results_dict( app, tool_test_results_dict ) # Get the installed repository record from the Galaxy database. required_repository = \ suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, 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: greg: Enhance the tool shed's install and test framework to populate and store information about the installation of each repository dependency in addition to the repository itself. This changeset also include miscellaneous typo fixes and code cleanup.
by commits-noreply＠bitbucket.org 06 Jan '14

06 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9df289e31120/ Changeset: 9df289e31120 User: greg Date: 2014-01-06 22:30:27 Summary: Enhance the tool shed's install and test framework to populate and store information about the installation of each repository dependency in addition to the repository itself. This changeset also include miscellaneous typo fixes and code cleanup. Affected #: 11 files diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -279,6 +279,10 @@ def is_deactivated_or_installed( self ): return self.status in [ self.installation_status.DEACTIVATED, self.installation_status.INSTALLED ] + + @property + def is_installed( self ): + return self.status == self.installation_status.INSTALLED @property def is_latest_installable_revision( self ): diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -171,7 +171,7 @@ :param tool_shed_url (required): the base URL of the Tool Shed from which to install the Repository :param name (required): the name of the Repository :param owner (required): the owner of the Repository - :param changset_revision (required): the changset_revision of the RepositoryMetadata object associated with the Repository + :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository :param new_tool_panel_section_label (optional): label of a new section to be added to the Galaxy tool panel in which to load tools contained in the Repository. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string or both must be an empty @@ -372,7 +372,7 @@ :param tool_shed_urls: the base URLs of the Tool Sheds from which to install a specified Repository :param names: the names of the Repositories to be installed :param owners: the owners of the Repositories to be installed - :param changset_revisions: the changset_revisions of each RepositoryMetadata object associated with each Repository to be installed + :param changeset_revisions: the changeset_revisions of each RepositoryMetadata object associated with each Repository to be installed :param new_tool_panel_section_label: optional label of a new section to be added to the Galaxy tool panel in which to load tools contained in the Repository. Either this parameter must be an empty string or the tool_panel_section_id parameter must be an empty string, as both cannot be used. @@ -454,7 +454,7 @@ :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed :param name (required): the name of the Repository :param owner (required): the owner of the Repository - :param changset_revision (required): the changset_revision of the RepositoryMetadata object associated with the Repository + :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository """ # Get the information about the repository to be installed from the payload. tool_shed_url = payload.get( 'tool_shed_url', '' ) diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -60,7 +60,7 @@ :param name: the name of the Repository :param owner: the owner of the Repository - :param changset_revision: the changset_revision of the RepositoryMetadata object associated with the Repository + :param changeset_revision: the changeset_revision of the RepositoryMetadata object associated with the Repository Returns a list of the following dictionaries:: - a dictionary defining the Repository. For example: diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -30,7 +30,7 @@ :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed :param name (required): the name of the Repository :param owner (required): the owner of the Repository - :param changset_revision (required): the changset_revision of the RepositoryMetadata object associated with the Repository + :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository :param export_repository_dependencies (optional): whether to export repository dependencies - defaults to False :param download_dir (optional): the local directory to which to download the archive - defaults to /tmp """ diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1273,8 +1273,8 @@ """Return a tool shed repository database record defined by the id.""" # This method is used only in Galaxy, not the tool shed. return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( trans.install_model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \ - .first() + .filter( trans.install_model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \ + .first() def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): """Return a tool shed repository database record defined by the combination of a tool_shed, repository name, repository owner and current changeet_revision.""" diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -415,10 +415,13 @@ tool_dependency_name=tool_dependency.name, tool_dependency_version=tool_dependency.version ) if remove_installation_path: - # This will be True only in the case where an exception was encountered during the installation process after the installation - # path was created, but before any information was written to the installation log, and the tool dependency status was not - # set to "Installed" or "Error". + # This will be True only in the case where an exception was encountered during the installation process after + # the installation path was created but before any information was written to the installation log and the + # tool dependency status was not set to "Installed" or "Error". if os.path.exists( install_dir ): + log.debug( 'Attempting to remove installation directory %s for version %s of tool dependency %s %s' % \ + ( str( install_dir ), str( tool_dependency.version ), str( tool_dependency.type ), str( tool_dependency.name ) ) ) + log.debug( 'due to the following installation error:\n%s' % str( error_message ) ) try: shutil.rmtree( install_dir ) except Exception, e: diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -41,13 +41,10 @@ self.shed_tools_dict = {} self.home() - def initiate_installation_process( self, - install_tool_dependencies=False, - install_repository_dependencies=True, - no_changes=True, + def initiate_installation_process( self, install_tool_dependencies=False, install_repository_dependencies=True, no_changes=True, new_tool_panel_section_label=None ): html = self.last_page() - # Since the installation process is by necessity asynchronous, we have to get the parameters to 'manually' initiate the + # Since the installation process is by necessity asynchronous we have to get the parameters to 'manually' initiate the # installation process. This regex will return the tool shed repository IDs in group(1), the encoded_kwd parameter in # group(2), and the reinstalling flag in group(3) and pass them to the manage_repositories method in the Galaxy # admin_toolshed controller. diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -289,12 +289,36 @@ else: return suc.INITIAL_CHANGELOG_HASH, error_message +def get_missing_repository_dependencies( repository ): + """ + Return the entire list of missing repository dependencies for the received repository. The entire + dependency tree will be inspected. + """ + log.debug( 'Checking revision %s of repository %s owned by %s for missing repository dependencies.' % \ + ( str( repository.changeset_revision ), str( repository.name ), str( repository.changeset_revision ) ) ) + missing_repository_dependencies = repository.missing_repository_dependencies + for missing_required_repository in missing_repository_dependencies: + log.debug( 'Revision %s of required repository %s owned by %s has status %s.' % \ + ( str( missing_required_repository.changeset_revision ), + str( missing_required_repository.name ), + str( missing_required_repository.owner ), + str( missing_required_repository.status ) ) ) + for repository_dependency in repository.repository_dependencies: + if repository_dependency.missing_repository_dependencies: + missing_repository_dependencies.extend( get_missing_repository_dependencies( repository_dependency ) ) + return missing_repository_dependencies + def get_missing_tool_dependencies( repository ): + """ + Return the entire list of missing tool dependencies for the received repository. The entire + dependency tree will be inspected. + """ log.debug( 'Checking revision %s of repository %s owned by %s for missing tool dependencies.' % \ ( str( repository.changeset_revision ), str( repository.name ), str( repository.changeset_revision ) ) ) missing_tool_dependencies = repository.missing_tool_dependencies - for tool_dependency in repository.tool_dependencies: - log.debug( 'Tool dependency %s version %s has status %s.' % ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) ) + for missing_tool_dependency in missing_tool_dependencies: + log.debug( 'Tool dependency %s version %s has status %s.' % \ + ( str( missing_tool_dependency.name ), str( missing_tool_dependency.version ), str( missing_tool_dependency.status ) ) ) for repository_dependency in repository.repository_dependencies: if repository_dependency.includes_tool_dependencies: missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) @@ -336,8 +360,7 @@ for baseline_repository_dict in baseline_repository_dicts: # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the # module that will generate the install methods. - repository_dict, error_message = \ - get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) + repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) if error_message: log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) else: @@ -439,6 +462,19 @@ extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) return extended_dict, error_message +def get_repository_dependencies_dicts( url, encoded_repository_metadata_id ): + """ + Return a list if dictionaries that define the repository dependencies of the repository defined by the + received repository_dict. + """ + error_message = '' + parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id, 'repository_dependencies' ] + api_url = get_api_url( base=url, parts=parts ) + repository_dependencies_dicts, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + return repository_dependencies_dicts, error_message + def get_repository_tuple_from_elem( elem ): attributes = elem.attrib name = attributes.get( 'name', None ) @@ -511,55 +547,6 @@ global_conf.update( get_static_settings() ) return global_conf -def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dicts, - tool_test_results_dict, params, can_update_tool_shed ): - """Handle missing repository or tool dependencies for an installed repository.""" - # If a tool dependency fails to install correctly, this should be considered an installation error, - # and functional tests should be skipped, since the tool dependency needs to be correctly installed - # for the test to be considered reliable. - log.debug( 'The following dependencies of revision %s of repository %s owned by %s are missing.' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) - # In keeping with the standard display layout, add the error message to the dict for each tool individually. - for dependency in repository.missing_tool_dependencies: - name = str( dependency.name ) - type = str( dependency.type ) - version = str( dependency.version ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing tool dependency %s of type %s version %s: %s' % ( name, type, version, error_message ) ) - missing_tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( missing_tool_dependency_info_dict ) - for dependency in repository.missing_repository_dependencies: - tool_shed = str( dependency.tool_shed ) - name = str( dependency.name ) - owner = str( dependency.owner ) - changeset_revision = str( dependency.changeset_revision ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ - ( name, changeset_revision, owner, error_message ) ) - missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, - name=name, - owner=owner, - changeset_revision=changeset_revision, - error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ]\ - .append( missing_repository_dependency_info_dict ) - # Record the status of this repository in the tool shed. - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ), str( tool_test_results_dict ) ) ) - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ), str( response_dict ) ) ) - log.debug('=============================================================' ) - def initialize_install_and_test_statistics_dict( test_framework ): # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = {} @@ -747,32 +734,42 @@ log.debug( 'The exclude file %s defines no repositories to be excluded from testing.' % str( xml_filename ) ) return exclude_list -def register_installed_and_missing_dependencies( app, repository, repository_identifier_dict, install_and_test_statistics_dict, - tool_test_results_dict ): - # The repository was successfully installed. - log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) +def populate_dependency_install_containers( app, repository, repository_identifier_dict, install_and_test_statistics_dict, + tool_test_results_dict ): + """ + Populate the installation containers (successful or errors) for the received repository's (which + itself was successfully installed) immediate repository and tool dependencies. The entire dependency + tree is not handled here. + """ + repository_name = str( repository.name ) + repository_owner = str( repository.owner ) + repository_changeset_revision = str( repository.changeset_revision ) install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) tool_test_results_dict[ 'successful_installations' ][ 'current_repository' ].append( repository_identifier_dict ) params = dict( test_install_error=False, do_not_test=False ) if repository.missing_repository_dependencies: + log.debug( 'The following repository dependencies for revision %s of repository %s owned by %s have installation errors:' % \ + ( repository_changeset_revision, repository_name, repository_owner ) ) params[ 'test_install_error' ] = True # Keep statistics for this repository's repository dependencies that resulted in installation errors. for missing_repository_dependency in repository.missing_repository_dependencies: tool_shed = str( missing_repository_dependency.tool_shed ) name = str( missing_repository_dependency.name ) owner = str( missing_repository_dependency.owner ) - changset_revision = str( missing_repository_dependency.changeset_revision ) + changeset_revision = str( missing_repository_dependency.changeset_revision ) error_message = unicodify( missing_repository_dependency.error_message ) + log.debug( 'Revision %s of repository %s owned by %s:\n%s' % ( changeset_revision, name, owner, error_message ) ) missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, name=name, owner=owner, - changset_revision=changset_revision, + changeset_revision=changeset_revision, error_message=error_message ) - install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( missing_repository_dependency_dict ) + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( missing_repository_dependency_info_dict ) tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) if repository.missing_tool_dependencies: + log.debug( 'The following tool dependencies for revision %s of repository %s owned by %s have installation errors:' % \ + ( repository_changeset_revision, repository_name, repository_owner ) ) params[ 'test_install_error' ] = True # Keep statistics for this repository's tool dependencies that resulted in installation errors. for missing_tool_dependency in repository.missing_tool_dependencies: @@ -780,6 +777,7 @@ type = str( missing_tool_dependency.type ) version = str( missing_tool_dependency.version ) error_message = unicodify( missing_tool_dependency.error_message ) + log.debug( 'Version %s of tool dependency %s %s:\n%s' % ( version, type, name, error_message ) ) missing_tool_dependency_info_dict = dict( type=type, name=name, version=version, @@ -787,12 +785,15 @@ install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( missing_tool_dependency_info_dict ) if repository.installed_repository_dependencies: + log.debug( 'The following repository dependencies for revision %s of repository %s owned by %s are installed:' % \ + ( repository_changeset_revision, repository_name, repository_owner ) ) # Keep statistics for this repository's tool dependencies that resulted in successful installations. for repository_dependency in repository.installed_repository_dependencies: tool_shed = str( repository_dependency.tool_shed ) name = str( repository_dependency.name ) owner = str( repository_dependency.owner ) changeset_revision = str( repository_dependency.changeset_revision ) + log.debug( 'Revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) repository_dependency_info_dict = dict( tool_shed=tool_shed, name=name, owner=owner, @@ -800,12 +801,15 @@ install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_dependency_info_dict ) tool_test_results_dict[ 'successful_installations' ][ 'repository_dependencies' ].append( repository_dependency_info_dict ) if repository.installed_tool_dependencies: + log.debug( 'The following tool dependencies for revision %s of repository %s owned by %s are installed:' % \ + ( repository_changeset_revision, repository_name, repository_owner ) ) # Keep statistics for this repository's tool dependencies that resulted in successful installations. for tool_dependency in repository.installed_tool_dependencies: name = str( tool_dependency.name ) type = str( tool_dependency.type ) version = str( tool_dependency.version ) installation_directory = tool_dependency.installation_directory( app ) + log.debug( 'Version %s of tool dependency %s %s is installed in: %s' % ( version, type, name, installation_directory ) ) tool_dependency_info_dict = dict( type=type, name=name, version=version, @@ -814,29 +818,98 @@ tool_test_results_dict[ 'successful_installations' ][ 'tool_dependencies' ].append( tool_dependency_info_dict ) return params, install_and_test_statistics_dict, tool_test_results_dict -def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ): +def populate_install_containers_for_repository_dependencies( app, repository, repository_metadata_id, install_and_test_statistics_dict, + can_update_tool_shed ): """ - Update the repository metadata tool_test_results and appropriate flags using the Tool Shed API. This method - updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags - to the appropriate values and updates the time_last_tested field to the value of the received time_tested. + The handle_repository_dependencies check box is always checked when a repository is installed, so the + tool_test_results dictionary must be inspected for each dependency to make sure installation containers + (success or errors) have been populated. Since multiple repositories can depend on the same repository, + some of the containers may have been populated during a previous installation. """ - if can_update_tool_shed: - metadata_revision_id = repository_dict.get( 'id', None ) - if metadata_revision_id is not None: - log.debug( 'Updating tool_test_results for repository_metadata id %s.' % str( metadata_revision_id ) ) - tool_test_results_dicts.insert( 0, tool_test_results_dict ) - params[ 'tool_test_results' ] = tool_test_results_dicts - # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. - params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' - url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) - try: - return update( tool_shed_api_key, url, params, return_formatted=False ) - except Exception, e: - log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' % \ - ( str( metadata_revision_id ), str( e ) ) ) - return {} + # Get the list of dictionaries that define the received repository's repository dependencies + # via the Tool Shed API. + repository_name = str( repository.name ) + repository_owner = str( repository.owner ) + repository_changeset_revision = str( repository.changeset_revision ) + repository_dependencies_dicts, error_message = get_repository_dependencies_dicts( galaxy_tool_shed_url, repository_metadata_id ) + if error_message: + log.debug( 'Cannot check or populate repository dependency install containers for version %s of repository %s owned by %s ' % \ + ( repository_changeset_revision, repository_name, repository_owner ) ) + log.debug( 'due to the following error getting repository_dependencies_dicts:\n%s' % str( error_message ) ) else: - return {} + for repository_dependencies_dict in repository_dependencies_dicts: + name = str( repository_dependencies_dict[ 'name' ] ) + owner = str( repository_dependencies_dict[ 'owner' ] ) + changeset_revision = str( repository_dependencies_dict[ 'changeset_revision' ] ) + log.debug( 'Checking installation containers for revision %s of required repository %s owned by %s' % \ + ( changeset_revision, name, owner ) ) + required_repository_metadata_id = repository_dependencies_dict[ 'id' ] + # Get the current list of tool_test_results dictionaries associated with the repository_metadata + # record in the tool shed. + tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, + required_repository_metadata_id ) + if error_message: + log.debug( 'Cannot check install container for version %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) ) + log.debug( 'due to the following error getting tool_test_results:\n%s' % str( error_message ) ) + else: + # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated + if len( tool_test_results_dicts ) == 0: + populated = False + tool_test_results_dict = initialize_tool_tests_results_dict( app, {} ) + else: + tool_test_results_dict = tool_test_results_dicts[ 0 ] + if len( tool_test_results_dict ) <= 1: + populated = False + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + elif len( tool_test_results_dict ) == 2 and \ + 'test_environment' in tool_test_results_dict and \ + 'missing_test_components' in tool_test_results_dict: + populated = False + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + else: + populated = True + if not populated: + # Get the installed repository record from the Galaxy database. + required_repository = \ + suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, + galaxy_tool_shed_url, + name, + owner, + changeset_revision ) + repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + if required_repository.is_installed: + # The required_repository was successfully installed, so populate the installation + # containers (success and error) for the repository's immediate dependencies. + params, install_and_test_statistics_dict, tool_test_results_dict = \ + populate_dependency_install_containers( app, + required_repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) + else: + # The required repository's installation failed. + tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) + params = dict( test_install_error=True, + do_not_test=False ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) @@ -853,3 +926,34 @@ test_runner = plug_runner result = test_runner.run( tests ) return result, test_config.plugins._plugins + +def save_test_results_for_changeset_revision( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, + params, can_update_tool_shed ): + """ + Update the repository metadata tool_test_results and appropriate flags using the Tool Shed API. This method + updates tool_test_results with the received tool_test_results_dict, sets the do_not_test and tools_functionally + correct flags to the appropriate values and updates the time_last_tested field. + """ + if can_update_tool_shed: + metadata_revision_id = repository_dict.get( 'id', None ) + if metadata_revision_id is not None: + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + log.debug('\n=============================================================\n' ) + log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) + log.debug( 'Updating tool_test_results for repository_metadata id %s.' % str( metadata_revision_id ) ) + tool_test_results_dicts.insert( 0, tool_test_results_dict ) + params[ 'tool_test_results' ] = tool_test_results_dicts + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' + url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + try: + return update( tool_shed_api_key, url, params, return_formatted=False ) + except Exception, e: + log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' % \ + ( str( metadata_revision_id ), str( e ) ) ) + return {} + else: + return {} diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -7,7 +7,7 @@ class InstallTestRepositories( InstallTestRepository ): - """Abstract test case that installs and uninstalls a predefined list of repositories.""" + """Abstract test case that installs a predefined list of repositories.""" def do_install( self, repository_dict ): self.logout() @@ -21,27 +21,34 @@ def generate_install_method( repository_dict=None ): """Generate abstract test cases for the defined list of repositories.""" + + def make_install_method( repository_dict ): + def test_install_repository( self ): + self.do_install( repository_dict ) + return test_install_repository + if repository_dict is None: return # Push all the toolbox tests to module level G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ) or key.startswith( 'TestForTool_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestForTool_' ): del G[ key ] - # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. - name = "TestInstallRepository_" + repository_dict[ 'name' ] + tool_shed = str( repository_dict[ 'tool_shed_url' ] ) + repository_name = str( repository_dict[ 'name' ] ) + repository_owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + # Create a new subclass with a method named install_repository_XXX that installs the repository defined + # by the received repository_dict along with all of its dependency hierarchy. + test_name = "TestInstallRepository_" + repository_name baseclasses = ( InstallTestRepositories, ) namespace = dict() - def make_install_method( repository_dict ): - def test_install_repository( self ): - self.do_install( repository_dict ) - return test_install_repository test_method = make_install_method( repository_dict ) - test_method.__doc__ = "Install the repository %s from %s." % \ - ( str( repository_dict[ 'name' ] ), str( repository_dict[ 'tool_shed_url' ] ) ) - namespace[ 'install_repository_%s' % str( repository_dict[ 'name' ] ) ] = test_method + test_method.__doc__ = "Installing revision %s of repository %s owned by %s from tool shed %s." % \ + ( changeset_revision, repository_name, repository_owner, tool_shed ) + namespace[ 'install_repository_%s' % repository_name ] = test_method # The new.classobj function returns a new class object with name name derived # from baseclasses (which should be a tuple of classes) and with namespace dict. - new_class_obj = new.classobj( str( name ), baseclasses, namespace ) - G[ name ] = new_class_obj + new_class_obj = new.classobj( str( test_name ), baseclasses, namespace ) + G[ test_name ] = new_class_obj diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -180,7 +180,8 @@ install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: - log.debug( error_message ) + log.debug( 'Cannot install version %s of repository %s owned by %s due to the following error getting tool_test_results:\n%s' % \ + ( changeset_revision, name, owner, str( error_message ) ) ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, @@ -194,18 +195,16 @@ # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) else: # See if the repository was installed in a previous test. repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) @@ -219,47 +218,54 @@ log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - params = dict( test_install_error=True ) - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + params = dict( test_install_error=True, + do_not_test=False ) + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) else: # The repository was successfully installed. log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) - params, install_and_test_statistics_dict, tool_test_results_dict = \ - install_and_test_base_util.register_installed_and_missing_dependencies( app, - repository, - repository_identifier_dict, - install_and_test_statistics_dict, - tool_test_results_dict ) # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are # missing test components. if 'missing_test_components' not in tool_test_results_dict: tool_test_results_dict[ 'missing_test_components' ] = [] + # Populate the installation containers (success and error) for the repository's immediate dependencies + # (the entire dependency tree is not handled here). + params, install_and_test_statistics_dict, tool_test_results_dict = \ + install_and_test_base_util.populate_dependency_install_containers( app, + repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) + # Populate the installation containers (success or error) for the repository's immediate repository + # dependencies whose containers are not yet populated. + install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, + repository, + encoded_repository_metadata_id, + install_and_test_statistics_dict, + can_update_tool_shed ) + # Execute the contained tool's functional tests only if the repository's entire dependency + # tree is successfully installed. + missing_repository_dependencies = install_and_test_base_util.get_missing_repository_dependencies( repository ) missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) - if missing_tool_dependencies or repository.missing_repository_dependencies: - install_and_test_base_util.handle_missing_dependencies( app=app, - repository=repository, - missing_tool_dependencies=missing_tool_dependencies, - repository_dict=repository_dict, - tool_test_results_dicts=tool_test_results_dicts, - tool_test_results_dict=tool_test_results_dict, - params=params, - can_update_tool_shed=can_update_tool_shed ) + if missing_repository_dependencies or missing_tool_dependencies: + log.debug( 'Cannot execute tests for tools in revision %s of repository %s owned by %s ' % \ + ( changeset_revision, name, owner ) ) + log.debug( 'because one or more dependencies has installation errors.' ) else: - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) + log.debug( 'Revision %s of repository %s owned by %s installed successfully, so running tool tests.' % \ + ( changeset_revision, name, owner ) ) # Generate the shed_tools_dict that specifies the location of test data contained within this repository. # and configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed @@ -287,19 +293,16 @@ install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) # Record the status of this repository in the tool shed. params[ 'tools_functionally_correct' ] = False - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) response_dict = \ - install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) else: log.debug( 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) ) @@ -661,21 +664,19 @@ params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) - # Call the register_test_result() method to execute a PUT request to the repository_revisions API - # controller with the status of the test. This also sets the do_not_test and tools_functionally - # correct flags and updates the time_last_tested field to today's date. - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + # Call the save_test_results_for_changeset_revision() method to execute a PUT request to the + # repository_revisions API controller with the status of the test. This also sets the do_not_test + # and tools_functionally correct flags and updates the time_last_tested field to today's date. + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) else: # The get_failed_test_dicts() method returns a list. log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ @@ -690,18 +691,16 @@ params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) # Remove the just-executed tests so twill will not find and re-test them along with the tools # contained in the next repository. remove_tests( app ) diff -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 -r 9df289e311209975ab34c288d8229096683af0e0 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -114,7 +114,8 @@ install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: - log.debug( error_message ) + log.debug( 'Cannot install version %s of repository %s owned by %s due to the following error getting tool_test_results:\n%s' % \ + ( changeset_revision, name, owner, str( error_message ) ) ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, @@ -128,18 +129,16 @@ ( changeset_revision, name, owner ) ) tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) else: # See if the repository was installed in a previous test. repository = install_and_test_base_util.get_repository( name, owner, changeset_revision ) @@ -153,41 +152,47 @@ log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - params = dict( test_install_error=True ) - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + params = dict( test_install_error=True, + do_not_test=False ) + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) else: # The repository was successfully installed. log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) + # Populate the installation containers (success and error) for the repository's immediate dependencies + # (the entire dependency tree is not handled here). params, install_and_test_statistics_dict, tool_test_results_dict = \ - install_and_test_base_util.register_installed_and_missing_dependencies( app, - repository, - repository_identifier_dict, - install_and_test_statistics_dict, - tool_test_results_dict ) - log.debug('=============================================================' ) - log.debug( 'Inserting the following into tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( tool_test_results_dict ) ) ) - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) + install_and_test_base_util.populate_dependency_install_containers( app, + repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) + response_dict = \ + install_and_test_base_util.save_test_results_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('=============================================================' ) + log.debug('\n=============================================================\n' ) + # Populate the installation containers (success or error) for the repository's immediate repository + # dependencies whose containers are not yet populated. + install_and_test_base_util.populate_install_containers_for_repository_dependencies( app, + repository, + encoded_repository_metadata_id, + install_and_test_statistics_dict, + can_update_tool_shed ) else: log.debug( 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Jan '14

06 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/49394b5fc1e9/ Changeset: 49394b5fc1e9 User: carlfeberhard Date: 2014-01-06 19:49:20 Summary: History view: replace mako gen. w/ js panel, allow importing to include deleted datasets (by using import when deleted datasets are visible); The original view page is still (temporarily) accessible by altering the url to history/original_view Affected #: 16 files diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -7,6 +7,7 @@ from galaxy.datatypes.data import nice_size from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings from galaxy.model.orm import and_, eagerload_all, func +from galaxy import util from galaxy.util import Params from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html @@ -86,7 +87,7 @@ ) operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=True ), - grids.GridOperation( "View", allow_multiple=False, inbound=True ), + grids.GridOperation( "View", allow_multiple=False ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False, inbound=True ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ), @@ -809,6 +810,9 @@ else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) + # include activatable/deleted datasets when copying? + include_deleted = util.string_as_bool( kwd.get( 'include_deleted', False ) ) + # Do import. if not id: return trans.show_error_message( "You must specify a history you want to import.<br>You can %s." % referer_message, use_panels=True ) @@ -822,7 +826,7 @@ #dan: I can import my own history. #if import_history.user_id == user.id: # return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) - new_history = import_history.copy( target_user=user ) + new_history = import_history.copy( target_user=user, activatable=include_deleted ) new_history.name = "imported: " + new_history.name new_history.user_id = user.id galaxy_session = trans.get_galaxy_session() @@ -840,7 +844,10 @@ return trans.show_ok_message( message="""History "%s" has been imported. <br>You can <a href="%s" onclick="parent.window.location='%s';">start using this history</a> or %s.""" % ( new_history.name, web.url_for( '/' ), web.url_for( '/' ), referer_message ), use_panels=True ) + elif not user_history or not user_history.datasets or confirm: + #TODO:?? should anon-users be allowed to include deleted datasets when importing? + #new_history = import_history.copy( activatable=include_deleted ) new_history = import_history.copy() new_history.name = "imported: " + new_history.name new_history.user_id = None @@ -863,8 +870,9 @@ history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) + # Replaced with view (below) but kept (available via manual URL editing) for now @web.expose - def view( self, trans, id=None, show_deleted=False, use_panels=True ): + def original_view( self, trans, id=None, show_deleted=False, use_panels=True ): """View a history. If a history is importable, then it is viewable by any user.""" # Get history to view. if not id: @@ -885,13 +893,67 @@ use_panels = galaxy.util.string_as_bool( use_panels ) except: pass # already a bool - return trans.stream_template_mako( "history/view.mako", + return trans.stream_template_mako( "history/original_view.mako", history = history_to_view, datasets = datasets, show_deleted = show_deleted, use_panels = use_panels ) @web.expose + def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): + """ + View a history. If a history is importable, then it is viewable by any user. + """ + # Get history to view. + if not id: + return trans.show_error_message( "You must specify a history you want to view." ) + + show_deleted = galaxy.util.string_as_bool( show_deleted ) + show_hidden = galaxy.util.string_as_bool( show_hidden ) + use_panels = galaxy.util.string_as_bool( use_panels ) + + history_dictionary = {} + hda_dictionaries = [] + try: + history_to_view = self.get_history( trans, id, False ) + if not history_to_view: + return trans.show_error_message( "The specified history does not exist." ) + + # Admin users can view any history + if( ( history_to_view.user != trans.user ) + and ( not trans.user_is_admin() ) + and ( not history_to_view.importable ) ): + #TODO: no check for shared with + return trans.show_error_message( "Either you are not allowed to view this history" + + " or the owner of this history has not made it accessible." ) + + hdas = self.get_history_datasets( trans, history_to_view, show_deleted=True, show_hidden=True ) + for hda in hdas: + hda_dict = {} + try: + hda_dict = self.get_hda_dict( trans, hda ) + + except Exception, exc: + # don't fail entire list if hda err's, record and move on + log.error( 'Error bootstrapping hda %d: %s', hda.id, str( exc ), exc_info=True ) + hda_dict = self.get_hda_dict_with_error( trans, hda, str( exc ) ) + + hda_dictionaries.append( hda_dict ) + + # re-use the hdas above to get the history data... + history_dictionary = self.get_history_dict( trans, history_to_view, hda_dictionaries=hda_dictionaries ) + + except Exception, exc: + user_id = str( trans.user.id ) if trans.user else '(anonymous)' + log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) + history_dictionary[ 'error' ] = ( 'An error occurred getting the history data from the server. ' + + 'Please contact a Galaxy administrator if the problem persists.' ) + + return trans.fill_template_mako( "history/view.mako", + history=history_dictionary, hdas=hda_dictionaries, + show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) + + @web.expose def display_by_username_and_slug( self, trans, username, slug ): """ Display history based on a username and slug. """ diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -93,13 +93,7 @@ // re-get web controller urls for functions relating to this hda. (new model data may have changed this) this.urls = this.model.urls(); - - // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. - var $newRender = $( HDABaseView.templates.skeleton( this.model.toJSON() ) ); - $newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() ); - $newRender.children( '.dataset-body' ).replaceWith( this._render_body() ); - this._setUpBehaviors( $newRender ); - //this._renderSelectable( $newRender ); + var $newRender = this._buildNewRender(); // fade the old render out (if desired) if( fade ){ @@ -128,6 +122,16 @@ }); return this; }, + + _buildNewRender : function(){ + // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. + var $newRender = $( HDABaseView.templates.skeleton( this.model.toJSON() ) ); + $newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() ); + $newRender.children( '.dataset-body' ).replaceWith( this._render_body() ); + this._setUpBehaviors( $newRender ); + //this._renderSelectable( $newRender ); + return $newRender; + }, /** set up js behaviors, event handlers for elements within the given container * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -261,6 +261,21 @@ } return $icon; }, + + // ......................................................................... render main + _buildNewRender : function(){ + var $newRender = hdaBase.HDABaseView.prototype._buildNewRender.call( this ); + + //TODO: this won't localize easily + $newRender.find( '.dataset-deleted-msg' ).append( + _l( 'Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it' + + ' or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk' )); + + $newRender.find( '.dataset-hidden-msg' ).append( + _l( 'Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it' )); + + return $newRender; + }, // ......................................................................... state body renderers /** Render an HDA where the metadata wasn't produced correctly. diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -710,7 +710,7 @@ ModeButton.prototype.init = function _init( element, options ){ options = options || {}; this.$element = $( element ); - this.options = jQuery.extend( true, this.defaults, options ); + this.options = jQuery.extend( true, {}, this.defaults, options ); var modeButton = this; this.$element.click( function _ModeButtonClick( event ){ @@ -774,20 +774,23 @@ jQuery.fn.extend({ modeButton : function $modeButton( options ){ var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); - return this.each( function(){ + //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)? + return this.map( function(){ var $this = $( this ), data = $this.data( 'mode-button' ); if( jQuery.type( options ) === 'object' ){ data = new ModeButton( $this, options ); $this.data( 'mode-button', data ); - } - if( data && jQuery.type( options ) === 'string' ){ + + } else if( data && jQuery.type( options ) === 'string' ){ var fn = data[ options ]; if( jQuery.type( fn ) === 'function' ){ return fn.apply( data, nonOptionsArgs ); } - } + } else if ( data ){ + return data; + } return this; }); } diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="'+this.linkTarget+'">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_buildNewRender:function(){var g=a.HDABaseView.prototype._buildNewRender.call(this);g.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));g.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return g},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('<a target="'+this.linkTarget+'">?</a>').attr("href",this.urls.edit))}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$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 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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 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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(){function a(j,p){var d=27,m=13,c=$(j),e=true,g={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(q){},minSearchLen:0,escWillClear:true,oninit:function(){}};function i(q){var r=$(this).parent().children("input");r.val("");r.trigger("clear:searchInput");p.onclear()}function o(r,q){$(this).trigger("search:searchInput",q);if(typeof p.onfirstsearch==="function"&&e){e=false;p.onfirstsearch(q)}else{p.onsearch(q)}}function f(){return['<input type="text" name="',p.name,'" placeholder="',p.placeholder,'" ','class="search-query ',p.classes,'" ',"/>"].join("")}function l(){return $(f()).focus(function(q){$(this).select()}).keyup(function(r){if(r.which===d&&p.escWillClear){i.call(this,r)}else{var q=$(this).val();if((r.which===m)||(p.minSearchLen&&q.length>=p.minSearchLen)){o.call(this,r,q)}else{if(!q.length){i.call(this,r)}}}}).val(p.initialVal)}function k(){return $(['<span class="search-clear fa fa-times-circle" ','title="',_l("clear search 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g=$(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";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}; \ No newline at end of file diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/packed/templates/compiled/history-templates.js --- a/static/scripts/packed/templates/compiled/history-templates.js +++ b/static/scripts/packed/templates/compiled/history-templates.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+='\n </div>\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';return A}function m(D,C){var A="",B;A+='\n <div class="dataset-summary">\n 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class="value">';if(B=p.misc_info){B=B.call(D,{hash:{},data:C})}else{B=D.misc_info;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function w(D,C){var A="",B;A+='\n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="dataset-display-applications">\n ';B=p.each.call(D,D.display_apps,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p.each.call(D,D.display_types,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-peek">\n ';B=p["if"].call(D,D.peek,{hash:{},inverse:o.noop,fn:o.program(19,s,C),data:C});if(B||B===0){A+=B}A+="\n </div>\n\n ";return A}function v(D,C){var A="",B;A+='\n <div class="display-application">\n <span class="display-application-location">';if(B=p.label){B=B.call(D,{hash:{},data:C})}else{B=D.label;B=typeof B===e?B.apply(D):B}A+=d(B)+'</span>\n <span class="display-application-links">\n 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\ No newline at end of file diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/packed/templates/compiled/template-hda-skeleton.js --- a/static/scripts/packed/templates/compiled/template-hda-skeleton.js +++ b/static/scripts/packed/templates/compiled/template-hda-skeleton.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-skeleton"]=b(function(f,r,p,k,w){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,f.helpers);w=w||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(B,A){var x="",z,y;x+='\n <div class="errormessagesmall">\n ';y={hash:{},inverse:o.noop,fn:o.program(2,m,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+=":\n ";y={hash:{},inverse:o.noop,fn:o.program(4,l,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </div>\n ";return x}function m(y,x){return"There was an error getting the data for this dataset"}function l(z,y){var x;if(x=p.error){x=x.call(z,{hash:{},data:y})}else{x=z.error;x=typeof x===e?x.apply(z):x}return d(x)}function j(A,z){var x="",y;x+="\n ";y=p["if"].call(A,A.purged,{hash:{},inverse:o.program(10,v,z),fn:o.program(7,i,z),data:z});if(y||y===0){x+=y}x+="\n ";return x}function i(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(8,g,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n\n ";return x}function g(y,x){return"This dataset has been deleted and removed from disk."}function v(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(11,u,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='\n \n \n Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it\n or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk\n </strong></div>\n ';return x}function u(y,x){return"This dataset has been deleted."}function t(B,A){var x="",z,y;x+='\n <div class="warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(14,s,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+='\n \n Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it\n </strong></div>\n ';return x}function s(y,x){return"This dataset has been hidden."}q+='<div class="dataset hda">\n <div class="dataset-warnings">\n ';h=p["if"].call(r,r.error,{hash:{},inverse:o.noop,fn:o.program(1,n,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p["if"].call(r,r.deleted,{hash:{},inverse:o.noop,fn:o.program(6,j,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p.unless.call(r,r.visible,{hash:{},inverse:o.noop,fn:o.program(13,t,w),data:w});if(h||h===0){q+=h}q+='\n </div>\n\n <div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>\n <div class="dataset-primary-actions"></div>\n \n <div class="dataset-title-bar clear" tabindex="0">\n <span class="dataset-state-icon state-icon"></span>\n <div class="dataset-title">\n <span class="hda-hid">';if(h=p.hid){h=h.call(r,{hash:{},data:w})}else{h=r.hid;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n <span class="dataset-name">';if(h=p.name){h=h.call(r,{hash:{},data:w})}else{h=r.name;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n </div>\n </div>\n\n <div class="dataset-body"></div>\n</div>';return q})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-skeleton"]=b(function(f,r,p,k,w){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,f.helpers);w=w||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(B,A){var x="",z,y;x+='\n <div class="errormessagesmall">\n ';y={hash:{},inverse:o.noop,fn:o.program(2,m,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+=":\n ";y={hash:{},inverse:o.noop,fn:o.program(4,l,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </div>\n ";return x}function m(y,x){return"There was an error getting the data for this dataset"}function l(z,y){var x;if(x=p.error){x=x.call(z,{hash:{},data:y})}else{x=z.error;x=typeof x===e?x.apply(z):x}return d(x)}function j(A,z){var x="",y;x+="\n ";y=p["if"].call(A,A.purged,{hash:{},inverse:o.program(10,v,z),fn:o.program(7,i,z),data:z});if(y||y===0){x+=y}x+="\n ";return x}function i(B,A){var x="",z,y;x+='\n <div class="dataset-purged-msg warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(8,g,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n\n ";return x}function g(y,x){return"This dataset has been deleted and removed from disk."}function v(B,A){var x="",z,y;x+='\n <div class="dataset-deleted-msg warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(11,u,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n ";return x}function u(y,x){return"This dataset has been deleted."}function t(B,A){var x="",z,y;x+='\n <div class="dataset-hidden-msg warningmessagesmall"><strong>\n ';y={hash:{},inverse:o.noop,fn:o.program(14,s,A),data:A};if(z=p.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!p.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n </strong></div>\n ";return x}function s(y,x){return"This dataset has been hidden."}q+='<div class="dataset hda">\n <div class="dataset-warnings">\n ';h=p["if"].call(r,r.error,{hash:{},inverse:o.noop,fn:o.program(1,n,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p["if"].call(r,r.deleted,{hash:{},inverse:o.noop,fn:o.program(6,j,w),data:w});if(h||h===0){q+=h}q+="\n\n ";h=p.unless.call(r,r.visible,{hash:{},inverse:o.noop,fn:o.program(13,t,w),data:w});if(h||h===0){q+=h}q+='\n </div>\n\n <div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>\n <div class="dataset-primary-actions"></div>\n \n <div class="dataset-title-bar clear" tabindex="0">\n <span class="dataset-state-icon state-icon"></span>\n <div class="dataset-title">\n <span class="hda-hid">';if(h=p.hid){h=h.call(r,{hash:{},data:w})}else{h=r.hid;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n <span class="dataset-name">';if(h=p.name){h=h.call(r,{hash:{},data:w})}else{h=r.name;h=typeof h===e?h.apply(r):h}q+=d(h)+'</span>\n </div>\n </div>\n\n <div class="dataset-body"></div>\n</div>';return q})})(); \ No newline at end of file diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -228,7 +228,7 @@ function program7(depth0,data) { var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; + buffer += "\n <div class=\"dataset-purged-msg warningmessagesmall\"><strong>\n "; options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } @@ -246,15 +246,13 @@ function program10(depth0,data) { var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; + buffer += "\n <div class=\"dataset-deleted-msg warningmessagesmall\"><strong>\n "; options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n " - + "\n " - + "\n Click <a href=\"javascript:void(0);\" class=\"dataset-undelete\">here</a> to undelete it\n or <a href=\"javascript:void(0);\" class=\"dataset-purge\">here</a> to immediately remove it from disk\n </strong></div>\n "; + buffer += "\n </strong></div>\n "; return buffer; } function program11(depth0,data) { @@ -266,14 +264,13 @@ function program13(depth0,data) { var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; + buffer += "\n <div class=\"dataset-hidden-msg warningmessagesmall\"><strong>\n "; options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n " - + "\n Click <a href=\"javascript:void(0);\" class=\"dataset-unhide\">here</a> to unhide it\n </strong></div>\n "; + buffer += "\n </strong></div>\n "; return buffer; } function program14(depth0,data) { @@ -305,131 +302,6 @@ }); })();(function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"errormessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":\n "; - options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n "; - return buffer; - } -function program2(depth0,data) { - - - return "There was an error getting the data for this dataset"; - } - -function program4(depth0,data) { - - var stack1; - if (stack1 = helpers.error) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.error; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - return escapeExpression(stack1); - } - -function program6(depth0,data) { - - var buffer = "", stack1; - buffer += "\n "; - stack1 = helpers['if'].call(depth0, depth0.purged, {hash:{},inverse:self.program(10, program10, data),fn:self.program(7, program7, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer; - } -function program7(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n\n "; - return buffer; - } -function program8(depth0,data) { - - - return "This dataset has been deleted and removed from disk."; - } - -function program10(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n " - + "\n " - + "\n Click <a href=\"javascript:void(0);\" class=\"dataset-undelete\">here</a> to undelete it\n or <a href=\"javascript:void(0);\" class=\"dataset-purge\">here</a> to immediately remove it from disk\n </strong></div>\n "; - return buffer; - } -function program11(depth0,data) { - - - return "This dataset has been deleted."; - } - -function program13(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n " - + "\n Click <a href=\"javascript:void(0);\" class=\"dataset-unhide\">here</a> to unhide it\n </strong></div>\n "; - return buffer; - } -function program14(depth0,data) { - - - return "This dataset has been hidden."; - } - - buffer += "<div class=\"dataset hda\">\n <div class=\"dataset-warnings\">\n "; - stack1 = helpers['if'].call(depth0, depth0.error, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n <div class=\"dataset-title-bar clear\" tabindex=\"0\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">"; - if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n <span class=\"dataset-name\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n </div>\n\n <div class=\"dataset-body\"></div>\n</div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-historyPanel-anon'] = template(function (Handlebars,depth0,helpers,partials,data) { this.compilerInfo = [4,'>= 1.0.0']; helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/templates/compiled/template-hda-skeleton.js --- a/static/scripts/templates/compiled/template-hda-skeleton.js +++ b/static/scripts/templates/compiled/template-hda-skeleton.js @@ -49,7 +49,7 @@ function program7(depth0,data) { var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; + buffer += "\n <div class=\"dataset-purged-msg warningmessagesmall\"><strong>\n "; options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } @@ -67,15 +67,13 @@ function program10(depth0,data) { var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; + buffer += "\n <div class=\"dataset-deleted-msg warningmessagesmall\"><strong>\n "; options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n " - + "\n " - + "\n Click <a href=\"javascript:void(0);\" class=\"dataset-undelete\">here</a> to undelete it\n or <a href=\"javascript:void(0);\" class=\"dataset-purge\">here</a> to immediately remove it from disk\n </strong></div>\n "; + buffer += "\n </strong></div>\n "; return buffer; } function program11(depth0,data) { @@ -87,14 +85,13 @@ function program13(depth0,data) { var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; + buffer += "\n <div class=\"dataset-hidden-msg warningmessagesmall\"><strong>\n "; options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n " - + "\n Click <a href=\"javascript:void(0);\" class=\"dataset-unhide\">here</a> to unhide it\n </strong></div>\n "; + buffer += "\n </strong></div>\n "; return buffer; } function program14(depth0,data) { diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d static/scripts/templates/hda-templates.html --- a/static/scripts/templates/hda-templates.html +++ b/static/scripts/templates/hda-templates.html @@ -11,26 +11,20 @@ {{#if deleted}} {{#if purged}} - <div class="warningmessagesmall"><strong> + <div class="dataset-purged-msg warningmessagesmall"><strong> {{#local}}This dataset has been deleted and removed from disk.{{/local}} </strong></div> {{else}}{{! deleted, not purged }} - <div class="warningmessagesmall"><strong> + <div class="dataset-deleted-msg warningmessagesmall"><strong> {{#local}}This dataset has been deleted.{{/local}} - {{! edit-only }} - {{! how in the hell would you localize this? }} - Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it - or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk </strong></div> {{/if}} {{/if}} {{#unless visible}} - <div class="warningmessagesmall"><strong> + <div class="dataset-hidden-msg warningmessagesmall"><strong> {{#local}}This dataset has been hidden.{{/local}} - {{! edit-only }} - Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it </strong></div> {{/unless}} </div> diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d templates/webapps/galaxy/history/history_panel.mako --- a/templates/webapps/galaxy/history/history_panel.mako +++ b/templates/webapps/galaxy/history/history_panel.mako @@ -92,12 +92,14 @@ ${h.js( "utils/localization", "mvc/base-mvc", - "mvc/tags", "mvc/annotations" + "mvc/tags", + "mvc/annotations" )} ##TODO: concat these ${h.templates( - "history-templates" + "history-templates", + "helpers-common-templates" )} ${localize_js_strings([ @@ -148,9 +150,9 @@ //require([ "/static/scripts/history-panel.min.js" ], function( historyPanel ){ require([ "mvc/history/history-panel" ], function( historyPanel ){ - onhistoryready.resolve( historyPanel ) + $(function(){ + onhistoryready.resolve( historyPanel ) + }); }); </script></%def> - - diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d templates/webapps/galaxy/history/original_view.mako --- /dev/null +++ b/templates/webapps/galaxy/history/original_view.mako @@ -0,0 +1,173 @@ +<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> +<%namespace file="/root/history_common.mako" import="render_dataset" /> +<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/galaxy/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "libs/jquery/jstorage" )} + <script type="text/javascript"> + $(function() { + init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); + $( '#switch-to-link' ).click( function( event ){ + var galaxy = window.Galaxy || window.parent.Galaxy; + if( galaxy ){ + galaxy.currHistoryPanel.switchToHistory( '${ trans.security.encode_id( history.id ) }' ); + } + }); + $( '#refresh' ).click( function( event ){ window.location.reload( true ); }) + }); + </script> +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "history", "autocomplete_tagging" )} + + <style type="text/css"> + + /* these don't appear to be used? */ + .page-body + { + padding: 10px; + float: left; + width: 65%; + } + .page-meta + { + float: right; + width: 27%; + padding: 0.5em; + margin: 0.25em; + vertical-align: text-top; + border: 2px solid #DDDDDD; + border-top: 4px solid #DDDDDD; + } + + + body { + padding: 0px; + margin: 0px; + } + + div.unified-panel-body { + position: absolute; + top: 0px; + width: 100%; + } + + #history-name-area { + margin: 12px 0px 0px 16px; + font-size: 120%; + } + #top-links { + margin: 4px 0px 8px 16px; + } + + .historyItemContainer { + /*padding-right: 3px;*/ + } + .historyItemBody { + display: none; + } + div.historyItemWrapper { + margin: 0px 4px 0px 4px ; + border-left: 1px solid #999999; + border-right: 1px solid #999999; + } + /* TODO: unify with other history css and into .less */ + </style> + + <noscript> + <style> + .historyItemBody { + display: block; + } + </style> + </noscript> +</%def> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False +%> +</%def> + +<%def name="body()"> + ${center_panel()} +</%def> + +<%def name="center_panel()"> + ## Get URL to other histories owned by user that owns this history. + <% + ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. + href_to_published_histories = h.url_for( controller='/history', action='list_published') + if history.user is not None: + href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') + else: + href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? + %> + + <div class="unified-panel-body"> + <div style="overflow: auto; height: 100%;"> + ## Render view of history. + <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> + <div id="history-name">${history.get_display_name()}</div> + </div> + + <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> + %if not history.purged and history.user != trans.user: + ##TODO: need to remove _top + <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}" + >import and start using history</a> | + <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | + %endif + %if not history.purged and history.user == trans.user: + <a id="switch-to-link" href="javascript:void(0)">${_('switch to this history')}</a> | + <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | + %endif + %if show_deleted: + <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | + %else: + <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | + %endif + <a href="#" class="toggle">collapse all</a> + </div> + + %if history.deleted: + <div class="warningmessagesmall"> + ${_('You are currently viewing a deleted history!')} + </div> + <p></p> + %endif + + %if not datasets: + <div class="infomessagesmall" id="emptyHistoryMessage"> + + %else: + ## Render requested datasets, ordered from newest to oldest + %for data in datasets: + %if data.visible: + <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} + </div> + %endif + %endfor + + <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> + %endif + ${_("Your history is empty. Click 'Get Data' on the left pane to start")} + </div> + </div> + </div> +</%def> diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -1,7 +1,7 @@ -<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> +<%namespace file="/history/history_panel.mako" import="history_panel_javascripts" /> +<%namespace file="/galaxy.masthead.mako" import="get_user_json" /> +## ---------------------------------------------------------------------------- <%! def inherit(context): if context.get('use_panels'): @@ -11,90 +11,6 @@ %><%inherit file="${inherit(context)}"/> -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); - $( '#switch-to-link' ).click( function( event ){ - var galaxy = window.Galaxy || window.parent.Galaxy; - if( galaxy ){ - galaxy.currHistoryPanel.switchToHistory( '${ trans.security.encode_id( history.id ) }' ); - } - }); - $( '#refresh' ).click( function( event ){ window.location.reload( true ); }) - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - - <style type="text/css"> - - /* these don't appear to be used? */ - .page-body - { - padding: 10px; - float: left; - width: 65%; - } - .page-meta - { - float: right; - width: 27%; - padding: 0.5em; - margin: 0.25em; - vertical-align: text-top; - border: 2px solid #DDDDDD; - border-top: 4px solid #DDDDDD; - } - - - body { - padding: 0px; - margin: 0px; - } - - div.unified-panel-body { - position: absolute; - top: 0px; - width: 100%; - } - - #history-name-area { - margin: 12px 0px 0px 16px; - font-size: 120%; - } - #top-links { - margin: 4px 0px 8px 16px; - } - - .historyItemContainer { - /*padding-right: 3px;*/ - } - .historyItemBody { - display: none; - } - div.historyItemWrapper { - margin: 0px 4px 0px 4px ; - border-left: 1px solid #999999; - border-right: 1px solid #999999; - } - /* TODO: unify with other history css and into .less */ - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - <%def name="init()"><% self.has_left_panel=False @@ -103,71 +19,171 @@ %></%def> +<%def name="center_panel()"> +</%def> + +## ---------------------------------------------------------------------------- <%def name="body()"> ${center_panel()} </%def> +## ---------------------------------------------------------------------------- +<%def name="title()"> + ${history[ 'name' ]} +</%def> + +## ---------------------------------------------------------------------------- +<%def name="stylesheets()"> +${parent.stylesheets()} +<style> +%if not use_panels: + body, html { + margin: 0px; + padding: 0px; + } +%endif +#header { + background-color: white; + border-bottom: 1px solid #DDD; + width: 100%; + height: 48px; +} +#history-view-controls { + margin: 10px 10px 10px 10px; +} +.history-panel { + /* this and the height of #header above are way too tweaky */ + margin-top: 18px; +} +.history-title { + font-size: 120%; +} +.history-title input { + font-size: 100%; +} +a.btn { + text-decoration: none; +} +</style> +</%def> + +## ---------------------------------------------------------------------------- +<%def name="javascripts()"> +${parent.javascripts()} +${history_panel_javascripts()} + +%if not use_panels: + ${h.js( 'mvc/user/user-model' )} +%endif + +<script type="text/javascript"> + var using_panels = ${ 'false' if not use_panels else 'true' }; + %if not use_panels: + window.Galaxy = {}; + Galaxy.currUser = new User(${h.to_json_string( get_user_json() )}); + %endif +</script> +</%def> + +## ---------------------------------------------------------------------------- <%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - ## Render view of history. - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> +<div id="header" class="clear"> + <div id="history-view-controls" class="pull-right"> + <% + show_deleted = context.get( 'show_deleted', None ) + show_hidden = context.get( 'show_hidden', None ) - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not history.purged and history.user != trans.user: - ##TODO: need to remove _top - <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}" - >import and start using history</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if not history.purged and history.user == trans.user: - <a id="switch-to-link" href="javascript:void(0)">${_('switch to this history')}</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if show_deleted: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | - %else: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | - %endif - <a href="#" class="toggle">collapse all</a> - </div> + show_deleted_js = 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) + show_hidden_js = 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) + %> + %if not history[ 'purged' ]: + <a id="import" class="btn btn-default" style="display: none;" + href="${h.url_for( controller='history', action='imp', id=history['id'], include_deleted=show_deleted )}"> + ${_('Import and start using history')} + </a> + %endif + <button id="toggle-deleted" class="btn btn-default"> + ${_('Exclude deleted') if show_deleted else _('Include deleted')} + </button> + <button id="toggle-hidden" class="btn btn-default"> + ${_('Exclude hidden') if show_hidden else _('Include hidden')} + </button> + </div> +</div> - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif +<div id="history-${ history[ 'id' ] }" class="history-panel unified-panel-body" style="overflow: auto;"></div> - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> +<script type="text/javascript"> + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, + historyJSON = ${h.to_json_string( history )}, + hdaJSON = ${h.to_json_string( hdas )}; + window.hdaJSON = hdaJSON; - %else: - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - %endif - %endfor + $( '#toggle-deleted' ).modeButton({ + initialMode : (${ show_deleted_js })?( 'exclude' ):( 'include' ), + modes: [ + { mode: 'exclude', html: _l( 'Exclude deleted' ) }, + { mode: 'include', html: _l( 'Include deleted' ) } + ] + }).click( function(){ + // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted datasets + // when importing or not; when deleted datasets are shown, they'll be imported + var $importBtn = $( '#import' ); + if( $importBtn.size() ){ + // a bit hacky + var href = $importBtn.attr( 'href' ), + includeDeleted = $( this ).modeButton()[0].getMode().mode === 'exclude'; + href = href.replace( /include_deleted=True|False/, ( includeDeleted )?( 'True' ):( 'False' ) ); + $importBtn.attr( 'href', href ); + $importBtn.text( includeDeleted ? _l( 'Import with deleted datasets and start using history' ) + : _l( 'Import and start using history' ) ); + } + }); - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </div> - </div> + $( '#toggle-hidden' ).modeButton({ + initialMode : (${ show_hidden_js })?( 'exclude' ):( 'include' ), + modes: [ + { mode: 'exclude', html: _l( 'Exclude hidden' ) }, + { mode: 'include', html: _l( 'Include hidden' ) } + ] + }); + + ##TODO: move to mako + if( Galaxy.currUser.id !== historyJSON.user_id ){ + $( '#import' ).show(); + } + + require.config({ + baseUrl : "${h.url_for( '/static/scripts' )}" + }); + require([ "mvc/history/history-panel" ], function( historyPanel ){ + // history module is already in the dpn chain from the panel. We can re-scope it here. + var historyModel = require( 'mvc/history/history-model' ), + hdaBaseView = require( 'mvc/dataset/hda-base' ); + + var history = new historyModel.History( historyJSON, hdaJSON, { + logger: ( debugging )?( console ):( null ) + }); + + window.historyPanel = new historyPanel.HistoryPanel({ + HDAViewClass : ( Galaxy.currUser.id === historyJSON.user_id )? + ( hdaBaseView.HDAEditView ):( hdaBaseView.HDABaseView ), + show_deleted : ${show_deleted_js}, + show_hidden : ${show_hidden_js}, + el : $( "#history-" + historyJSON.id ), + model : history, + onready : function(){ + var panel = this; + $( '#toggle-deleted' ).on( 'click', function(){ + panel.toggleShowDeleted(); + }); + $( '#toggle-hidden' ).on( 'click', function(){ + panel.toggleShowHidden(); + }); + this.render(); + } + }); + }); +</script> + </%def> diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 49394b5fc1e92322cc84d645d1de213658453a3d templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -21,13 +21,10 @@ ## ----------------------------------------------------------------------------- <%def name="javascripts()"> ${parent.javascripts()} +${history_panel_javascripts()} ${h.js( - "libs/require", - "mvc/base-mvc", - "utils/localization", "mvc/user/user-model" )} -${h.templates( "helpers-common-templates" )} <script type="text/javascript"> if( !window.Galaxy ){ @@ -40,8 +37,6 @@ }); </script> -${history_panel_javascripts()} - <script type="text/javascript"> onhistoryready.done( function( historyPanel ){ https://bitbucket.org/galaxy/galaxy-central/commits/7ebebaa348c3/ Changeset: 7ebebaa348c3 User: carlfeberhard Date: 2014-01-06 19:50:13 Summary: Merge Affected #: 2 files diff -r 49394b5fc1e92322cc84d645d1de213658453a3d -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 test/tool_shed/functional/test_0520_import_export_circular_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0520_import_export_circular_dependencies.py @@ -0,0 +1,84 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common + +import logging +log = logging.getLogger( __name__ ) + +filtering_repository_name = 'filtering_0520' +filtering_repository_description = "Galaxy's filtering tool for test 0520" +filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0520" +freebayes_repository_name = 'freebayes_0520' +freebayes_repository_description = "Galaxy's freebayes tool" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0520" + +category_name = 'Test 0520 Circular Dependency Import Export' +category_description = 'Test script 0520 for importing and exporting repositories with circular dependencies.' + +''' +1) Upload a capsule with 2 repositories that define simple repository dependencies on each other, resulting in circular + dependencies to a tool shed. +2) Make sure each repository contains an invalid repository dependency after the capsule has been uploaded (they should + be invalid because their toolshed and changeset_revision attributes could not be auto-populated). +3) Make sure each repository's repository_metadata record has the downloadable column marked as False. +''' + + +class TestExportImportRepository( ShedTwillTestCase ): + '''Test exporting and importing repositories.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = self.test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = self.test_db_util.get_private_role( admin_user ) + + def test_0005_import_repository_capsule( self ): + """Import the filter_0520 repository capsule with dependencies.""" + ''' + This is step 1 - Upload a capsule with 2 repositories that define simple repository dependencies on each other, resulting in + circular dependencies to a tool shed. + ''' + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.import_capsule( self.get_filename( 'repository_capsules/0520_filtering.tar.gz' ), + strings_displayed=[ filtering_repository_name, freebayes_repository_name, '<b>Exists' ], + strings_not_displayed=[ ' Exists' ], + strings_displayed_after_submit=[ 'Repository <b>filtering_0520</b> has been created.' ], + strings_not_displayed_after_submit=[ 'Import not necessary' ] ) + + def test_0010_verify_invalid_dependency( self ): + '''Verify that the repository dependencies are marked as invalid.''' + ''' + This is step 2 - Make sure each repository contains an invalid repository dependency after the capsule has been uploaded + (they should be invalid because their toolshed and changeset_revision attributes could not be auto-populated). + ''' + freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + strings_displayed = [ 'Ignoring repository dependency definition', self.url, 'filtering_0520', 'name is invalid' ] + self.display_manage_repository_page( freebayes_repository, + strings_displayed=strings_displayed, + strings_not_displayed=[ 'Repository dependencies' ] ) + self.display_manage_repository_page( filtering_repository, + strings_displayed=[ 'Repository dependencies', self.get_repository_tip( freebayes_repository ) ], + strings_not_displayed=[] ) + + def test_0015_verify_repository_metadata( self ): + '''Verify that the repositories are not marked as downloadable.''' + ''' + This is step 3 - Make sure each repository's repository_metadata record has the downloadable column marked as False. + ''' + freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_metadata = self.get_repository_metadata_by_changeset_revision( freebayes_repository, self.get_repository_tip( freebayes_repository ) ) + filtering_metadata = self.get_repository_metadata_by_changeset_revision( filtering_repository, self.get_repository_tip( filtering_repository ) ) + assert not filtering_metadata.downloadable, 'Repository filtering_0520 is incorrectly marked as downloadable.' + assert not freebayes_metadata.downloadable, 'Repository freebayes_0520 is incorrectly marked as downloadable.' diff -r 49394b5fc1e92322cc84d645d1de213658453a3d -r 7ebebaa348c316203ff7aee7ffa67fdc2db3ff88 test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz Binary file test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Functional test for importing an exported repository capsule where a circular repository dependency has been defined.
by commits-noreply＠bitbucket.org 06 Jan '14

06 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5c6c916b0b98/ Changeset: 5c6c916b0b98 User: inithello Date: 2014-01-06 19:48:17 Summary: Functional test for importing an exported repository capsule where a circular repository dependency has been defined. Affected #: 2 files diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 5c6c916b0b9862cf572af3a70e87a1f20546e6fe test/tool_shed/functional/test_0520_import_export_circular_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0520_import_export_circular_dependencies.py @@ -0,0 +1,84 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common + +import logging +log = logging.getLogger( __name__ ) + +filtering_repository_name = 'filtering_0520' +filtering_repository_description = "Galaxy's filtering tool for test 0520" +filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0520" +freebayes_repository_name = 'freebayes_0520' +freebayes_repository_description = "Galaxy's freebayes tool" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0520" + +category_name = 'Test 0520 Circular Dependency Import Export' +category_description = 'Test script 0520 for importing and exporting repositories with circular dependencies.' + +''' +1) Upload a capsule with 2 repositories that define simple repository dependencies on each other, resulting in circular + dependencies to a tool shed. +2) Make sure each repository contains an invalid repository dependency after the capsule has been uploaded (they should + be invalid because their toolshed and changeset_revision attributes could not be auto-populated). +3) Make sure each repository's repository_metadata record has the downloadable column marked as False. +''' + + +class TestExportImportRepository( ShedTwillTestCase ): + '''Test exporting and importing repositories.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin user.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = self.test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email + admin_user_private_role = self.test_db_util.get_private_role( admin_user ) + + def test_0005_import_repository_capsule( self ): + """Import the filter_0520 repository capsule with dependencies.""" + ''' + This is step 1 - Upload a capsule with 2 repositories that define simple repository dependencies on each other, resulting in + circular dependencies to a tool shed. + ''' + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.import_capsule( self.get_filename( 'repository_capsules/0520_filtering.tar.gz' ), + strings_displayed=[ filtering_repository_name, freebayes_repository_name, '<b>Exists' ], + strings_not_displayed=[ ' Exists' ], + strings_displayed_after_submit=[ 'Repository <b>filtering_0520</b> has been created.' ], + strings_not_displayed_after_submit=[ 'Import not necessary' ] ) + + def test_0010_verify_invalid_dependency( self ): + '''Verify that the repository dependencies are marked as invalid.''' + ''' + This is step 2 - Make sure each repository contains an invalid repository dependency after the capsule has been uploaded + (they should be invalid because their toolshed and changeset_revision attributes could not be auto-populated). + ''' + freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + strings_displayed = [ 'Ignoring repository dependency definition', self.url, 'filtering_0520', 'name is invalid' ] + self.display_manage_repository_page( freebayes_repository, + strings_displayed=strings_displayed, + strings_not_displayed=[ 'Repository dependencies' ] ) + self.display_manage_repository_page( filtering_repository, + strings_displayed=[ 'Repository dependencies', self.get_repository_tip( freebayes_repository ) ], + strings_not_displayed=[] ) + + def test_0015_verify_repository_metadata( self ): + '''Verify that the repositories are not marked as downloadable.''' + ''' + This is step 3 - Make sure each repository's repository_metadata record has the downloadable column marked as False. + ''' + freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_metadata = self.get_repository_metadata_by_changeset_revision( freebayes_repository, self.get_repository_tip( freebayes_repository ) ) + filtering_metadata = self.get_repository_metadata_by_changeset_revision( filtering_repository, self.get_repository_tip( filtering_repository ) ) + assert not filtering_metadata.downloadable, 'Repository filtering_0520 is incorrectly marked as downloadable.' + assert not freebayes_metadata.downloadable, 'Repository freebayes_0520 is incorrectly marked as downloadable.' diff -r 1d57caac677cbbd8465c149b6a091684b21af1f8 -r 5c6c916b0b9862cf572af3a70e87a1f20546e6fe test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz Binary file test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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