November 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by Bitbucket 08 Nov '12

08 Nov '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c2e7520982ef/ changeset: c2e7520982ef user: carlfeberhard date: 2012-11-08 20:42:26 summary: (alt)history: move show_deleted, show_hidden to the client. galaxy.util: added string_as_bool_or_none which parses True/False/None values from controller args. affected #: 11 files diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -339,6 +339,24 @@ else: return False +def string_as_bool_or_none( string ): + """ + Returns True, None or False based on the argument: + True if passed True, 'True', 'Yes', or 'On' + None if passed None or 'None' + False otherwise + + Note: string comparison is case-insensitive so lowecase versions of those + function equivalently. + """ + string = str( string ).lower() + if string in ( 'true', 'yes', 'on' ): + return True + elif string == 'none': + return None + else: + return False + def listify( item ): """ Make a single item a single item list, or return a list if passed a diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -98,7 +98,8 @@ return trans.fill_template_mako( "/my_data.mako" ) @web.expose - def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None, **kwd ): + #def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None, **kwd ): + def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): """ Display the current history, creating a new history if necessary. NOTE: No longer accepts "id" or "template" options for security reasons. @@ -116,9 +117,9 @@ show_deleted=util.string_as_bool( show_deleted ), show_hidden=util.string_as_bool( show_hidden ) ) else: - show_deleted = util.string_as_bool( show_deleted ) - show_hidden = util.string_as_bool( show_hidden ) - show_purged = util.string_as_bool( show_deleted ) + show_deleted = util.string_as_bool_or_none( show_deleted ) + show_purged = show_deleted + show_hidden = util.string_as_bool_or_none( show_hidden ) datasets = [] history_panel_template = "root/history.mako" @@ -128,6 +129,7 @@ if 'USE_ALTERNATE' in locals(): datasets = self.get_history_datasets( trans, history, show_deleted=True, show_hidden=True, show_purged=True ) + #datasets = self.get_history_datasets( trans, history, show_deleted, show_hidden, show_purged ) history_panel_template = "root/alternate_history.mako" else: diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -17,10 +17,10 @@ name : '', state : '', - //TODO: wire these to items (or this) - show_deleted : false, - show_hidden : false, - + ////TODO: wire these to items (or this) + //show_deleted : false, + //show_hidden : false, + // diskSize : 0, deleted : false, diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -8,6 +8,8 @@ anon user, mako template init: bug: rename url seems to be wrong url + BUG: shouldn't have tag/anno buttons (on hdas) + logged in, mako template: BUG: meter is not updating RELIABLY on change:nice_size BUG: am able to start upload even if over quota - 'runs' forever @@ -54,6 +56,8 @@ show_deleted/hidden: use storage on/off ui + need urls + change template move histview fadein/out in render to app? don't draw body until it's first expand event localize all @@ -124,10 +128,30 @@ // data that needs to be persistant over page refreshes // (note the key function which uses the history id as well) - this.storage = new PersistantStorage( - 'HistoryView.' + this.model.get( 'id' ), - { expandedHdas : {} } - ); + this.storage = new PersistantStorage( 'HistoryView.' + this.model.get( 'id' ), { + expandedHdas : {}, + show_deleted : false, + show_hidden : false + }); + this.log( 'this.storage:', this.storage.get() ); + + // get the show_deleted/hidden settings giving priority to values passed into initialize, but + // using web storage otherwise + this.log( 'show_deleted:', attributes.show_deleted, 'show_hidden', attributes.show_hidden ); + // if the page has specifically requested show_deleted/hidden, these will be either true or false + // (as opposed to undefined, null) - and we give priority to that setting + if( ( attributes.show_deleted === true ) || ( attributes.show_deleted === false ) ){ + // save them to web storage + this.storage.set( 'show_deleted', attributes.show_deleted ); + } + if( ( attributes.show_hidden === true ) || ( attributes.show_hidden === false ) ){ + this.storage.set( 'show_hidden', attributes.show_hidden ); + } + // pull show_deleted/hidden from the web storage if the page hasn't specified whether to show_deleted/hidden, + this.show_deleted = this.storage.get( 'show_deleted' ); + this.show_hidden = this.storage.get( 'show_hidden' ); + this.log( 'this.show_deleted:', this.show_deleted, 'show_hidden', this.show_hidden ); + this.log( '(now) this.storage:', this.storage.get() ); // bind events from the model's hda collection //this.model.bind( 'change', this.render, this ); @@ -189,7 +213,8 @@ // render the main template, tooltips //NOTE: this is done before the items, since item views should handle theirs themselves newRender.append( HistoryPanel.templates.historyPanel( modelJson ) ); - newRender.find( '.tooltip' ).tooltip(); + newRender.find( '.tooltip' ).tooltip({ placement: 'bottom' }); + this.setUpActionButton( newRender.find( '#history-action-popup' ) ); // render hda views (if any and any shown (show_deleted/hidden) if( !this.model.hdas.length @@ -227,13 +252,26 @@ return this; }, + setUpActionButton : function( $button ){ + var historyPanel = this, + show_deletedText = ( this.storage.get( 'show_deleted' ) )?( 'Hide deleted' ):( 'Show deleted' ), + show_hiddenText = ( this.storage.get( 'show_hidden' ) )?( 'Hide hidden' ):( 'Show hidden' ), + menuActions = {}; + menuActions[ _l( 'refresh' ) ] = function(){ window.location.reload(); }; + menuActions[ _l( 'collapse all' ) ] = function(){ historyPanel.hideAllHdaBodies(); }; + menuActions[ _l( show_deletedText ) ] = function(){ historyPanel.toggleShowDeleted(); }; + menuActions[ _l( show_hiddenText ) ] = function(){ historyPanel.toggleShowHidden(); }; + make_popupmenu( $button, menuActions ); + }, + // set up a view for each item to be shown, init with model and listeners, cache to map ( model.id : view ) renderItems : function( $whereTo ){ this.hdaViews = {}; var historyView = this, - show_deleted = this.model.get( 'show_deleted' ), - show_hidden = this.model.get( 'show_hidden' ), - visibleHdas = this.model.hdas.getVisible( show_deleted, show_hidden ); + visibleHdas = this.model.hdas.getVisible( + this.storage.get( 'show_deleted' ), + this.storage.get( 'show_hidden' ) + ); // only render the shown hdas _.each( visibleHdas, function( hda ){ @@ -293,6 +331,8 @@ async_save_text( "history-annotation-container", "history-annotation", this.urls.annotate, "new_annotation", 18, true, 4 ); + + //this.$( 'button' ).button(); }, // update the history size display (curr. upper right of panel) @@ -300,6 +340,10 @@ this.$el.find( '#history-size' ).text( this.model.get( 'nice_size' ) ); }, + events : { + 'click #history-tag' : 'loadAndDisplayTags' + }, + //TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here showQuotaMessage : function( userData ){ var msg = this.$el.find( '#quota-message-container' ); @@ -314,9 +358,14 @@ if( !msg.is( ':hidden' ) ){ msg.slideUp( 'fast' ); } }, - events : { - 'click #history-collapse-all' : 'hideAllHdaBodies', - 'click #history-tag' : 'loadAndDisplayTags' + toggleShowDeleted : function( x, y, z ){ + this.storage.set( 'show_deleted', !this.storage.get( 'show_deleted' ) ); + this.render(); + }, + + toggleShowHidden : function(){ + this.storage.set( 'show_hidden', !this.storage.get( 'show_hidden' ) ); + this.render(); }, // collapse all hda bodies diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/dataset/hda-edit.js --- /dev/null +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -0,0 +1,1 @@ +var HDAView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this._clearReferences();this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null;this.showParamsButton=null;this.rerunButton=null;this.visualizationsButton=null;this.tagButton=null;this.annotateButton=null},_render_warnings:function(){return $(jQuery.trim(HDAView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={icon_class:"display"};if(this.model.get("purged")){a.enabled=false;a.title="Cannot display datasets removed from disk"}else{a.title="Display data in browser";a.href=this.urls.display}if(this.model.get("for_editing")){a.target="galaxy_main"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title="Cannot edit attributes of datasets removed from disk"}else{if(a){b.title="Undelete dataset to edit attributes"}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((!this.model.get("for_editing"))||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={title:"Delete",href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDAView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDAView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HDAView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a&&a.length)||!(f)){return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:"Visualize",href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[h]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.tags.get)){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.annotation.get)){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HDAView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b,a){var c=this.$el.find(".historyItemBody");a=(a===undefined)?(!c.is(":visible")):(a);if(a){c.slideDown("fast")}else{c.slideUp("fast")}this.trigger("toggleBodyVisibility",this.model.get("id"),a)},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(e){var f=window.parent;f.show_modal("View Data in a New or Saved Visualization","",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal("Add Data to Saved Visualization",e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/dataset/hda-model.js --- /dev/null +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -0,0 +1,1 @@ +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"",state:"",data_type:null,file_size:0,meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:false,for_editing:true},url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",OK:"ok",EMPTY:"empty",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return}var b=this;_.each(a,function(e,c){var d=b.get(e);d.fetch()})},toString:function(){return("HDACollection("+this.ids().join(",")+")")}}); \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/history/history-model.js --- /dev/null +++ b/static/scripts/packed/mvc/history/history-model.js @@ -0,0 +1,1 @@ +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",show_deleted:false,show_hidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/history/history-panel.js --- /dev/null +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -0,0 +1,1 @@ +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{}});this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip();if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},renderItems:function(c){this.hdaViews={};var b=this,a=this.model.get("show_deleted"),e=this.model.get("show_hidden"),d=this.model.hdas.getVisible(a,e);_.each(d,function(h){var g=h.get("id"),f=b.storage.get("expandedHdas").get(g);b.hdaViews[g]=new HDAView({model:h,expanded:f,urlTemplates:b.hdaUrlTemplates});b.setUpHdaListeners(b.hdaViews[g]);c.prepend(b.hdaViews[g].render().$el)});return d.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}});b.bind("rendered:ready",function(){a.trigger("hda:rendered:ready")})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},events:{"click #history-collapse-all":"hideAllHdaBodies","click #history-tag":"loadAndDisplayTags"},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 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 @@ -7,232 +7,157 @@ function program1(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\"\n title=\"Click to rename history\">"; + buffer += "\n <div id=\"history-name\" class=\"tooltip editable-text\"\n title=\"Click to rename history\">"; foundHelper = helpers.name; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n "; + buffer += escapeExpression(stack1) + "</div>\n "; return buffer;} function program3(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip\"\n title=\"You must be logged in to edit your history name\">"; + buffer += "\n <div id=\"history-name\" class=\"tooltip\"\n title=\"You must be logged in to edit your history name\">"; foundHelper = helpers.name; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n "; + buffer += escapeExpression(stack1) + "</div>\n "; return buffer;} function program5(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-secondary-links\" style=\"float: right;\">\n <a id=\"history-tag\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; + return buffer;} +function program6(depth0,data) { - return "refresh";} + + return "Edit history tags";} -function program7(depth0,data) { +function program8(depth0,data) { - return "collapse all";} + return "Edit history annotation";} -function program9(depth0,data) { +function program10(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <a id=\"history-tag\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + buffer += "\n "; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + buffer += "\n "; + return buffer;} +function program11(depth0,data) { + + var stack1, foundHelper; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; - return buffer;} -function program10(depth0,data) { - - - return "Edit history tags";} - + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} function program12(depth0,data) { - return "Edit history annotation";} + return "You are currently viewing a deleted history!";} function program14(depth0,data) { - var buffer = "", stack1, foundHelper; - buffer += "\n <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_deleted; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } + var buffer = "", stack1; + buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + stack1 = depth0.annotation; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(17, program17, data),fn:self.program(15, program15, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; + buffer += "\n </div>\n </div>\n </div>\n </div>\n "; return buffer;} function program15(depth0,data) { - - return "hide deleted";} + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.annotation; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n "; + return buffer;} function program17(depth0,data) { - var buffer = "", stack1, foundHelper; - buffer += "\n <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_hidden; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; - return buffer;} -function program18(depth0,data) { - - return "hide hidden";} + return "\n <em>Describe or add notes to history</em>\n ";} -function program20(depth0,data) { +function program19(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n"; - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n"; - return buffer;} -function program21(depth0,data) { - - var stack1, foundHelper; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }} -function program22(depth0,data) { - - - return "You are currently viewing a deleted history!";} - -function program24(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; - stack1 = depth0.annotation; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n </div>\n </div>\n "; - return buffer;} -function program25(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - foundHelper = helpers.annotation; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\n "; - return buffer;} - -function program27(depth0,data) { - - - return "\n <em>Describe or add notes to history</em>\n ";} - -function program29(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n<div id=\"message-container\">\n <div class=\""; + buffer += "\n <div id=\"message-container\">\n <div class=\""; foundHelper = helpers.status; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "message\">\n "; + buffer += escapeExpression(stack1) + "message\">\n "; foundHelper = helpers.message; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\n </div><br />\n</div>\n"; + buffer += escapeExpression(stack1) + "\n </div><br />\n </div>\n "; return buffer;} -function program31(depth0,data) { +function program21(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start";} - buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; - buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; + buffer += "\n<div id=\"history-controls\">\n <div id=\"history-title-area\" class=\"historyLinks\">\n\n <div id=\"history-name-container\" style=\"float: left;\">\n "; + buffer += "\n "; + stack1 = depth0.user; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n\n <a id=\"history-action-popup\" href=\"javascript:void(0);\" style=\"float: right;\">\n <span class=\"ficon cog large\"></span>\n </a>\n <div style=\"clear: both;\"></div>\n </div>\n\n <div id=\"history-subtitle-area\">\n <div id=\"history-size\" style=\"float:left;\">"; foundHelper = helpers.nice_size; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</div>\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + buffer += "\n <div style=\"clear: both;\"></div>\n </div>\n\n "; + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.base; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n "; + buffer += "\n\n "; + buffer += "\n "; + buffer += "\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n</div>\n<div style=\"clear: both;\"></div>\n\n"; - buffer += "\n<div class=\"historyLinks\">\n "; - stack1 = depth0.show_deleted; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - stack1 = depth0.show_hidden; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); + buffer += "\n\n "; + stack1 = depth0.message; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n\n"; - stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - buffer += "\n"; - buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n "; - stack1 = depth0.user; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n\n"; - stack1 = depth0.message; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n<div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n</div>\n\n<div id=\""; + buffer += "\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n </div>\n</div>\n\n<div id=\""; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>"; return buffer;}); diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -106,86 +106,80 @@ --><script type="text/template" class="template-history" id="template-history-historyPanel"> {{! history name (if any) }} -<div id="history-name-area" class="historyLinks"> - <div id="history-name-container" style="position: relative;"> - {{! TODO: factor out conditional css }} - <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{nice_size}}</div> - {{#if user.email}} - <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" +<div id="history-controls"> + <div id="history-title-area" class="historyLinks"> + + <div id="history-name-container" style="float: left;"> + {{! TODO: factor out conditional css }} + {{#if user.email}} + <div id="history-name" class="tooltip editable-text" title="Click to rename history">{{name}}</div> - {{else}} - <div id="history-name" style="margin-right: 50px;" class="tooltip" + {{else}} + <div id="history-name" class="tooltip" title="You must be logged in to edit your history name">{{name}}</div> - {{/if}} - </div> -</div> -<div style="clear: both;"></div> + {{/if}} + </div> -<div id="top-links" class="historyLinks"> - <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{urls.base}}"></a> - <a title='{{#local}}collapse all{{/local}}' id="history-collapse-all" - class='icon-button toggle tooltip' href='javascript:void(0);'></a> - <div style="width: 40px; float: right; white-space: nowrap;"> - {{#if user.email}} - <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" - class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a> - <a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" - class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a> - {{/if}} - </div> -</div> -<div style="clear: both;"></div> - -{{! TODO: move to js with no reload - use each with historyLinks }} -<div class="historyLinks"> - {{#if show_deleted}} - <a href="{{urls.hide_deleted}}">{{#local}}hide deleted{{/local}}</a> - {{/if}} - {{#if show_hidden}} - <a href="{{urls.hide_hidden}}">{{#local}}hide hidden{{/local}}</a> - {{/if}} -</div> - -{{#if deleted}} -{{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} -{{/if}} - -{{! tags and annotations }} -{{! TODO: move inline styles out }} -<div style="margin: 0px 5px 10px 5px"> - - {{#if user.email}} - <div id="history-tag-area" style="display: none"> - <strong>Tags:</strong> - <div class="tag-elt"></div> + <a id="history-action-popup" href="javascript:void(0);" style="float: right;"> + <span class="ficon cog large"></span> + </a> + <div style="clear: both;"></div></div> - <div id="history-annotation-area" style="display: none"> - <strong>Annotation / Notes:</strong> - <div id="history-annotation-container"> - <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> - {{#if annotation}} - {{annotation}} - {{else}} - <em>Describe or add notes to history</em> - {{/if}} + <div id="history-subtitle-area"> + <div id="history-size" style="float:left;">{{nice_size}}</div> + {{#if user.email}} + <div id="history-secondary-links" style="float: right;"> + <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" + class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a> + <a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" + class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a></div> + {{/if}} + <div style="clear: both;"></div> + </div> + + {{#if deleted}} + {{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} + {{/if}} + + {{! tags and annotations }} + {{! TODO: move inline styles out }} + {{#if user.email}} + <div id="history-tag-annotation"> + + <div id="history-tag-area" style="display: none"> + <strong>Tags:</strong> + <div class="tag-elt"></div> + </div> + + <div id="history-annotation-area" style="display: none"> + <strong>Annotation / Notes:</strong> + <div id="history-annotation-container"> + <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> + {{#if annotation}} + {{annotation}} + {{else}} + <em>Describe or add notes to history</em> + {{/if}} + </div> + </div></div></div> {{/if}} -</div> -{{#if message}} -<div id="message-container"> - <div class="{{status}}message"> - {{message}} - </div><br /> -</div> -{{/if}} + {{#if message}} + <div id="message-container"> + <div class="{{status}}message"> + {{message}} + </div><br /> + </div> + {{/if}} -<div id="quota-message-container" style="display: none"> - <div id="quota-message" class="errormessage"> - You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. + <div id="quota-message-container" style="display: none"> + <div id="quota-message" class="errormessage"> + You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. + </div></div></div> diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -42,9 +42,9 @@ 'No data: ', 'format: ', 'database: ', - # localized data.dbkey?? - localize in the datasetup above + #TODO localized data.dbkey?? 'Info: ', - # localized display_app.display_name?? - localize above + #TODO localized display_app.display_name?? # _( link_app.name ) # localized peek...ugh 'Error: unknown dataset state', @@ -63,12 +63,6 @@ encoded_id_template = '<%= id %>' url_dict = { - # TODO:?? next 3 needed? - 'base' : h.url_for( controller="/history" ), - ##TODO: move these into the historyMV - 'hide_deleted' : h.url_for( controller="/history", show_deleted=False ), - 'hide_hidden' : h.url_for( controller="/history", show_hidden=False ), - ##TODO: into their own MVs 'rename' : h.url_for( controller="/history", action="rename_async", id=encoded_id_template ), @@ -294,15 +288,14 @@ // add user data to history // i don't like this history+user relationship, but user authentication changes views/behaviour history.user = user; - // is page sending in show settings? if so override history's - //TODO: move into historyPanel - history.show_deleted = ${ 'true' if show_deleted else 'false' }; - history.show_hidden = ${ 'true' if show_hidden else 'false' }; var historyPanel = new HistoryPanel({ - model : new History( history, hdas ), - urlTemplates: galaxy_paths.attributes, - logger : console + model : new History( history, hdas ), + urlTemplates : galaxy_paths.attributes, + logger : console, + // is page sending in show settings? if so override history's + show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, + show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) } }); historyPanel.render(); if( !Galaxy.currHistoryPanel ){ Galaxy.currHistoryPanel = historyPanel; } @@ -317,6 +310,7 @@ // QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history) // create it and join them here for now (via events) //TODO: this really belongs in the masthead + //TODO: and the quota message (curr. in the history panel) belongs somewhere else //window.currUser.logger = console; var quotaMeter = new UserQuotaMeter({ @@ -351,30 +345,50 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css("base", "history", "autocomplete_tagging" )} + ${h.css( + "base", + "history", + "autocomplete_tagging" + )} <style> ## TODO: move to base.less .historyItemBody { display: none; } - div.form-row { - padding: 5px 5px 5px 0px; + + #history-controls { + /*border: 1px solid white;*/ + margin-bottom: 5px; + padding: 5px; } - #top-links { - margin-bottom: 15px; - } - #history-name-container { - color: gray; - font-weight: bold; + + #history-title-area { + margin: 0px 0px 5px 0px; + /*border: 1px solid red;*/ } #history-name { word-wrap: break-word; + font-weight: bold; + color: black; } .editable-text { border: solid transparent 1px; - padding: 3px; - margin: -4px; } + #history-name-container input { + width: 90%; + margin: -2px 0px -3px -4px; + font-weight: bold; + color: black; + } + + #history-subtitle-area { + /*border: 1px solid green;*/ + } + #history-size { + } + #history-secondary-links { + } + </style><noscript> https://bitbucket.org/galaxy/galaxy-central/changeset/6344832c535a/ changeset: 6344832c535a user: carlfeberhard date: 2012-11-08 20:43:26 summary: pack scripts affected #: 4 files diff -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 -r 6344832c535aab0a8cc4a57be1414fc179e8540b static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",show_deleted:false,show_hidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file diff -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 -r 6344832c535aab0a8cc4a57be1414fc179e8540b 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{}});this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip();if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},renderItems:function(c){this.hdaViews={};var b=this,a=this.model.get("show_deleted"),e=this.model.get("show_hidden"),d=this.model.hdas.getVisible(a,e);_.each(d,function(h){var g=h.get("id"),f=b.storage.get("expandedHdas").get(g);b.hdaViews[g]=new HDAView({model:h,expanded:f,urlTemplates:b.hdaUrlTemplates});b.setUpHdaListeners(b.hdaViews[g]);c.prepend(b.hdaViews[g].render().$el)});return d.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}});b.bind("rendered:ready",function(){a.trigger("hda:rendered:ready")})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},events:{"click #history-collapse-all":"hideAllHdaBodies","click #history-tag":"loadAndDisplayTags"},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());this.log("show_deleted:",a.show_deleted,"show_hidden",a.show_hidden);if((a.show_deleted===true)||(a.show_deleted===false)){this.storage.set("show_deleted",a.show_deleted)}if((a.show_hidden===true)||(a.show_hidden===false)){this.storage.set("show_hidden",a.show_hidden)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("this.show_deleted:",this.show_deleted,"show_hidden",this.show_hidden);this.log("(now) this.storage:",this.storage.get());this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});this.setUpActionButton(c.find("#history-action-popup"));if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},setUpActionButton:function(e){var c=this,d=(this.storage.get("show_deleted"))?("Hide deleted"):("Show deleted"),a=(this.storage.get("show_hidden"))?("Hide hidden"):("Show hidden"),b={};b[_l("refresh")]=function(){window.location.reload()};b[_l("collapse all")]=function(){c.hideAllHdaBodies()};b[_l(d)]=function(){c.toggleShowDeleted()};b[_l(a)]=function(){c.toggleShowHidden()};make_popupmenu(e,b)},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a.setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}});b.bind("rendered:ready",function(){a.trigger("hda:rendered:ready")})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},events:{"click #history-tag":"loadAndDisplayTags"},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},toggleShowDeleted:function(a,c,b){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 -r 6344832c535aab0a8cc4a57be1414fc179e8540b 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(l,z,x,s,G){x=x||l.helpers;var y="",o,n,f="function",e=this.escapeExpression,v=this,c=x.blockHelperMissing;function u(L,K){var I="",J,H;I+='\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text"\n title="Click to rename history">';H=x.name;if(H){J=H.call(L,{hash:{}})}else{J=L.name;J=typeof J===f?J():J}I+=e(J)+"</div>\n ";return I}function t(L,K){var I="",J,H;I+='\n <div id="history-name" style="margin-right: 50px;" class="tooltip"\n title="You must be logged in to edit your history name">';H=x.name;if(H){J=H.call(L,{hash:{}})}else{J=L.name;J=typeof J===f?J():J}I+=e(J)+"</div>\n ";return I}function r(I,H){return"refresh"}function q(I,H){return"collapse all"}function k(L,K){var I="",J,H;I+='\n <a id="history-tag" title="';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(10,F,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(10,F,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(12,E,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(12,E,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n ';return I}function F(I,H){return"Edit history tags"}function E(I,H){return"Edit history annotation"}function D(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_deleted;J=typeof J===f?J():J;I+=e(J)+'">';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(15,C,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(15,C,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function C(I,H){return"hide deleted"}function B(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_hidden;J=typeof J===f?J():J;I+=e(J)+'">';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(18,A,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(18,A,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function A(I,H){return"hide hidden"}function p(L,K){var I="",J,H;I+="\n";H=x.warningmessagesmall;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(21,m,K)})}else{J=L.warningmessagesmall;J=typeof J===f?J():J}if(!x.warningmessagesmall){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(21,m,K)})}if(J||J===0){I+=J}I+="\n";return I}function m(K,J){var I,H;H=x.local;if(H){I=H.call(K,{hash:{},inverse:v.noop,fn:v.program(22,j,J)})}else{I=K.local;I=typeof I===f?I():I}if(!x.local){I=c.call(K,I,{hash:{},inverse:v.noop,fn:v.program(22,j,J)})}if(I||I===0){return I}else{return""}}function j(I,H){return"You are currently viewing a deleted history!"}function i(K,J){var H="",I;H+='\n <div id="history-tag-area" style="display: none">\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';I=K.annotation;I=x["if"].call(K,I,{hash:{},inverse:v.program(27,g,J),fn:v.program(25,h,J)});if(I||I===0){H+=I}H+="\n </div>\n </div>\n </div>\n ";return H}function h(L,K){var I="",J,H;I+="\n ";H=x.annotation;if(H){J=H.call(L,{hash:{}})}else{J=L.annotation;J=typeof J===f?J():J}I+=e(J)+"\n ";return I}function g(I,H){return"\n <em>Describe or add notes to history</em>\n "}function d(L,K){var I="",J,H;I+='\n<div id="message-container">\n <div class="';H=x.status;if(H){J=H.call(L,{hash:{}})}else{J=L.status;J=typeof J===f?J():J}I+=e(J)+'message">\n ';H=x.message;if(H){J=H.call(L,{hash:{}})}else{J=L.message;J=typeof J===f?J():J}I+=e(J)+"\n </div><br />\n</div>\n";return I}function w(I,H){return"Your history is empty. 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o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") 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j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(v,w){v.update_radius_bounds(r[w])});g.each(this.chords_views,function(v){v.update_radius_bounds(r[0])});var q=this.circular_views.length,u=(t.get("track_type")==="LineTrack"?d:e),n=new u({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var e=f.extend({get_data_bounds:function(o){var n=g.map(o,function(p){if(typeof p==="string"||!p.max){return 0}return p.max});return[0,(n&&typeof n!=="string"?this._quantile(values,0.98):0)]}});var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});return{CircsterView:a}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var A=(y.get("track_type")==="LineTrack"?d:e),x=new A({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(v,w){v.update_radius_bounds(r[w])});g.each(this.chords_views,function(v){v.update_radius_bounds(r[0])});var q=this.circular_views.length,u=(t.get("track_type")==="LineTrack"?d:e),n=new u({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var e=f.extend({get_data_bounds:function(o){var n=g.map(o,function(p){if(typeof p==="string"||!p.max){return 0}return p.max});return[0,(n&&typeof n!=="string"?this._quantile(values,0.98):0)]}});var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});return{CircsterView:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the shed_tool_data_table_config to the functional test's app.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/86fbf6e15f79/ changeset: 86fbf6e15f79 user: greg date: 2012-11-08 17:41:21 summary: Add the shed_tool_data_table_config to the functional test's app. affected #: 1 file diff -r 762d4010a9a534ce5237d7a0bb6d317a9d9501ac -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -169,6 +169,7 @@ tool_data_table_config_path = 'tool_data_table_conf.test.xml' else: tool_data_table_config_path = 'tool_data_table_conf.xml' + shed_tool_data_table_config = 'shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) @@ -266,6 +267,7 @@ tool_parse_help = False, test_conf = "test.conf", tool_data_table_config_path = tool_data_table_config_path, + shed_tool_data_table_config = shed_tool_data_table_config, log_destination = "stdout", use_heartbeat = False, allow_user_creation = True, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Provide a warning message when uploading files to a toolshed repository and a tool_dependencies.xml has been provided, but tool_dependencies metadata has not been generated.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/762d4010a9a5/ changeset: 762d4010a9a5 user: dan date: 2012-11-08 16:52:45 summary: Provide a warning message when uploading files to a toolshed repository and a tool_dependencies.xml has been provided, but tool_dependencies metadata has not been generated. affected #: 1 file diff -r d3054b066218eacd366e618cc97535d059d8bf6a -r 762d4010a9a534ce5237d7a0bb6d317a9d9501ac lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -160,6 +160,7 @@ # Get the new repository tip. if tip == repository.tip: message = 'No changes to repository. ' + status = 'warning' else: if ( isgzip or isbz2 ) and uncompress_file: uncompress_str = ' uncompressed and ' @@ -182,6 +183,16 @@ message += " %d files were removed from the repository root. " % len( files_to_remove ) kwd[ 'message' ] = message set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) + #provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to e.g. a requirement tag mismatch + if get_config_from_disk( 'tool_dependencies.xml', repo_dir ): + if repository.metadata_revisions: + metadata_dict = repository.metadata_revisions[0].metadata + else: + metadata_dict = {} + if 'tool_dependencies' not in metadata_dict: + message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml". ' + status = 'warning' + log.debug( 'Error in tool dependencies for repository %s: %s.' % ( repository.id, repository.name ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository', 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: Add the new ched_tool_data_table_config setting to the tool shed's config object.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d3054b066218/ changeset: d3054b066218 user: greg date: 2012-11-08 16:32:30 summary: Add the new ched_tool_data_table_config setting to the tool shed's config object. affected #: 1 file diff -r b5ce9451c5d190f0507f3b2c484afe937f12a045 -r d3054b066218eacd366e618cc97535d059d8bf6a lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -48,6 +48,7 @@ self.tool_secret = kwargs.get( "tool_secret", "" ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() ) self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) + self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) # Location for dependencies if 'tool_dependency_dir' in kwargs: 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: Attempt to make sure .sample files included in an installed tool shed repository are only copied to ~/tool-data if they are sample data index files.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b5ce9451c5d1/ changeset: b5ce9451c5d1 user: greg date: 2012-11-08 16:01:08 summary: Attempt to make sure .sample files included in an installed tool shed repository are only copied to ~/tool-data if they are sample data index files. affected #: 1 file diff -r 5ff899b77dffce59580991a4b1d4dfbcdc091090 -r b5ce9451c5d190f0507f3b2c484afe937f12a045 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -7,6 +7,7 @@ from galaxy.web.form_builder import SelectField from galaxy.tools import parameters from galaxy.datatypes.checkers import * +from galaxy.datatypes.sniff import is_column_based from galaxy.util.json import * from galaxy.util import inflector from galaxy.tools.search import ToolBoxSearch @@ -546,15 +547,20 @@ shutil.copy( full_source_path, os.path.join( dest_path, copied_file ) ) def copy_sample_files( app, sample_files, tool_path=None, sample_files_copied=None, dest_path=None ): """ - Copy all files to dest_path in the local Galaxy environment that have not already been copied. Those that have been copied - are contained in sample_files_copied. The default value for dest_path is ~/tool-data. + Copy all appropriate files to dest_path in the local Galaxy environment that have not already been copied. Those that have been copied + are contained in sample_files_copied. The default value for dest_path is ~/tool-data. We need to be careful to copy only appropriate + files here because tool shed repositories can contain files ending in .sample that should not be copied to the ~/tool-data directory. """ + filenames_not_to_copy = [ 'tool_data_table_conf.xml.sample' ] sample_files_copied = util.listify( sample_files_copied ) for filename in sample_files: - if filename not in sample_files_copied: + filename_sans_path = os.path.split( filename )[ 1 ] + if filename_sans_path not in filenames_not_to_copy and filename not in sample_files_copied: if tool_path: filename=os.path.join( tool_path, filename ) - copy_sample_file( app, filename, dest_path=dest_path ) + # Attempt to ensure we're copying an appropriate file. + if is_data_index_sample_file( filename ): + copy_sample_file( app, filename, dest_path=dest_path ) def create_repo_info_dict( repository, owner, repository_clone_url, changeset_revision, ctx_rev, metadata ): repo_info_dict = {} repo_info_dict[ repository.name ] = ( repository.description, @@ -1539,9 +1545,11 @@ if shed_tool_conf == file_name: return index, shed_tool_conf_dict def get_tool_index_sample_files( sample_files ): + """Try to return the list of all appropriate tool data sample files included in the repository.""" tool_index_sample_files = [] for s in sample_files: - if s.endswith( '.loc.sample' ): + # The problem with this is that Galaxy does not follow a standard naming convention for file names. + if s.endswith( '.loc.sample' ) or s.endswith( '.xml.sample' ) or s.endswith( '.txt.sample' ): tool_index_sample_files.append( s ) return tool_index_sample_files def get_tool_dependency( trans, id ): @@ -1846,6 +1854,29 @@ parent_id=tool_version_using_parent_id.id ) sa_session.add( tool_version_association ) sa_session.flush() +def is_data_index_sample_file( file_path ): + """ + Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when a tool shed repository is being installed + into a Galaxy instance. + """ + # Currently most data index files are tabular, so check that first. We'll assume that if the file is tabular, it's ok to copy. + if is_column_based( file_path ): + return True + # If the file is any of the following, don't copy it. + if check_html( file_path ): + return False + if check_image( file_path ): + return False + if check_binary( name=file_path ): + return False + if is_bz2( file_path ): + return False + if is_gzip( file_path ): + return False + if check_zip( file_path ): + return False + # Default to copying the file if none of the above are true. + return True def is_downloadable( metadata_dict ): return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ): 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: dan: Add shed_tool_data_table_conf.xml.sample to buildbot_setup.sh.
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5ff899b77dff/ changeset: 5ff899b77dff user: dan date: 2012-11-08 03:16:17 summary: Add shed_tool_data_table_conf.xml.sample to buildbot_setup.sh. affected #: 1 file diff -r 982b9522efca2abf46637870e06c7abf1204be6d -r 5ff899b77dffce59580991a4b1d4dfbcdc091090 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -68,6 +68,7 @@ datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample +shed_tool_data_table_conf.xml.sample migrated_tools_conf.xml.sample tool-data/shared/ensembl/builds.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample 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: dan: Fix for params_to_incoming.
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/982b9522efca/ changeset: 982b9522efca user: dan date: 2012-11-08 03:06:54 summary: Fix for params_to_incoming. affected #: 2 files diff -r ec51a727a497d5912fdd4269571d7c26d7523436 -r 982b9522efca2abf46637870e06c7abf1204be6d lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -115,5 +115,5 @@ incoming[ new_name_prefix + input.test_param.name ] = values[ input.test_param.name ] params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix ) else: - incoming[ name_prefix + input.name ] = input.to_string( input_values.get( input.name ), app ) + incoming[ name_prefix + input.name ] = input.to_html_value( input_values.get( input.name ), app ) diff -r ec51a727a497d5912fdd4269571d7c26d7523436 -r 982b9522efca2abf46637870e06c7abf1204be6d lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -106,6 +106,10 @@ """ return value + def to_html_value( self, value, app ): + """Convert an object value to the value expected from an html post""" + return self.to_string( value, app ) + def to_string( self, value, app ): """Convert a value to a string representation suitable for persisting""" return str( value ) @@ -370,6 +374,11 @@ return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) + def to_html_value( self, value, app ): + if value: + return [ 'true', 'true' ] + else: + return [ 'true' ] def to_python( self, value, app ): return ( value == 'True' ) def get_initial_value( self, trans, context ): 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: clements: Modified docstrings so that Sphinx would not complain about them. However, I couldn't get Sphinx to be happy with all docstrings, so we are still getting 10 warnings (down from over 70 though).
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ec51a727a497/ changeset: ec51a727a497 user: clements date: 2012-11-02 07:25:39 summary: Modified docstrings so that Sphinx would not complain about them. However, I couldn't get Sphinx to be happy with all docstrings, so we are still getting 10 warnings (down from over 70 though). affected #: 25 files diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/converters/fastq_to_fqtoc.py --- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py +++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py @@ -6,11 +6,13 @@ def main(): """ - The format of the file is JSON: - { "sections" : [ - { "start" : "x", "end" : "y", "sequences" : "z" }, - ... - ]} + The format of the file is JSON:: + + { "sections" : [ + { "start" : "x", "end" : "y", "sequences" : "z" }, + ... + ]} + This works only for UNCOMPRESSED fastq files. The Python GzipFile does not provide seekable offsets via tell(), so clients just have to split the slow way """ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/converters/interval_to_fli.py --- a/lib/galaxy/datatypes/converters/interval_to_fli.py +++ b/lib/galaxy/datatypes/converters/interval_to_fli.py @@ -1,12 +1,16 @@ ''' Creates a feature location index (FLI) for a given BED/GFF file. -FLI index has the form: +FLI index has the form:: + [line_length] <symbol1_in_lowercase><tab><symbol1><tab><location><symbol2_in_lowercase><tab><symbol2><tab><location> ... + where location is formatted as: + contig:start-end + and symbols are sorted in lexigraphical order. ''' @@ -94,4 +98,4 @@ out.close() if __name__ == '__main__': - main() \ No newline at end of file + main() diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py --- a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py +++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py @@ -78,10 +78,14 @@ """ need to work with rgenetics composite datatypes so in and out are html files with data in extrafiles path - <command interpreter="python"> - pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh' - '$output1' '$output1.files_path' 'plink' - </command> + + .. raw:: xml + + <command interpreter="python"> + pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh' + '$output1' '$output1.files_path' 'plink' + </command> + """ nparm = 7 if len(sys.argv) < nparm: diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -800,11 +800,12 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=[] ): """ - Returns the first LINE_COUNT lines wrapped to WIDTH:: + Returns the first LINE_COUNT lines wrapped to WIDTH - ## >>> fname = get_test_fname('4.bed') - ## >>> get_file_peek(fname) - ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' + ## >>> fname = get_test_fname('4.bed') + ## >>> get_file_peek(fname) + ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' + """ # Set size for file.readline() to a negative number to force it to # read until either a newline or EOF. Needed for datasets with very diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -46,6 +46,7 @@ process all data lines. Items of interest: + 1. We treat 'overwrite' as always True (we always want to set tabular metadata when called). 2. If a tabular file has no data, it will have one column of type 'str'. 3. We used to check only the first 100 lines when setting metadata and this class's @@ -356,15 +357,18 @@ Determines whether the file is in SAM format A file in SAM format consists of lines of tab-separated data. - The following header line may be the first line: - @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL - or - @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT + The following header line may be the first line:: + + @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL + or + @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT + Data in the OPT column is optional and can consist of tab-separated data For complete details see http://samtools.sourceforge.net/SAM1.pdf - Rules for sniffing as True: + Rules for sniffing as True:: + There must be 11 or more columns of data on each line Columns 2 (FLAG), 4(POS), 5 (MAPQ), 8 (MPOS), and 9 (ISIZE) must be numbers (9 can be negative) We will only check that up to the first 5 alignments are correctly formatted. @@ -579,10 +583,11 @@ A file in ELAND export format consists of lines of tab-separated data. There is no header. - Rules for sniffing as True: - There must be 22 columns on each line - LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct - We will only check that up to the first 5 alignments are correctly formatted. + Rules for sniffing as True:: + + - There must be 22 columns on each line + - LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct + - We will only check that up to the first 5 alignments are correctly formatted. """ import gzip try: diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -51,6 +51,7 @@ store, False otherwise. FIELD DESCRIPTIONS (these apply to all the methods in this class): + :type obj: object :param obj: A Galaxy object with an assigned database ID accessible via the .id attribute. @@ -118,6 +119,7 @@ """ Deletes the object identified by `obj`. See `exists` method for the description of other fields. + :type entire_dir: bool :param entire_dir: If True, delete the entire directory pointed to by extra_dir. For safety reasons, this option applies diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/quota/__init__.py --- a/lib/galaxy/quota/__init__.py +++ b/lib/galaxy/quota/__init__.py @@ -41,6 +41,7 @@ def get_quota( self, user, nice_size=False ): """ Calculated like so: + 1. Anonymous users get the default quota. 2. Logged in users start with the highest of their associated '=' quotas or the default quota, if there are no associated '=' diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -173,17 +173,21 @@ which the request is sent. We cannot use trans.user_is_admin() because the controller is what is important since admin users do not necessarily have permission to do things on items outside of the admin view. + If cntrller is from the admin side ( e.g., library_admin ): - -if item is public, all roles, including private roles, are legitimate. - -if item is restricted, legitimate roles are derived from the users and groups associated - with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or - LIBRARY_MANAGE ) on item. Legitimate roles will include private roles. + + - if item is public, all roles, including private roles, are legitimate. + - if item is restricted, legitimate roles are derived from the users and groups associated + with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or + LIBRARY_MANAGE ) on item. Legitimate roles will include private roles. + If cntrller is not from the admin side ( e.g., root, library ): - -if item is public, all non-private roles, except for the current user's private role, - are legitimate. - -if item is restricted, legitimate roles are derived from the users and groups associated - with each role that is associated with the access permission on item. Private roles, except - for the current user's private role, will be excluded. + + - if item is public, all non-private roles, except for the current user's private role, + are legitimate. + - if item is restricted, legitimate roles are derived from the users and groups associated + with each role that is associated with the access permission on item. Private roles, except + for the current user's private role, will be excluded. """ admin_controller = cntrller in [ 'library_admin' ] roles = set() @@ -1063,9 +1067,10 @@ comma-separated string of folder ids. This method works with the show_library_item() method below, and it returns libraries for which the received user has permission to perform the received actions. Here is an example call to this method to return all - libraries for which the received user has LIBRARY_ADD permission: - libraries = trans.app.security_agent.get_permitted_libraries( trans, user, - [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries for which the received user has LIBRARY_ADD permission:: + + libraries = trans.app.security_agent.get_permitted_libraries( trans, user, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) """ all_libraries = trans.sa_session.query( trans.app.model.Library ) \ .filter( trans.app.model.Library.table.c.deleted == False ) \ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -250,10 +250,11 @@ def set_environment( app, elem, tool_shed_repository ): """ Create a ToolDependency to set an environment variable. This is different from the process used to set an environment variable that is associated - with a package. An example entry in a tool_dependencies.xml file is: - <set_environment version="1.0"> - <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> + with a package. An example entry in a tool_dependencies.xml file is:: + + <set_environment version="1.0"> + <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> """ sa_session = app.model.context.current tool_dependency = None diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -112,16 +112,20 @@ def init_tools( self, config_filename ): """ Read the configuration file and load each tool. The following tags are currently supported: - <toolbox> - <tool file="data_source/upload.xml"/> # tools outside sections - <label text="Basic Tools" id="basic_tools" /> # labels outside sections - <workflow id="529fd61ab1c6cc36" /> # workflows outside sections - <section name="Get Data" id="getext"> # sections - <tool file="data_source/biomart.xml" /> # tools inside sections - <label text="In Section" id="in_section" /> # labels inside sections - <workflow id="adb5f5c93f827949" /> # workflows inside sections - </section> - </toolbox> + + .. raw:: xml + + <toolbox> + <tool file="data_source/upload.xml"/> # tools outside sections + <label text="Basic Tools" id="basic_tools" /> # labels outside sections + <workflow id="529fd61ab1c6cc36" /> # workflows outside sections + <section name="Get Data" id="getext"> # sections + <tool file="data_source/biomart.xml" /> # tools inside sections + <label text="In Section" id="in_section" /> # labels inside sections + <workflow id="adb5f5c93f827949" /> # workflows inside sections + </section> + </toolbox> + """ if self.app.config.get_bool( 'enable_tool_tags', False ): log.info("removing all tool tag associations (" + str( self.sa_session.query( self.app.model.ToolTagAssociation ).count() ) + ")" ) @@ -740,7 +744,8 @@ class ToolOutput( object ): """ Represents an output datasets produced by a tool. For backward - compatibility this behaves as if it were the tuple: + compatibility this behaves as if it were the tuple:: + (format, metadata_source, parent) """ @@ -1079,7 +1084,7 @@ else: self.trackster_conf = None def parse_inputs( self, root ): - """ + r""" Parse the "<inputs>" element and create appropriate `ToolParameter`s. This implementation supports multiple pages and grouping constructs. """ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -31,10 +31,11 @@ def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): """ This method is called under 3 conditions: - 1) When the ToolDataTableManager is initialized (see __init__ above). - 2) Just after the ToolDataTableManager is initialized and the additional entries defined by shed_tool_data_table_conf.xml + + 1. When the ToolDataTableManager is initialized (see __init__ above). + 2. Just after the ToolDataTableManager is initialized and the additional entries defined by shed_tool_data_table_conf.xml are being loaded into the ToolDataTableManager.data_tables. - 3) When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local + 3. When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local Galaxy instance. In this case, we have 2 entry types to handle, files whose root tag is <tables>, for example: """ tree = util.parse_xml( config_filename ) @@ -57,20 +58,24 @@ def add_new_entries_from_config_file( self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False ): """ This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being - installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example: - <tables> + installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example:: + + <tables> +  + <table name="tmap_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/tmap_index.loc" /> + </table> + </tables> + + and files whose root tag is <table>, for example:: + <table name="tmap_indexes" comment_char="#"><columns>value, dbkey, name, path</columns><file path="tool-data/tmap_index.loc" /></table> - </tables> - and files whose root tag is <table>, for example: -  - <table name="tmap_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/tmap_index.loc" /> - </table> + """ tree = util.parse_xml( config_filename ) root = tree.getroot() @@ -119,13 +124,14 @@ class TabularToolDataTable( ToolDataTable ): """ Data stored in a tabular / separated value format on disk, allows multiple - files to be merged but all must have the same column definitions. + files to be merged but all must have the same column definitions:: - <table type="tabular" name="test"> - <column name='...' index = '...' /> - <file path="..." /> - <file path="..." /> - </table> + <table type="tabular" name="test"> + <column name='...' index = '...' /> + <file path="..." /> + <file path="..." /> + </table> + """ type_key = 'tabular' diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -64,16 +64,20 @@ Type: data_meta - When no 'from_' source has been specified in the <options> tag, this will populate the options list with (meta_value, meta_value, False). + When no 'from' source has been specified in the <options> tag, this will populate the options list with (meta_value, meta_value, False). Otherwise, options which do not match the metadata value in the column are discarded. Required Attributes: - ref: Name of input dataset - key: Metadata key to use for comparison - column: column in options to compare with (not required when not associated with input options) + + - ref: Name of input dataset + - key: Metadata key to use for comparison + - column: column in options to compare with (not required when not associated with input options) + Optional Attributes: - multiple: Option values are multiple, split column by separator (True) - separator: When multiple split by this (,) + + - multiple: Option values are multiple, split column by separator (True) + - separator: When multiple split by this (,) + """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) @@ -132,12 +136,16 @@ Type: param_value Required Attributes: - ref: Name of input value - column: column in options to compare with + + - ref: Name of input value + - column: column in options to compare with + Optional Attributes: - keep: Keep columns matching value (True) - Discard columns matching value (False) - ref_attribute: Period (.) separated attribute chain of input (ref) to use as value for filter + + - keep: Keep columns matching value (True) + Discard columns matching value (False) + - ref_attribute: Period (.) separated attribute chain of input (ref) to use as value for filter + """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) @@ -294,13 +302,15 @@ Type: remove_value - Required Attributes: + Required Attributes:: + value: value to remove from select list or ref: param to refer to or meta_ref: dataset to refer to key: metadata key to compare to + """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/util/heartbeat.py --- a/lib/galaxy/util/heartbeat.py +++ b/lib/galaxy/util/heartbeat.py @@ -134,7 +134,9 @@ Scans a given backtrace stack frames, returns a single quadraple of [filename, line, function-name, text] of the single, deepest, most interesting frame. - Interesting being: + + Interesting being:: + inside the galaxy source code ("/lib/galaxy"), prefreably not an egg. """ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -2397,11 +2397,13 @@ def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ): """ Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates - to an installed tool shed repository. The original_dependency_dict is a single tool dependency definition, an example of which is: - {"name": "bwa", - "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", - "type": "package", - "version": "0.6.2"} + to an installed tool shed repository. The original_dependency_dict is a single tool dependency definition, an example of which is:: + + {"name": "bwa", + "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", + "type": "package", + "version": "0.6.2"} + The new_dependencies_dict is the dictionary generated by the generate_tool_dependency_metadata method. """ new_tool_dependency = None diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/util/topsort.py --- a/lib/galaxy/util/topsort.py +++ b/lib/galaxy/util/topsort.py @@ -9,18 +9,24 @@ value is a list, representing a total ordering that respects all the input constraints. E.g., + topsort( [(1,2), (3,3)] ) + may return any of (but nothing other than) + [3, 1, 2] [1, 3, 2] [1, 2, 3] + because those are the permutations of the input elements that respect the "1 precedes 2" and "3 precedes 3" input constraints. Note that a constraint of the form (x, x) is really just a trick to make sure x appears *somewhere* in the output list. If there's a cycle in the constraints, say + topsort( [(1,2), (2,1)] ) + then CycleError is raised, and the exception object supports many methods to help analyze and break the cycles. This requires a good deal more code than topsort itself! diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -610,11 +610,16 @@ def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ - Returns a dict with the following attributes: + Returns a dict with the following attributes:: + data - a list of variants with the format + + .. raw:: text + [<guid>, <start>, <end>, <name>, cigar, seq] message - error/informative message + """ rval = [] message = None @@ -893,13 +898,17 @@ def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ - Returns a dict with the following attributes: + Returns a dict with the following attributes:: + data - a list of reads with the format - [<guid>, <start>, <end>, <name>, <read_1>, <read_2>, [empty], <mapq_scores>] + [<guid>, <start>, <end>, <name>, <read_1>, <read_2>, [empty], <mapq_scores>] + where <read_1> has the format [<start>, <end>, <cigar>, <strand>, <read_seq>] + and <read_2> has the format [<start>, <end>, <cigar>, <strand>, <read_seq>] + Field 7 is empty so that mapq scores' location matches that in single-end reads. For single-end reads, read has format: [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>, <mapq_score>] @@ -910,6 +919,7 @@ max_low - lowest coordinate for the returned reads max_high - highest coordinate for the returned reads message - error/informative message + """ # No iterator indicates no reads. if iterator is None: diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/visualization/data_providers/phyloviz/newickparser.py --- a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py @@ -112,9 +112,12 @@ def parseNode(self, string, depth): """ Recursive method for parsing newick string, works by stripping down the string into substring of newick contained with brackers, which is used to call itself. - Eg ... ( A, B, (D, E)C, F, G ) ... + + Eg ... ( A, B, (D, E)C, F, G ) ... + We will make the preceeding nodes first A, B, then the internal node C, its children D, E, - and finally the succeeding nodes F, G""" + and finally the succeeding nodes F, G + """ # Base case where there is only an empty string if string == "": diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -708,9 +708,12 @@ selected_value='none', refresh_on_change=False, multiple=False, display=None, size=None ): """ Build a SelectField given a set of objects. The received params are: + - objs: the set of objects used to populate the option list - label_attr: the attribute of each obj (e.g., name, email, etc ) whose value is used to populate each option label. + - If the string 'self' is passed as label_attr, each obj in objs is assumed to be a string, so the obj itself is used + - select_field_name: the name of the SelectField - initial_value: the value of the first option in the SelectField - allows for an option telling the user to select something - selected_value: the value of the currently selected option diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -624,6 +624,7 @@ def handle_user_login( self, user ): """ Login a new user (possibly newly created) + - create a new session - associate new session with user - if old session had a history and it was not associated with a user, associate it with the new session, diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -140,7 +140,7 @@ def get_database_engine_options( kwargs ): """ Allow options for the SQLAlchemy database engine to be passed by using - the prefix "database_engine_option_". + the prefix "database_engine_option". """ conversions = { 'convert_unicode': string_as_bool, diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -48,25 +48,25 @@ POST /api/genomes Download and/or index a genome. - Parameters: + Parameters:: - dbkey DB key of the build to download, ignored unless 'UCSC' is specified as the source - ncbi_name NCBI's genome identifier, ignored unless NCBI is specified as the source - ensembl_dbkey Ensembl's genome identifier, ignored unless Ensembl is specified as the source - url_dbkey DB key to use for this build, ignored unless URL is specified as the source - source Data source for this build. Can be: UCSC, Ensembl, NCBI, URL - indexers POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) - func Allowed values: - 'download' Download and index - 'index' Index only - - Returns: + dbkey DB key of the build to download, ignored unless 'UCSC' is specified as the source + ncbi_name NCBI's genome identifier, ignored unless NCBI is specified as the source + ensembl_dbkey Ensembl's genome identifier, ignored unless Ensembl is specified as the source + url_dbkey DB key to use for this build, ignored unless URL is specified as the source + source Data source for this build. Can be: UCSC, Ensembl, NCBI, URL + indexers POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) + func Allowed values: + 'download' Download and index + 'index' Index only + + Returns:: - If no error: - dict( status: 'ok', job: <job ID> ) + If no error: + dict( status: 'ok', job: <job ID> ) - If error: - dict( status: 'error', error: <error message> ) + If error: + dict( status: 'error', error: <error message> ) """ params = util.Params( payload ) diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -13,12 +13,15 @@ @web.expose_api def index( self, trans, **kwds ): """ - GET /api/tools: returns a list of tools defined by parameters + GET /api/tools: returns a list of tools defined by parameters:: + parameters: + in_panel - if true, tools are returned in panel structure, including sections and labels trackster - if true, only tools that are compatible with Trackster are returned + """ # Read params. diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1980,8 +1980,8 @@ def edgelist_for_workflow_steps( steps ): """ - Create a list of tuples representing edges between `WorkflowSteps` based - on associated `WorkflowStepConnection`s + Create a list of tuples representing edges between ``WorkflowSteps`` based + on associated ``WorkflowStepConnection``s """ edges = [] steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -56,7 +56,7 @@ def get_database_engine_options( kwargs ): """ Allow options for the SQLAlchemy database engine to be passed by using - the prefix "database_engine_option_". + the prefix "database_engine_option". """ conversions = { 'convert_unicode': string_as_bool, diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/mimeparse.py --- a/lib/mimeparse.py +++ b/lib/mimeparse.py @@ -39,18 +39,21 @@ return (type.strip(), subtype.strip(), params) def parse_media_range(range): - """Carves up a media range and returns a tuple of the - (type, subtype, params) where 'params' is a dictionary - of all the parameters for the media range. - For example, the media range 'application/*;q=0.5' would - get parsed into: + r""" + Carves up a media range and returns a tuple of the + (type, subtype, params) where 'params' is a dictionary + of all the parameters for the media range. + For example, the media range 'application/*;q=0.5' would + get parsed into: - ('application', '*', {'q', '0.5'}) + .. raw:: text - In addition this function also guarantees that there - is a value for 'q' in the params dictionary, filling it - in with a proper default if necessary. - """ + ('application', '*', {'q', '0.5'}) + + In addition this function also guarantees that there + is a value for 'q' in the params dictionary, filling it + in with a proper default if necessary. + """ (type, subtype, params) = parse_mime_type(range) if not params.has_key('q') or not params['q'] or \ not float(params['q']) or float(params['q']) > 1\ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTab
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bc5fa254bafc/ changeset: bc5fa254bafc user: greg date: 2012-11-07 22:36:28 summary: Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly. affected #: 11 files diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -76,8 +76,13 @@ self.genomes = Genomes( self ) # Data providers registry. self.data_provider_registry = DataProviderRegistry() - # Tool data tables - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path, self.config.tool_data_table_config_path ) + # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( tool_data_path=self.config.tool_data_path, + config_filename=self.config.tool_data_table_config_path ) + # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. + self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, + tool_data_path=self.tool_data_tables.tool_data_path, + from_shed_config=True ) # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs: diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -66,6 +66,7 @@ tcf = 'tool_conf.xml' self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) + self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) try: self.hours_between_check = int( kwargs.get( 'hours_between_check', 12 ) ) diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -184,7 +184,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -41,8 +41,13 @@ self.datatypes_registry = galaxy.datatypes.registry.Registry() # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) - # Tool data tables - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path, self.config.tool_data_table_config_path ) + # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( tool_data_path=self.config.tool_data_path, + config_filename=self.config.tool_data_table_config_path ) + # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. + self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, + tool_data_path=self.tool_data_tables.tool_data_path, + from_shed_config=True ) # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs: diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -15,17 +15,28 @@ """Manages a collection of tool data tables""" def __init__( self, tool_data_path, config_filename=None ): self.tool_data_path = tool_data_path - self.data_tables = {} - # Store config elements for on-the-fly persistence. - self.data_table_elems = [] + # This stores all defined data table entries from both the tool_data_table_conf.xml file and the shed_tool_data_table_conf.xml file + # at server startup. If tool shed repositories are installed that contain a valid file named tool_data_table_conf.xml.sample, entries + # from that file are inserted into this dict at the time of installation. + self.data_tables = {} + # Store config elements for on-the-fly persistence to the defined shed_tool_data_table_config file name. + self.shed_data_table_elems = [] self.data_table_elem_names = [] if config_filename: - self.load_from_config_file( config_filename, self.tool_data_path ) + self.load_from_config_file( config_filename, self.tool_data_path, from_shed_config=False ) def __getitem__( self, key ): return self.data_tables.__getitem__( key ) def __contains__( self, key ): return self.data_tables.__contains__( key ) - def load_from_config_file( self, config_filename, tool_data_path ): + def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): + """ + This method is called under 3 conditions: + 1) When the ToolDataTableManager is initialized (see __init__ above). + 2) Just after the ToolDataTableManager is initialized and the additional entries defined by shed_tool_data_table_conf.xml + are being loaded into the ToolDataTableManager.data_tables. + 3) When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local + Galaxy instance. In this case, we have 2 entry types to handle, files whose root tag is <tables>, for example: + """ tree = util.parse_xml( config_filename ) root = tree.getroot() table_elems = [] @@ -36,13 +47,14 @@ table_elem_name = table_elem.get( 'name', None ) if table_elem_name and table_elem_name not in self.data_table_elem_names: self.data_table_elem_names.append( table_elem_name ) - self.data_table_elems.append( table_elem ) + if from_shed_config: + self.shed_data_table_elems.append( table_elem ) table = tool_data_table_types[ type ]( table_elem, tool_data_path ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Loaded tool data table '%s'", table.name ) return table_elems - def add_new_entries_from_config_file( self, config_filename, tool_data_path, tool_data_table_config_path, persist=False ): + def add_new_entries_from_config_file( self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False ): """ This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example: @@ -65,7 +77,9 @@ # Make a copy of the current list of data_table_elem_names so we can persist later if changes to the config file are necessary. original_data_table_elem_names = [ name for name in self.data_table_elem_names ] if root.tag == 'tables': - table_elems = self.load_from_config_file( config_filename, tool_data_path ) + table_elems = self.load_from_config_file( config_filename=config_filename, + tool_data_path=tool_data_path, + from_shed_config=True ) else: table_elems = [] type = root.get( 'type', 'tabular' ) @@ -74,23 +88,22 @@ table_elem_name = root.get( 'name', None ) if table_elem_name and table_elem_name not in self.data_table_elem_names: self.data_table_elem_names.append( table_elem_name ) - self.data_table_elems.append( root ) + self.shed_data_table_elems.append( root ) table = tool_data_table_types[ type ]( root, tool_data_path ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Added new tool data table '%s'", table.name ) if persist and self.data_table_elem_names != original_data_table_elem_names: # Persist Galaxy's version of the changed tool_data_table_conf.xml file. - self.to_xml_file( tool_data_table_config_path ) + self.to_xml_file( shed_tool_data_table_config ) return table_elems - def to_xml_file( self, tool_data_table_config_path ): - """Write the current in-memory version of the tool_data-table_conf.xml file to disk.""" - full_path = os.path.abspath( tool_data_table_config_path ) + def to_xml_file( self, shed_tool_data_table_config ): + """Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.""" + full_path = os.path.abspath( shed_tool_data_table_config ) fd, filename = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) - os.write( fd, "\n" ) os.write( fd, '<tables>\n' ) - for elem in self.data_table_elems: + for elem in self.shed_data_table_elems: os.write( fd, '%s' % util.xml_to_string( elem ) ) os.write( fd, '</tables>\n' ) os.close( fd ) diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -753,12 +753,15 @@ tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, shed_config_dict={}, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False ): + resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be an absolute path to a temporary directory containing a clone). If it is an absolute path, the value of relative_install_dir must contain repository.repo_path. + + The value of persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries + should ultimately be persisted to the file referred to by app.config.shed_tool_data_table_config. """ if updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository installed into a local Galaxy instance for which @@ -810,9 +813,9 @@ relative_path, filename = os.path.split( sample_file ) if filename == 'tool_data_table_conf.xml.sample': new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=sample_file, - tool_data_path=app.config.tool_data_path, - tool_data_table_config_path=app.config.tool_data_table_config_path, - persist=False ) + tool_data_path=original_tool_data_path, + shed_tool_data_table_config=app.config.shed_tool_data_table_config, + persist=persist ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -1768,15 +1771,15 @@ return tool, message, sample_files def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ - Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur) - if call is from the Galaxy side (not the tool shed), the new entries will be appended to Galaxy's tool_data_table_conf.xml file on disk. + Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur + if call is from the Galaxy side, not the tool shed), the new entries will be appended to Galaxy's shed_tool_data_table_conf.xml file on disk. """ error = False message = '' try: new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=filename, tool_data_path=app.config.tool_data_path, - tool_data_table_config_path=app.config.tool_data_table_config_path, + shed_tool_data_table_config=app.config.shed_tool_data_table_config, persist=persist ) except Exception, e: message = str( e ) @@ -2143,7 +2146,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: update_in_shed_tool_config( trans.app, repository ) @@ -2221,7 +2225,8 @@ relative_install_dir=repo_dir, repository_files_dir=work_dir, resetting_all_metadata_on_repository=True, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -10,9 +10,8 @@ from galaxy.util.shed_util import generate_clone_url_for_repository_in_tool_shed, generate_message_for_invalid_tools, generate_metadata_for_changeset_revision from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_file_context_from_ctx, get_named_tmpfile_from_ctx from galaxy.util.shed_util import get_parent_id, get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision -from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config -from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, is_downloadable, load_tool_from_config, remove_dir -from galaxy.util.shed_util import reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH +from galaxy.util.shed_util import is_downloadable, load_tool_from_config, remove_dir, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * from galaxy.web.base.controllers.admin import * from galaxy.webapps.community import model @@ -640,7 +639,8 @@ relative_install_dir=repo_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) if metadata_dict: downloadable = is_downloadable( metadata_dict ) repository_metadata = None diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -447,6 +447,12 @@ @web.expose @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): + """ + Handle all changes when a tool shed repository is being deactivated or uninstalled. Notice that if the repository contents include + a file named tool_data_table_conf.xml.sample, it's entries are not removed from the defined config.shed_tool_data_table_config. This + is because it becomes a bit complex to determine if other installed repositories include tools that require the same entry. For now + we'll never delete entries from config.shed_tool_data_table_config, but we may choose to do so in the future if it becomes necessary. + """ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -753,7 +759,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -1491,7 +1498,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: update_in_shed_tool_config( trans.app, repository ) @@ -1675,7 +1683,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=True ) + updating_installed_repository=True, + persist=True ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 run.sh --- a/run.sh +++ b/run.sh @@ -13,6 +13,7 @@ reports_wsgi.ini.sample shed_tool_conf.xml.sample tool_conf.xml.sample + shed_tool_data_table_conf.xml.sample tool_data_table_conf.xml.sample tool_sheds_conf.xml.sample openid_conf.xml.sample diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 shed_tool_data_table_conf.xml.sample --- /dev/null +++ b/shed_tool_data_table_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<tables> +</tables> diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -149,6 +149,16 @@ #enable_tool_shed_check = False #hours_between_check = 12 +# XML config file that contains data table entries for the ToolDataTableManager. This file is manually +# maintained by the Galaxy administrator. +#tool_data_table_config_path = tool_data_table_conf.xml + +# XML config file that contains additional data table entries for the ToolDataTableManager. This file +# is automatically generated based on the current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically +# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +#shed_tool_data_table_config = shed_tool_data_table_conf.xml + # Directory where data used by tools is located, see the samples in that # directory and the wiki for help: # http://wiki.g2.bx.psu.edu/Admin/Data%20Integration 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: dan: Allow unhiding all datasets in the current history.
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dbff28bde968/ changeset: dbff28bde968 user: dan date: 2012-11-07 19:50:06 summary: Allow unhiding all datasets in the current history. affected #: 3 files diff -r 932585f1dd8d67c28d2c22003af0d9ae318ef947 -r dbff28bde968a05b787dd53cfca182c53a81eeb7 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -694,6 +694,9 @@ @property def get_disk_size_bytes( self ): return self.get_disk_size( nice_size=False ) + def unhide_datasets( self ): + for dataset in self.datasets: + dataset.mark_unhidden() def get_disk_size( self, nice_size=False ): # unique datasets only db_session = object_session( self ) diff -r 932585f1dd8d67c28d2c22003af0d9ae318ef947 -r dbff28bde968a05b787dd53cfca182c53a81eeb7 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -550,6 +550,20 @@ return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] ) @web.expose + def unhide_datasets( self, trans, current=False, ids=None ): + """Unhide the datasets in the active history -- this does not require a logged in user.""" + if not ids and util.string_as_bool( current ): + histories = [ trans.get_history() ] + refresh_frames = ['history'] + else: + raise NotImplementedError( "You can currently only unhide all the datasets of the current history." ) + for history in histories: + history.unhide_datasets() + trans.sa_session.add( history ) + trans.sa_session.flush() + return trans.show_ok_message( "Your datasets have been unhidden.", refresh_frames=refresh_frames ) + + @web.expose @web.require_login( "rate items" ) @web.json def rate_async( self, trans, id, rating ): diff -r 932585f1dd8d67c28d2c22003af0d9ae318ef947 -r dbff28bde968a05b787dd53cfca182c53a81eeb7 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -43,6 +43,11 @@ "${_("Show Hidden Datasets")}": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}"; }, + "${_("Unhide Hidden Datasets")}": function() { + if ( confirm( "Really unhide all hidden datasets?" ) ) { + galaxy_main.location = "${h.url_for( controller='history', action='unhide_datasets', current=True )}"; + } + }, "${_("Purge Deleted Datasets")}": function() { if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) { galaxy_main.location = "${h.url_for( controller='history', action='purge_deleted_datasets' )}"; 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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