[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fdea658292c9/ changeset: fdea658292c9 user: carlfeberhard date: 2012-11-06 21:54:47 summary: (alt)history: split files up, rework names, add global Galaxy namespace affected #: 6 files diff -r 3d27b35e1c1fa629ec4175f5e613b5a771152377 -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 static/scripts/mvc/dataset/hda-edit.js --- /dev/null +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -0,0 +1,862 @@ +//define([ +// "../mvc/base-mvc" +//], function(){ +//============================================================================== +/** View for editing (working with - as opposed to viewing/read-only) an hda + * + */ +var HDAView = BaseView.extend( LoggableMixin ).extend({ + //??TODO: add alias in initialize this.hda = this.model? + // view for HistoryDatasetAssociation model above + + // uncomment this out see log messages + //logger : console, + + tagName : "div", + className : "historyItemContainer", + + // ................................................................................ SET UP + initialize : function( attributes ){ + this.log( this + '.initialize:', attributes ); + + // render urlTemplates (gen. provided by GalaxyPaths) to urls + if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } + this.urls = this.renderUrls( attributes.urlTemplates, this.model.toJSON() ); + + // whether the body of this hda is expanded (shown) + this.expanded = attributes.expanded || false; + + // re-render the entire view on any model change + this.model.bind( 'change', this.render, this ); + //this.bind( 'all', function( event ){ + // this.log( event ); + //}, this ); + }, + + // urlTemplates is a map (or nested map) of underscore templates (currently, anyhoo) + // use the templates to create the apropo urls for each action this ds could use + renderUrls : function( urlTemplates, modelJson ){ + var hdaView = this, + urls = {}; + _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ + // object == nested templates: recurse + if( _.isObject( urlTemplateOrObj ) ){ + urls[ urlKey ] = hdaView.renderUrls( urlTemplateOrObj, modelJson ); + + // string == template: + } else { + // meta_down load is a special case (see renderMetaDownloadUrls) + //TODO: should be a better (gen.) way to handle this case + if( urlKey === 'meta_download' ){ + urls[ urlKey ] = hdaView.renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); + } else { + urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); + } + } + }); + return urls; + }, + + // there can be more than one meta_file to download, so return a list of url and file_type for each + renderMetaDownloadUrls : function( urlTemplate, modelJson ){ + return _.map( modelJson.meta_files, function( meta_file ){ + return { + url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), + file_type : meta_file.file_type + }; + }); + }, + + // ................................................................................ RENDER MAIN + render : function(){ + var view = this, + id = this.model.get( 'id' ), + state = this.model.get( 'state' ), + itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ), + initialRender = ( this.$el.children().size() === 0 ); + + //console.debug( this + '.render, initial?:', initialRender ); + + this._clearReferences(); + this.$el.attr( 'id', 'historyItemContainer-' + id ); + + itemWrapper + .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) + .addClass( 'historyItem-' + state ); + + itemWrapper.append( this._render_warnings() ); + itemWrapper.append( this._render_titleBar() ); + this.body = $( this._render_body() ); + itemWrapper.append( this.body ); + + //TODO: move to own function: setUpBehaviours + // we can potentially skip this step and call popupmenu directly on the download button + make_popup_menus( itemWrapper ); + + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) + itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); + + // transition... + this.$el.fadeOut( 'fast', function(){ + view.$el.children().remove(); + view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ + view.log( view + ' rendered:', view.$el ); + var renderedEventName = 'rendered'; + + if( initialRender ){ + renderedEventName += ':initial'; + } else if( view.model.inReadyState() ){ + renderedEventName += ':ready'; + } + view.trigger( renderedEventName ); + }); + }); + return this; + }, + + //NOTE: button renderers have the side effect of caching their IconButtonViews to this view + // clear out cached sub-views, dom refs, etc. from prev. render + _clearReferences : function(){ + //??TODO: we should reset these in the button logic checks (i.e. if not needed this.button = null; return null) + //?? do we really need these - not so far + //TODO: at least move these to a map + 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 + // hda warnings including: is deleted, is purged, is hidden (including links to further actions (undelete, etc.)) + _render_warnings : function(){ + // jQ errs on building dom with whitespace - if there are no messages, trim -> '' + return $( jQuery.trim( HDAView.templates.messages( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); + }, + + // ................................................................................ RENDER TITLEBAR + // the part of an hda always shown (whether the body is expanded or not): title link, title buttons + _render_titleBar : function(){ + var titleBar = $( '<div class="historyItemTitleBar" style="overflow: hidden"></div>' ); + titleBar.append( this._render_titleButtons() ); + titleBar.append( '<span class="state-icon"></span>' ); + titleBar.append( this._render_titleLink() ); + return titleBar; + }, + + // ................................................................................ display, edit attr, delete + // icon-button group for the common, most easily accessed actions + //NOTE: these are generally displayed for almost every hda state (tho poss. disabled) + _render_titleButtons : function(){ + // render the display, edit attr and delete icon-buttons + var buttonDiv = $( '<div class="historyItemButtons"></div>' ); + buttonDiv.append( this._render_displayButton() ); + buttonDiv.append( this._render_editButton() ); + buttonDiv.append( this._render_deleteButton() ); + return buttonDiv; + }, + + // icon-button to display this hda in the galaxy main iframe + _render_displayButton : function(){ + // don't show display if not in ready state, error'd, or not accessible + if( ( !this.model.inReadyState() ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } + + var displayBtnData = { + icon_class : 'display' + }; + + // show a disabled display if the data's been purged + if( this.model.get( 'purged' ) ){ + displayBtnData.enabled = false; + displayBtnData.title = 'Cannot display datasets removed from disk'; + + } else { + displayBtnData.title = 'Display data in browser'; + displayBtnData.href = this.urls.display; + } + + if( this.model.get( 'for_editing' ) ){ + displayBtnData.target = 'galaxy_main'; + } + + this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); + return this.displayButton.render().$el; + }, + + // icon-button to edit the attributes (format, permissions, etc.) this hda + _render_editButton : function(){ + // don't show edit while uploading, or if editable + 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 purged = this.model.get( 'purged' ), + deleted = this.model.get( 'deleted' ), + editBtnData = { + title : 'Edit attributes', + href : this.urls.edit, + target : 'galaxy_main', + icon_class : 'edit' + }; + + // disable if purged or deleted and explain why in the tooltip + //TODO: if for_editing + if( deleted || purged ){ + editBtnData.enabled = false; + if( purged ){ + editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; + } else if( deleted ){ + editBtnData.title = 'Undelete dataset to edit attributes'; + } + } + + this.editButton = new IconButtonView({ model : new IconButton( editBtnData ) }); + return this.editButton.render().$el; + }, + + // icon-button to delete this hda + _render_deleteButton : function(){ + // don't show delete if... + if( ( !this.model.get( 'for_editing' ) ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) ){ + return null; + } + + var deleteBtnData = { + title : 'Delete', + href : this.urls[ 'delete' ], + id : 'historyItemDeleter-' + this.model.get( 'id' ), + icon_class : 'delete' + }; + if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ + deleteBtnData = { + title : 'Dataset is already deleted', + icon_class : 'delete', + enabled : false + }; + } + this.deleteButton = new IconButtonView({ model : new IconButton( deleteBtnData ) }); + return this.deleteButton.render().$el; + }, + + // ................................................................................ titleLink + // render the hid and hda.name as a link (that will expand the body) + _render_titleLink : function(){ + return $( jQuery.trim( HDAView.templates.titleLink( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); + }, + + // ................................................................................ RENDER BODY + // render the data/metadata summary (format, size, misc info, etc.) + _render_hdaSummary : function(){ + var modelData = _.extend( this.model.toJSON(), { urls: this.urls } ); + // if there's no dbkey and it's editable : pass a flag to the template to render a link to editing in the '?' + if( this.model.get( 'metadata_dbkey' ) === '?' + && !this.model.isDeletedOrPurged() ){ + _.extend( modelData, { dbkey_unknown_and_editable : true }); + } + return HDAView.templates.hdaSummary( modelData ); + }, + + // ................................................................................ primary actions + // render the icon-buttons gen. placed underneath the hda summary + _render_primaryActionButtons : function( buttonRenderingFuncs ){ + var primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ), + view = this; + _.each( buttonRenderingFuncs, function( fn ){ + primaryActionButtons.append( fn.call( view ) ); + }); + return primaryActionButtons; + }, + + // icon-button/popupmenu to down the data (and/or the associated meta files (bai, etc.)) for this hda + _render_downloadButton : function(){ + // don't show anything if the data's been purged + if( this.model.get( 'purged' ) ){ return null; } + + // return either: a single download icon-button (if there are no meta files) + // or a popupmenu with links to download assoc. meta files (if there are meta files) + var downloadLinkHTML = HDAView.templates.downloadLinks( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ); + //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); + return $( downloadLinkHTML ); + }, + + // icon-button to show the input and output (stdout/err) for the job that created this hda + _render_errButton : function(){ + if( ( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ) + || ( !this.model.get( 'for_editing' ) ) ){ return null; } + + this.errButton = new IconButtonView({ model : new IconButton({ + title : 'View or report this error', + href : this.urls.report_error, + target : 'galaxy_main', + icon_class : 'bug' + })}); + return this.errButton.render().$el; + }, + + // icon-button to show the input and output (stdout/err) for the job that created this hda + _render_showParamsButton : function(){ + // gen. safe to show in all cases + 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().$el; + }, + + // icon-button to re run the job that created this hda + _render_rerunButton : function(){ + if( !this.model.get( 'for_editing' ) ){ return null; } + this.rerunButton = new IconButtonView({ model : new IconButton({ + title : 'Run this job again', + href : this.urls.rerun, + target : 'galaxy_main', + icon_class : 'arrow-circle' + }) }); + return this.rerunButton.render().$el; + }, + + // build an icon-button or popupmenu based on the number of applicable visualizations + // also map button/popup clicks to viz setup functions + _render_visualizationsButton : function(){ + var dbkey = this.model.get( 'dbkey' ), + visualizations = this.model.get( 'visualizations' ), + visualization_url = this.urls.visualization, + popup_menu_dict = {}, + params = { + dataset_id: this.model.get( 'id' ), + hda_ldda: 'hda' + }; + + if( !( this.model.hasData() ) + || !( this.model.get( 'for_editing' ) ) + || !( visualizations && visualizations.length ) + || !( visualization_url ) ){ + //console.warn( 'NOT rendering visualization icon' ) + return null; + } + + // render the icon from template + this.visualizationsButton = new IconButtonView({ model : new IconButton({ + title : 'Visualize', + href : visualization_url, + icon_class : 'chart_curve' + })}); + var $icon = this.visualizationsButton.render().$el; + $icon.addClass( 'visualize-icon' ); // needed? + + //TODO: make this more concise + // map a function to each visualization in the icon's attributes + // create a popupmenu from that map + // Add dbkey to params if it exists. + if( dbkey ){ params.dbkey = dbkey; } + + function create_viz_action( visualization ) { + switch( visualization ){ + case 'trackster': + return create_trackster_action_fn( visualization_url, params, dbkey ); + case 'scatterplot': + return create_scatterplot_action_fn( visualization_url, params ); + default: + return function(){ + window.parent.location = visualization_url + '/' + visualization + '?' + $.param( params ); }; + } + } + + // No need for popup menu because there's a single visualization. + if ( visualizations.length === 1 ) { + $icon.attr( 'title', visualizations[0] ); + $icon.click( create_viz_action( visualizations[0] ) ); + + // >1: Populate menu dict with visualization fns, make the popupmenu + } else { + _.each( visualizations, function( visualization ) { + //TODO: move to utils + var titleCaseVisualization = visualization.charAt( 0 ).toUpperCase() + visualization.slice( 1 ); + popup_menu_dict[ titleCaseVisualization ] = create_viz_action( visualization ); + }); + make_popupmenu( $icon, popup_menu_dict ); + } + return $icon; + }, + + // ................................................................................ secondary actions + // secondary actions: currently tagging and annotation (if user is allowed) + _render_secondaryActionButtons : function( buttonRenderingFuncs ){ + // move to the right (same level as primary) + var secondaryActionButtons = $( '<div/>' ), + view = this; + secondaryActionButtons + .attr( 'style', 'float: right;' ) + .attr( 'id', 'secondary-actions-' + this.model.get( 'id' ) ); + + _.each( buttonRenderingFuncs, function( fn ){ + secondaryActionButtons.append( fn.call( view ) ); + }); + return secondaryActionButtons; + }, + + // icon-button to load and display tagging html + //TODO: these should be a sub-MV + _render_tagButton : function(){ + if( !( this.model.hasData() ) + || !( this.model.get( 'for_editing' ) ) + || ( !this.urls.tags.get ) ){ return null; } + + this.tagButton = new IconButtonView({ model : new IconButton({ + title : 'Edit dataset tags', + target : 'galaxy_main', + href : this.urls.tags.get, + icon_class : 'tags' + })}); + return this.tagButton.render().$el; + }, + + // icon-button to load and display annotation html + //TODO: these should be a sub-MV + _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; + }, + + // ................................................................................ other elements + // render links to external genome display applications (igb, gbrowse, etc.) + //TODO: not a fan of the style on these + _render_displayApps : function(){ + if( !this.model.hasData() ){ return null; } + + var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); + if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ + //this.log( this + 'display_types:', this.model.get( 'urls' ).display_types ); + //TODO:?? does this ever get used? + displayAppsDiv.append( + HDAView.templates.displayApps({ displayApps : this.model.get( 'display_types' ) }) + ); + } + if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ + //this.log( this + 'display_apps:', this.model.get( 'urls' ).display_apps ); + displayAppsDiv.append( + HDAView.templates.displayApps({ displayApps : this.model.get( 'display_apps' ) }) + ); + } + return displayAppsDiv; + }, + + //TODO: into sub-MV + // render the area used to load tag display + _render_tagArea : function(){ + if( !this.urls.tags.set ){ return null; } + //TODO: move to mvc/tags.js + return $( HDAView.templates.tagArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + )); + }, + + //TODO: into sub-MV + // render the area used to load annotation display + _render_annotationArea : function(){ + if( !this.urls.annotation.get ){ return null; } + //TODO: move to mvc/annotations.js + return $( HDAView.templates.annotationArea( + _.extend( this.model.toJSON(), { urls: this.urls } ) + )); + }, + + // render the data peek + //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible + _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' ) ) + ); + }, + + // ................................................................................ state body renderers + // _render_body fns for the various states + //TODO: only render these on expansion (or already expanded) + _render_body_not_viewable : function( parent ){ + //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right + parent.append( $( '<div>You do not have permission to view dataset.</div>' ) ); + }, + + _render_body_uploading : function( parent ){ + parent.append( $( '<div>Dataset is uploading</div>' ) ); + }, + + _render_body_queued : function( parent ){ + parent.append( $( '<div>Job is waiting to run.</div>' ) ); + parent.append( this._render_primaryActionButtons([ + this._render_showParamsButton, + this._render_rerunButton + ])); + }, + + _render_body_running : function( parent ){ + parent.append( '<div>Job is currently running.</div>' ); + parent.append( this._render_primaryActionButtons([ + this._render_showParamsButton, + this._render_rerunButton + ])); + }, + + _render_body_error : function( parent ){ + if( !this.model.get( 'purged' ) ){ + parent.append( $( '<div>' + this.model.get( 'misc_blurb' ) + '</div>' ) ); + } + parent.append( ( 'An error occurred running this job: ' + + '<i>' + $.trim( this.model.get( 'misc_info' ) ) + '</i>' ) ); + parent.append( this._render_primaryActionButtons([ + this._render_downloadButton, + this._render_errButton, + this._render_showParamsButton, + this._render_rerunButton + ])); + }, + + _render_body_discarded : function( parent ){ + parent.append( '<div>The job creating this dataset was cancelled before completion.</div>' ); + parent.append( this._render_primaryActionButtons([ + this._render_showParamsButton, + this._render_rerunButton + ])); + }, + + _render_body_setting_metadata : function( parent ){ + parent.append( $( '<div>Metadata is being auto-detected.</div>' ) ); + }, + + _render_body_empty : function( parent ){ + //TODO: replace i with dataset-misc-info class + //?? why are we showing the file size when we know it's zero?? + parent.append( $( '<div>No data: <i>' + this.model.get( 'misc_blurb' ) + '</i></div>' ) ); + parent.append( this._render_primaryActionButtons([ + this._render_showParamsButton, + this._render_rerunButton + ])); + }, + + _render_body_failed_metadata : function( parent ){ + //TODO: the css for this box is broken (unlike the others) + // add a message box about the failure at the top of the body... + parent.append( $( HDAView.templates.failedMetadata( this.model.toJSON() ) ) ); + //...then render the remaining body as STATES.OK (only diff between these states is the box above) + this._render_body_ok( parent ); + }, + + _render_body_ok : function( parent ){ + // most common state renderer and the most complicated + parent.append( this._render_hdaSummary() ); + + // return shortened form if del'd + //TODO: is this correct? maybe only on purged + if( this.model.isDeletedOrPurged() ){ + parent.append( this._render_primaryActionButtons([ + this._render_downloadButton, + this._render_showParamsButton, + this._render_rerunButton + ])); + return; + } + + //NOTE: change the order here + parent.append( this._render_primaryActionButtons([ + this._render_downloadButton, + this._render_errButton, + this._render_showParamsButton, + this._render_rerunButton, + this._render_visualizationsButton + ])); + parent.append( this._render_secondaryActionButtons([ + this._render_tagButton, + this._render_annotateButton + ])); + parent.append( '<div class="clear"/>' ); + + parent.append( this._render_tagArea() ); + parent.append( this._render_annotationArea() ); + + parent.append( this._render_displayApps() ); + parent.append( this._render_peek() ); + + //TODO??: still needed? + //// If Mozilla, hide scrollbars in hidden items since they cause animation bugs + //if ( $.browser.mozilla ) { + // $( "div.historyItemBody" ).each( function() { + // if ( !$(this).is(":visible") ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); } + // }); + //} + }, + + _render_body : function(){ + //this.log( this + '_render_body' ); + //this.log( 'state:', state, 'for_editing', for_editing ); + + //TODO: incorrect id (encoded - use hid?) + var body = $( '<div/>' ) + .attr( 'id', 'info-' + this.model.get( 'id' ) ) + .addClass( 'historyItemBody' ) + .attr( 'style', 'display: block' ); + + //TODO: not a fan of this dispatch + switch( this.model.get( 'state' ) ){ + case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : + this._render_body_not_viewable( body ); + break; + case HistoryDatasetAssociation.STATES.UPLOAD : + this._render_body_uploading( body ); + break; + case HistoryDatasetAssociation.STATES.QUEUED : + this._render_body_queued( body ); + break; + case HistoryDatasetAssociation.STATES.RUNNING : + this._render_body_running( body ); + break; + case HistoryDatasetAssociation.STATES.ERROR : + this._render_body_error( body ); + break; + case HistoryDatasetAssociation.STATES.DISCARDED : + this._render_body_discarded( body ); + break; + case HistoryDatasetAssociation.STATES.SETTING_METADATA : + this._render_body_setting_metadata( body ); + break; + case HistoryDatasetAssociation.STATES.EMPTY : + this._render_body_empty( body ); + break; + case HistoryDatasetAssociation.STATES.FAILED_METADATA : + this._render_body_failed_metadata( body ); + break; + case HistoryDatasetAssociation.STATES.OK : + this._render_body_ok( body ); + break; + default: + //??: no body? + body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) ); + } + body.append( '<div style="clear: both"></div>' ); + + if( this.expanded ){ + body.show(); + } else { + body.hide(); + } + return body; + }, + + // ................................................................................ EVENTS + events : { + 'click .historyItemTitle' : 'toggleBodyVisibility', + 'click a.icon-button.tags' : 'loadAndDisplayTags', + 'click a.icon-button.annotate' : 'loadAndDisplayAnnotation' + }, + + // ................................................................................ STATE CHANGES / MANIPULATION + // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide + //TODO: into sub-MV + loadAndDisplayTags : function( event ){ + //BUG: broken with latest + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this + '.loadAndDisplayTags', event ); + var tagArea = this.$el.find( '.tag-area' ), + tagElt = tagArea.find( '.tag-elt' ); + + // Show or hide tag area; if showing tag area and it's empty, fill it. + if( tagArea.is( ":hidden" ) ){ + if( !jQuery.trim( tagElt.html() ) ){ + // Need to fill tag element. + $.ajax({ + //TODO: the html from this breaks a couple of times + url: this.urls.tags.get, + error: function() { alert( "Tagging failed" ); }, + success: function(tag_elt_html) { + tagElt.html(tag_elt_html); + tagElt.find(".tooltip").tooltip(); + tagArea.slideDown("fast"); + } + }); + } else { + // Tag element is filled; show. + tagArea.slideDown("fast"); + } + } else { + // Hide. + tagArea.slideUp("fast"); + } + return false; + }, + + // find the annotation area and, if initial: (via ajax) load the html for displaying it; otherwise, unhide/hide + //TODO: into sub-MV + loadAndDisplayAnnotation : function( event ){ + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this + '.loadAndDisplayAnnotation', event ); + var annotationArea = this.$el.find( '.annotation-area' ), + annotationElem = annotationArea.find( '.annotation-elt' ), + setAnnotationUrl = this.urls.annotation.set; + + // Show or hide annotation area; if showing annotation area and it's empty, fill it. + if ( annotationArea.is( ":hidden" ) ){ + if( !jQuery.trim( annotationElem.html() ) ){ + // Need to fill annotation element. + $.ajax({ + url: this.urls.annotation.get, + error: function(){ alert( "Annotations failed" ); }, + success: function( htmlFromAjax ){ + if( htmlFromAjax === "" ){ + htmlFromAjax = "<em>Describe or add notes to dataset</em>"; + } + annotationElem.html( htmlFromAjax ); + annotationArea.find(".tooltip").tooltip(); + + async_save_text( + annotationElem.attr("id"), annotationElem.attr("id"), + setAnnotationUrl, + "new_annotation", 18, true, 4 + ); + annotationArea.slideDown("fast"); + } + }); + } else { + annotationArea.slideDown("fast"); + } + + } else { + // Hide. + annotationArea.slideUp("fast"); + } + return false; + }, + + // expand/collapse body + //side effect: trigger event + toggleBodyVisibility : function( event, expanded ){ + var $body = this.$el.find( '.historyItemBody' ); + expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); + //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); + + if( expanded ){ + $body.slideDown( 'fast' ); + } else { + $body.slideUp( 'fast' ); + } + this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), expanded ); + }, + + // ................................................................................ UTILTIY + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'HDAView(' + modelString + ')'; + } +}); + +//------------------------------------------------------------------------------ +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' ] +}; + +//============================================================================== +//TODO: these belong somewhere else + +//TODO: should be imported from scatterplot.js +//TODO: OR abstracted to 'load this in the galaxy_main frame' +function create_scatterplot_action_fn( url, params ){ + action = function() { + var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ), + final_url = url + '/scatterplot?' + $.param(params); + galaxy_main.attr( 'src', final_url ); + //TODO: this needs to go away + $( 'div.popmenu-wrapper' ).remove(); + return false; + }; + return action; +} + +// ----------------------------------------------------------------------------- +// Create trackster action function. +//TODO: should be imported from trackster.js +function create_trackster_action_fn(vis_url, dataset_params, dbkey) { + return function() { + var params = {}; + if (dbkey) { params.dbkey = dbkey; } + $.ajax({ + url: vis_url + '/list_tracks?f-' + $.param(params), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + success: function(table_html) { + var parent = window.parent; + + parent.show_modal("View Data in a New or Saved Visualization", "", { + "Cancel": function() { + parent.hide_modal(); + }, + "View in saved visualization": function() { + // Show new modal with saved visualizations. + parent.show_modal("Add Data to Saved Visualization", table_html, { + "Cancel": function() { + parent.hide_modal(); + }, + "Add to visualization": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + dataset_params.id = vis_id; + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + }); + } + }); + }, + "View in new visualization": function() { + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + } + }); + } + }); + return false; + }; +} + +//============================================================================== +//return { +// HDAView : HDAView, +//};}); diff -r 3d27b35e1c1fa629ec4175f5e613b5a771152377 -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 static/scripts/mvc/dataset/hda-model.js --- /dev/null +++ b/static/scripts/mvc/dataset/hda-model.js @@ -0,0 +1,223 @@ +//define([ +// "../mvc/base-mvc" +//], function(){ +//============================================================================== +/** + * + */ +var HistoryDatasetAssociation = BaseModel.extend( LoggableMixin ).extend({ + // a single HDA model + + // uncomment this out see log messages + //logger : console, + + defaults : { + // ---these are part of an HDA proper: + + // parent (containing) history + history_id : null, + // often used with tagging + model_class : 'HistoryDatasetAssociation', + // index within history (??) + hid : 0, + + // ---whereas these are Dataset related/inherited + + id : null, + name : '', + // one of HistoryDatasetAssociation.STATES + state : '', + // sniffed datatype (sam, tabular, bed, etc.) + data_type : null, + // size in bytes + file_size : 0, + + // array of associated file types (eg. [ 'bam_index', ... ]) + meta_files : [], + + misc_blurb : '', + misc_info : '', + + deleted : false, + purged : false, + // aka. !hidden + visible : false, + // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset )) + accessible : false, + + //TODO: this needs to be removed (it is a function of the view type (e.g. HDAForEditingView)) + for_editing : true + }, + + // fetch location of this history in the api + url : function(){ + //TODO: get this via url router + return 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); + }, + + // (curr) only handles changing state of non-accessible hdas to STATES.NOT_VIEWABLE + //TODO:? use initialize (or validate) to check purged AND deleted -> purged XOR deleted + initialize : function(){ + this.log( this + '.initialize', this.attributes ); + this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); + + //!! this state is not in trans.app.model.Dataset.states - set it here - + //TODO: change to server side. + if( !this.get( 'accessible' ) ){ + this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); + } + + // if the state has changed and the new state is a ready state, fire an event + this.on( 'change:state', function( currModel, newState ){ + this.log( this + ' has changed state:', currModel, newState ); + if( this.inReadyState() ){ + this.trigger( 'state:ready', this.get( 'id' ), newState, this.previous( 'state' ), currModel ); + } + }); + + // debug on change events + //this.on( 'change', function( currModel, changedList ){ + // this.log( this + ' has changed:', currModel, changedList ); + //}); + //this.bind( 'all', function( event ){ + // this.log( this + '', arguments ); + //}); + }, + + isDeletedOrPurged : function(){ + return ( this.get( 'deleted' ) || this.get( 'purged' ) ); + }, + + // based on show_deleted, show_hidden (gen. from the container control), would this ds show in the list of ds's? + //TODO: too many visibles + isVisible : function( show_deleted, show_hidden ){ + var isVisible = true; + if( ( !show_deleted ) + && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){ + isVisible = false; + } + if( ( !show_hidden ) + && ( !this.get( 'visible' ) ) ){ + isVisible = false; + } + return isVisible; + }, + + // 'ready' states are states where no processing (for the ds) is left to do on the server + inReadyState : function(){ + var state = this.get( 'state' ); + return ( + ( state === HistoryDatasetAssociation.STATES.NEW ) + || ( state === HistoryDatasetAssociation.STATES.OK ) + || ( state === HistoryDatasetAssociation.STATES.EMPTY ) + || ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA ) + || ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( state === HistoryDatasetAssociation.STATES.DISCARDED ) + || ( state === HistoryDatasetAssociation.STATES.ERROR ) + ); + }, + + // convenience fn to match hda.has_data + hasData : function(){ + //TODO:?? is this equivalent to all possible hda.has_data calls? + return ( this.get( 'file_size' ) > 0 ); + }, + + toString : function(){ + var nameAndId = this.get( 'id' ) || ''; + if( this.get( 'name' ) ){ + nameAndId += ':"' + this.get( 'name' ) + '"'; + } + return 'HistoryDatasetAssociation(' + nameAndId + ')'; + } +}); + +//------------------------------------------------------------------------------ +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', // not in trans.app.model.Dataset.states + DISCARDED : 'discarded', + ERROR : 'error' +}; + +//============================================================================== +/** + * + */ +var HDACollection = Backbone.Collection.extend( LoggableMixin ).extend({ + model : HistoryDatasetAssociation, + + //logger : console, + + initialize : function(){ + //this.bind( 'all', function( event ){ + // this.log( this + '', arguments ); + //}); + }, + + // return the ids of every hda in this collection + ids : function(){ + return this.map( function( item ){ return item.id; }); + }, + + // return an HDA collection containing every 'shown' hda based on show_deleted/hidden + getVisible : function( show_deleted, show_hidden ){ + return this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }); + }, + + // get a map where <possible hda state> : [ <list of hda ids in that state> ] + getStateLists : function(){ + var stateLists = {}; + _.each( _.values( HistoryDatasetAssociation.STATES ), function( state ){ + stateLists[ state ] = []; + }); + //NOTE: will err on unknown state + this.each( function( item ){ + stateLists[ item.get( 'state' ) ].push( item.get( 'id' ) ); + }); + return stateLists; + }, + + // returns the id of every hda still running (not in a ready state) + running : function(){ + var idList = []; + this.each( function( item ){ + if( !item.inReadyState() ){ + idList.push( item.get( 'id' ) ); + } + }); + return idList; + }, + + // update (fetch -> render) the hdas with the ids given + update : function( ids ){ + this.log( this + 'update:', ids ); + + if( !( ids && ids.length ) ){ return; } + + var collection = this; + _.each( ids, function( id, index ){ + var historyItem = collection.get( id ); + historyItem.fetch(); + }); + }, + + toString : function(){ + return ( 'HDACollection(' + this.ids().join(',') + ')' ); + } +}); + +//============================================================================== +//return { +// HistoryDatasetAssociation : HistoryDatasetAssociation, +// HDACollection : HDACollection, +//};}); diff -r 3d27b35e1c1fa629ec4175f5e613b5a771152377 -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ /dev/null @@ -1,1611 +0,0 @@ -//define([ -// "../mvc/base-mvc" -// -//], function(){ -/* ============================================================================= -Backbone.js implementation of history panel - -TODO: - bug: - anon, mako: - tooltips not rendered - anno, tags rendered - title editable - bug: - when over quota history is re-rendered, over quota msg is not displayed - bc the quota:over event isn't fired - bc the user state hasn't changed - - anon user, mako template init: - bug: rename url seems to be wrong url - - currently, adding a dataset (via tool execute, etc.) creates a new dataset and refreshes the page - logged in, mako template: - BUG: am able to start upload even if over quota - 'runs' forever - - BUG: from above sit, delete uploading hda - now in state 'discarded'! ...new state to handle - bug: quotaMeter bar rendering square in chrome - BUG: quotaMsg not showing when 100% (on load) - BUG: upload, history size, doesn't change - TODO: on hdas state:ready, update ONLY the size...from what? histories.py? in js? - BUG: imported, shared history with unaccessible dataset errs in historycontents when getting history - (entire history is inaccessible) - ??: still happening? - - from loadFromApi: - BUG: not showing previous annotations - - fixed: - BUG: historyItem, error'd ds show display, download? - FIXED: removed - bug: loading hdas (alt_hist) - FIXED: added anon user api request ( trans.user == None and trans.history.id == requested id ) - bug: quota meter not updating on upload/tool run - FIXED: quotaMeter now listens for 'state:ready' from glx_history in alternate_history.mako - bug: use of new HDACollection with event listener in init doesn't die...keeps reporting - FIXED: change getVisible to return an array - BUG: history, broken intial hist state (running, updater, etc.) - ??: doesn't seem to happen anymore - BUG: collapse all should remove all expanded from storage - FIXED: hideAllItemBodies now resets storage.expandedItems - BUG: historyItem, shouldn't allow tag, annotate, peek on purged datasets - FIXED: ok state now shows only: info, rerun - BUG: history?, some ids aren't returning encoded... - FIXED:??? - BUG: history, showing deleted ds - FIXED - UGH: historyItems have to be decorated with history_ids (api/histories/:history_id/contents/:id) - FIXED by adding history_id to history_contents.show - BUG: history, if hist has err'd ds, hist has perm state 'error', updater on following ds's doesn't run - FIXED by reordering history state from ds' states here and histories - BUG: history, broken annotation on reload (can't get thru api (sets fine, tho)) - FIXED: get thru api for now - - to relational model? - HDACollection, meta_files, display_apps, etc. - - - quota mgr - show_deleted/hidden: - use storage - on/off ui - move histview fadein/out in render to app? - don't draw body until it's first expand event - localize all - break this file up - ?: render url templates on init or render? - ?: history, annotation won't accept unicode - - hierarchy: - dataset -> hda - history -> historyForEditing, historyForViewing - display_structured? - - btw: get an error'd ds by running fastqc on fastq (when you don't have it installed) - - meta: - css/html class/id 'item' -> hda - add classes, ids on empty divs - events (local/ui and otherwise) - list in docs as well - require.js - convert function comments to jsDoc style, complete comments - move inline styles into base.less - watch the magic strings - watch your globals - - features: - lineage - hide button - show permissions in info - show shared/sharing status on ds, history - maintain scroll position on refresh (storage?) - selection, multi-select (and actions common to selected (ugh)) - searching - sorting, re-shuffling - -============================================================================= */ -var HistoryDatasetAssociation = BaseModel.extend( LoggableMixin ).extend({ - // a single HDA model - - // uncomment this out see log messages - //logger : console, - - defaults : { - // ---these are part of an HDA proper: - - // parent (containing) history - history_id : null, - // often used with tagging - model_class : 'HistoryDatasetAssociation', - // index within history (??) - hid : 0, - - // ---whereas these are Dataset related/inherited - - id : null, - name : '', - // one of HistoryDatasetAssociation.STATES - state : '', - // sniffed datatype (sam, tabular, bed, etc.) - data_type : null, - // size in bytes - file_size : 0, - - // array of associated file types (eg. [ 'bam_index', ... ]) - meta_files : [], - - misc_blurb : '', - misc_info : '', - - deleted : false, - purged : false, - // aka. !hidden - visible : false, - // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset )) - accessible : false, - - //TODO: this needs to be removed (it is a function of the view type (e.g. HDAForEditingView)) - for_editing : true - }, - - // fetch location of this history in the api - url : function(){ - //TODO: get this via url router - return 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); - }, - - // (curr) only handles changing state of non-accessible hdas to STATES.NOT_VIEWABLE - //TODO:? use initialize (or validate) to check purged AND deleted -> purged XOR deleted - initialize : function(){ - this.log( this + '.initialize', this.attributes ); - this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); - - //!! this state is not in trans.app.model.Dataset.states - set it here - - //TODO: change to server side. - if( !this.get( 'accessible' ) ){ - this.set( 'state', HistoryDatasetAssociation.STATES.NOT_VIEWABLE ); - } - - // if the state has changed and the new state is a ready state, fire an event - this.on( 'change:state', function( currModel, newState ){ - this.log( this + ' has changed state:', currModel, newState ); - if( this.inReadyState() ){ - this.trigger( 'state:ready', this.get( 'id' ), newState, this.previous( 'state' ), currModel ); - } - }); - - // debug on change events - //this.on( 'change', function( currModel, changedList ){ - // this.log( this + ' has changed:', currModel, changedList ); - //}); - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); - }, - - isDeletedOrPurged : function(){ - return ( this.get( 'deleted' ) || this.get( 'purged' ) ); - }, - - // based on show_deleted, show_hidden (gen. from the container control), would this ds show in the list of ds's? - //TODO: too many visibles - isVisible : function( show_deleted, show_hidden ){ - var isVisible = true; - if( ( !show_deleted ) - && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){ - isVisible = false; - } - if( ( !show_hidden ) - && ( !this.get( 'visible' ) ) ){ - isVisible = false; - } - return isVisible; - }, - - // 'ready' states are states where no processing (for the ds) is left to do on the server - inReadyState : function(){ - var state = this.get( 'state' ); - return ( - ( state === HistoryDatasetAssociation.STATES.NEW ) - || ( state === HistoryDatasetAssociation.STATES.OK ) - || ( state === HistoryDatasetAssociation.STATES.EMPTY ) - || ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA ) - || ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( state === HistoryDatasetAssociation.STATES.DISCARDED ) - || ( state === HistoryDatasetAssociation.STATES.ERROR ) - ); - }, - - // convenience fn to match hda.has_data - hasData : function(){ - //TODO:?? is this equivalent to all possible hda.has_data calls? - return ( this.get( 'file_size' ) > 0 ); - }, - - toString : function(){ - var nameAndId = this.get( 'id' ) || ''; - if( this.get( 'name' ) ){ - nameAndId += ':"' + this.get( 'name' ) + '"'; - } - return 'HistoryDatasetAssociation(' + nameAndId + ')'; - } -}); - -//------------------------------------------------------------------------------ -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', // not in trans.app.model.Dataset.states - DISCARDED : 'discarded', - ERROR : 'error' -}; - -//============================================================================== -var HDACollection = Backbone.Collection.extend( LoggableMixin ).extend({ - model : HistoryDatasetAssociation, - - //logger : console, - - initialize : function(){ - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); - }, - - // return the ids of every hda in this collection - ids : function(){ - return this.map( function( item ){ return item.id; }); - }, - - // return an HDA collection containing every 'shown' hda based on show_deleted/hidden - getVisible : function( show_deleted, show_hidden ){ - return this.filter( function( item ){ return item.isVisible( show_deleted, show_hidden ); }); - }, - - // get a map where <possible hda state> : [ <list of hda ids in that state> ] - getStateLists : function(){ - var stateLists = {}; - _.each( _.values( HistoryDatasetAssociation.STATES ), function( state ){ - stateLists[ state ] = []; - }); - //NOTE: will err on unknown state - this.each( function( item ){ - stateLists[ item.get( 'state' ) ].push( item.get( 'id' ) ); - }); - return stateLists; - }, - - // returns the id of every hda still running (not in a ready state) - running : function(){ - var idList = []; - this.each( function( item ){ - if( !item.inReadyState() ){ - idList.push( item.get( 'id' ) ); - } - }); - return idList; - }, - - // update (fetch -> render) the hdas with the ids given - update : function( ids ){ - this.log( this + 'update:', ids ); - - if( !( ids && ids.length ) ){ return; } - - var collection = this; - _.each( ids, function( id, index ){ - var historyItem = collection.get( id ); - historyItem.fetch(); - }); - }, - - toString : function(){ - return ( 'HDACollection(' + this.ids().join(',') + ')' ); - } -}); - - -//============================================================================== -var History = BaseModel.extend( LoggableMixin ).extend({ - //TODO: bind change events from items and collection to this (itemLengths, states) - - // uncomment this out see log messages - //logger : console, - - // values from api (may need more) - defaults : { - id : '', - name : '', - state : '', - - //TODO: wire these to items (or this) - show_deleted : false, - show_hidden : false, - - diskSize : 0, - deleted : false, - - tags : [], - annotation : null, - - //TODO: quota msg and message? how to get those over the api? - message : null, - quotaMsg : false - }, - - url : function(){ - // api location of history resource - //TODO: hardcoded - return 'api/histories/' + this.get( 'id' ); - }, - - initialize : function( initialSettings, initialHdas ){ - this.log( this + ".initialize:", initialSettings, initialHdas ); - - this.hdas = new HDACollection(); - - // if we've got hdas passed in the constructor, load them and set up updates if needed - if( initialHdas && initialHdas.length ){ - this.hdas.reset( initialHdas ); - this.checkForUpdates(); - } - - //this.on( 'change', function( currModel, changedList ){ - // this.log( this + ' has changed:', currModel, changedList ); - //}); - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); - }, - - // get data via the api (alternative to sending options,hdas to initialize) - loadFromApi : function( historyId, callback ){ - var history = this; - - // fetch the history AND the user (mainly to see if they're logged in at this point) - history.attributes.id = historyId; - //TODO:?? really? fetch user here? - jQuery.when( jQuery.ajax( 'api/users/current' ), history.fetch() - - ).then( function( userResponse, historyResponse ){ - //console.warn( 'fetched user, history: ', userResponse, historyResponse ); - history.attributes.user = userResponse[0]; //? meh. - history.log( history ); - - }).then( function(){ - // ...then the hdas (using contents?ids=...) - jQuery.ajax( history.url() + '/contents?' + jQuery.param({ - ids : history.itemIdsFromStateIds().join( ',' ) - - // reset the collection to the hdas returned - })).success( function( hdas ){ - //console.warn( 'fetched hdas' ); - history.hdas.reset( hdas ); - history.checkForUpdates(); - callback(); - }); - }); - }, - - // reduce the state_ids map of hda id lists -> a single list of ids - //...ugh - seems roundabout; necessary because the history doesn't have a straightforward list of ids - // (and history_contents/index curr returns a summary only) - hdaIdsFromStateIds : function(){ - return _.reduce( _.values( this.get( 'state_ids' ) ), function( reduction, currIdList ){ - return reduction.concat( currIdList ); - }); - }, - - // get the history's state from it's cummulative ds states, delay + update if needed - checkForUpdates : function( datasets ){ - // get overall History state from collection, run updater if History has running/queued hdas - // boiling it down on the client to running/not - if( this.hdas.running().length ){ - this.stateUpdater(); - } - return this; - }, - - // update this history, find any hda's running/queued, update ONLY those that have changed states, - // set up to run this again in some interval of time - stateUpdater : function(){ - var history = this, - oldState = this.get( 'state' ), - // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state - oldStateIds = this.get( 'state_ids' ); - - // pull from the history api - //TODO: fetch? - jQuery.ajax( 'api/histories/' + this.get( 'id' ) - - ).success( function( response ){ - //this.log( 'historyApiRequest, response:', response ); - history.set( response ); - history.log( 'current history state:', history.get( 'state' ), - '(was)', oldState, - 'new size:', history.get( 'nice_size' ) ); - - //TODO: revisit this - seems too elaborate, need something straightforward - // for each state, check for the difference between old dataset states and new - // the goal here is to check ONLY those datasets that have changed states (not all datasets) - var changedIds = []; - _.each( _.keys( response.state_ids ), function( state ){ - var diffIds = _.difference( response.state_ids[ state ], oldStateIds[ state ] ); - // aggregate those changed ids - changedIds = changedIds.concat( diffIds ); - }); - - // send the changed ids (if any) to dataset collection to have them fetch their own model changes - if( changedIds.length ){ - history.hdas.update( changedIds ); - } - - // set up to keep pulling if this history in run/queue state - //TODO: magic number here - if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ - setTimeout( function(){ - history.stateUpdater(); - }, 4000 ); - } - - }).error( function( xhr, status, error ){ - if( console && console.warn ){ - console.warn( 'Error getting history updates from the server:', xhr, status, error ); - } - alert( 'Error getting history updates from the server.\n' + error ); - }); - }, - - toString : function(){ - var nameString = ( this.get( 'name' ) )? - ( ',' + this.get( 'name' ) ) : ( '' ); - return 'History(' + this.get( 'id' ) + nameString + ')'; - } -}); - -//============================================================================== -var HDAView = BaseView.extend( LoggableMixin ).extend({ - //??TODO: add alias in initialize this.hda = this.model? - // view for HistoryDatasetAssociation model above - - // uncomment this out see log messages - //logger : console, - - tagName : "div", - className : "historyItemContainer", - - // ................................................................................ SET UP - initialize : function( attributes ){ - this.log( this + '.initialize:', attributes ); - - // render urlTemplates (gen. provided by GalaxyPaths) to urls - if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } - this.urls = this.renderUrls( attributes.urlTemplates, this.model.toJSON() ); - - // whether the body of this hda is expanded (shown) - this.expanded = attributes.expanded || false; - - // re-render the entire view on any model change - this.model.bind( 'change', this.render, this ); - //this.bind( 'all', function( event ){ - // this.log( event ); - //}, this ); - }, - - // urlTemplates is a map (or nested map) of underscore templates (currently, anyhoo) - // use the templates to create the apropo urls for each action this ds could use - renderUrls : function( urlTemplates, modelJson ){ - var hdaView = this, - urls = {}; - _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ - // object == nested templates: recurse - if( _.isObject( urlTemplateOrObj ) ){ - urls[ urlKey ] = hdaView.renderUrls( urlTemplateOrObj, modelJson ); - - // string == template: - } else { - // meta_down load is a special case (see renderMetaDownloadUrls) - //TODO: should be a better (gen.) way to handle this case - if( urlKey === 'meta_download' ){ - urls[ urlKey ] = hdaView.renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); - } else { - urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); - } - } - }); - return urls; - }, - - // there can be more than one meta_file to download, so return a list of url and file_type for each - renderMetaDownloadUrls : function( urlTemplate, modelJson ){ - return _.map( modelJson.meta_files, function( meta_file ){ - return { - url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), - file_type : meta_file.file_type - }; - }); - }, - - // ................................................................................ RENDER MAIN - render : function(){ - var view = this, - id = this.model.get( 'id' ), - state = this.model.get( 'state' ), - itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ), - initialRender = ( this.$el.children().size() === 0 ); - - //console.debug( this + '.render, initial?:', initialRender ); - - this._clearReferences(); - this.$el.attr( 'id', 'historyItemContainer-' + id ); - - itemWrapper - .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) - .addClass( 'historyItem-' + state ); - - itemWrapper.append( this._render_warnings() ); - itemWrapper.append( this._render_titleBar() ); - this.body = $( this._render_body() ); - itemWrapper.append( this.body ); - - //TODO: move to own function: setUpBehaviours - // we can potentially skip this step and call popupmenu directly on the download button - make_popup_menus( itemWrapper ); - - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); - - // transition... - this.$el.fadeOut( 'fast', function(){ - view.$el.children().remove(); - view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ - view.log( view + ' rendered:', view.$el ); - var renderedEventName = 'rendered'; - - if( initialRender ){ - renderedEventName += ':initial'; - } else if( view.model.inReadyState() ){ - renderedEventName += ':ready'; - } - view.trigger( renderedEventName ); - }); - }); - return this; - }, - - //NOTE: button renderers have the side effect of caching their IconButtonViews to this view - // clear out cached sub-views, dom refs, etc. from prev. render - _clearReferences : function(){ - //??TODO: we should reset these in the button logic checks (i.e. if not needed this.button = null; return null) - //?? do we really need these - not so far - //TODO: at least move these to a map - 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 - // hda warnings including: is deleted, is purged, is hidden (including links to further actions (undelete, etc.)) - _render_warnings : function(){ - // jQ errs on building dom with whitespace - if there are no messages, trim -> '' - return $( jQuery.trim( HDAView.templates.messages( - _.extend( this.model.toJSON(), { urls: this.urls } ) - ))); - }, - - // ................................................................................ RENDER TITLEBAR - // the part of an hda always shown (whether the body is expanded or not): title link, title buttons - _render_titleBar : function(){ - var titleBar = $( '<div class="historyItemTitleBar" style="overflow: hidden"></div>' ); - titleBar.append( this._render_titleButtons() ); - titleBar.append( '<span class="state-icon"></span>' ); - titleBar.append( this._render_titleLink() ); - return titleBar; - }, - - // ................................................................................ display, edit attr, delete - // icon-button group for the common, most easily accessed actions - //NOTE: these are generally displayed for almost every hda state (tho poss. disabled) - _render_titleButtons : function(){ - // render the display, edit attr and delete icon-buttons - var buttonDiv = $( '<div class="historyItemButtons"></div>' ); - buttonDiv.append( this._render_displayButton() ); - buttonDiv.append( this._render_editButton() ); - buttonDiv.append( this._render_deleteButton() ); - return buttonDiv; - }, - - // icon-button to display this hda in the galaxy main iframe - _render_displayButton : function(){ - // don't show display if not in ready state, error'd, or not accessible - if( ( !this.model.inReadyState() ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( !this.model.get( 'accessible' ) ) ){ - return null; - } - - var displayBtnData = { - icon_class : 'display' - }; - - // show a disabled display if the data's been purged - if( this.model.get( 'purged' ) ){ - displayBtnData.enabled = false; - displayBtnData.title = 'Cannot display datasets removed from disk'; - - } else { - displayBtnData.title = 'Display data in browser'; - displayBtnData.href = this.urls.display; - } - - if( this.model.get( 'for_editing' ) ){ - displayBtnData.target = 'galaxy_main'; - } - - this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); - return this.displayButton.render().$el; - }, - - // icon-button to edit the attributes (format, permissions, etc.) this hda - _render_editButton : function(){ - // don't show edit while uploading, or if editable - 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 purged = this.model.get( 'purged' ), - deleted = this.model.get( 'deleted' ), - editBtnData = { - title : 'Edit attributes', - href : this.urls.edit, - target : 'galaxy_main', - icon_class : 'edit' - }; - - // disable if purged or deleted and explain why in the tooltip - //TODO: if for_editing - if( deleted || purged ){ - editBtnData.enabled = false; - if( purged ){ - editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; - } else if( deleted ){ - editBtnData.title = 'Undelete dataset to edit attributes'; - } - } - - this.editButton = new IconButtonView({ model : new IconButton( editBtnData ) }); - return this.editButton.render().$el; - }, - - // icon-button to delete this hda - _render_deleteButton : function(){ - // don't show delete if... - if( ( !this.model.get( 'for_editing' ) ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( !this.model.get( 'accessible' ) ) ){ - return null; - } - - var deleteBtnData = { - title : 'Delete', - href : this.urls[ 'delete' ], - id : 'historyItemDeleter-' + this.model.get( 'id' ), - icon_class : 'delete' - }; - if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ - deleteBtnData = { - title : 'Dataset is already deleted', - icon_class : 'delete', - enabled : false - }; - } - this.deleteButton = new IconButtonView({ model : new IconButton( deleteBtnData ) }); - return this.deleteButton.render().$el; - }, - - // ................................................................................ titleLink - // render the hid and hda.name as a link (that will expand the body) - _render_titleLink : function(){ - return $( jQuery.trim( HDAView.templates.titleLink( - _.extend( this.model.toJSON(), { urls: this.urls } ) - ))); - }, - - // ................................................................................ RENDER BODY - // render the data/metadata summary (format, size, misc info, etc.) - _render_hdaSummary : function(){ - var modelData = _.extend( this.model.toJSON(), { urls: this.urls } ); - // if there's no dbkey and it's editable : pass a flag to the template to render a link to editing in the '?' - if( this.model.get( 'metadata_dbkey' ) === '?' - && !this.model.isDeletedOrPurged() ){ - _.extend( modelData, { dbkey_unknown_and_editable : true }); - } - return HDAView.templates.hdaSummary( modelData ); - }, - - // ................................................................................ primary actions - // render the icon-buttons gen. placed underneath the hda summary - _render_primaryActionButtons : function( buttonRenderingFuncs ){ - var primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ), - view = this; - _.each( buttonRenderingFuncs, function( fn ){ - primaryActionButtons.append( fn.call( view ) ); - }); - return primaryActionButtons; - }, - - // icon-button/popupmenu to down the data (and/or the associated meta files (bai, etc.)) for this hda - _render_downloadButton : function(){ - // don't show anything if the data's been purged - if( this.model.get( 'purged' ) ){ return null; } - - // return either: a single download icon-button (if there are no meta files) - // or a popupmenu with links to download assoc. meta files (if there are meta files) - var downloadLinkHTML = HDAView.templates.downloadLinks( - _.extend( this.model.toJSON(), { urls: this.urls } ) - ); - //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); - return $( downloadLinkHTML ); - }, - - // icon-button to show the input and output (stdout/err) for the job that created this hda - _render_errButton : function(){ - if( ( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ) - || ( !this.model.get( 'for_editing' ) ) ){ return null; } - - this.errButton = new IconButtonView({ model : new IconButton({ - title : 'View or report this error', - href : this.urls.report_error, - target : 'galaxy_main', - icon_class : 'bug' - })}); - return this.errButton.render().$el; - }, - - // icon-button to show the input and output (stdout/err) for the job that created this hda - _render_showParamsButton : function(){ - // gen. safe to show in all cases - 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().$el; - }, - - // icon-button to re run the job that created this hda - _render_rerunButton : function(){ - if( !this.model.get( 'for_editing' ) ){ return null; } - this.rerunButton = new IconButtonView({ model : new IconButton({ - title : 'Run this job again', - href : this.urls.rerun, - target : 'galaxy_main', - icon_class : 'arrow-circle' - }) }); - return this.rerunButton.render().$el; - }, - - // build an icon-button or popupmenu based on the number of applicable visualizations - // also map button/popup clicks to viz setup functions - _render_visualizationsButton : function(){ - var dbkey = this.model.get( 'dbkey' ), - visualizations = this.model.get( 'visualizations' ), - visualization_url = this.urls.visualization, - popup_menu_dict = {}, - params = { - dataset_id: this.model.get( 'id' ), - hda_ldda: 'hda' - }; - - if( !( this.model.hasData() ) - || !( this.model.get( 'for_editing' ) ) - || !( visualizations && visualizations.length ) - || !( visualization_url ) ){ - //console.warn( 'NOT rendering visualization icon' ) - return null; - } - - // render the icon from template - this.visualizationsButton = new IconButtonView({ model : new IconButton({ - title : 'Visualize', - href : visualization_url, - icon_class : 'chart_curve' - })}); - var $icon = this.visualizationsButton.render().$el; - $icon.addClass( 'visualize-icon' ); // needed? - - //TODO: make this more concise - // map a function to each visualization in the icon's attributes - // create a popupmenu from that map - // Add dbkey to params if it exists. - if( dbkey ){ params.dbkey = dbkey; } - - function create_viz_action( visualization ) { - switch( visualization ){ - case 'trackster': - return create_trackster_action_fn( visualization_url, params, dbkey ); - case 'scatterplot': - return create_scatterplot_action_fn( visualization_url, params ); - default: - return function(){ - window.parent.location = visualization_url + '/' + visualization + '?' + $.param( params ); }; - } - } - - // No need for popup menu because there's a single visualization. - if ( visualizations.length === 1 ) { - $icon.attr( 'title', visualizations[0] ); - $icon.click( create_viz_action( visualizations[0] ) ); - - // >1: Populate menu dict with visualization fns, make the popupmenu - } else { - _.each( visualizations, function( visualization ) { - //TODO: move to utils - var titleCaseVisualization = visualization.charAt( 0 ).toUpperCase() + visualization.slice( 1 ); - popup_menu_dict[ titleCaseVisualization ] = create_viz_action( visualization ); - }); - make_popupmenu( $icon, popup_menu_dict ); - } - return $icon; - }, - - // ................................................................................ secondary actions - // secondary actions: currently tagging and annotation (if user is allowed) - _render_secondaryActionButtons : function( buttonRenderingFuncs ){ - // move to the right (same level as primary) - var secondaryActionButtons = $( '<div/>' ), - view = this; - secondaryActionButtons - .attr( 'style', 'float: right;' ) - .attr( 'id', 'secondary-actions-' + this.model.get( 'id' ) ); - - _.each( buttonRenderingFuncs, function( fn ){ - secondaryActionButtons.append( fn.call( view ) ); - }); - return secondaryActionButtons; - }, - - // icon-button to load and display tagging html - //TODO: these should be a sub-MV - _render_tagButton : function(){ - if( !( this.model.hasData() ) - || !( this.model.get( 'for_editing' ) ) - || ( !this.urls.tags.get ) ){ return null; } - - this.tagButton = new IconButtonView({ model : new IconButton({ - title : 'Edit dataset tags', - target : 'galaxy_main', - href : this.urls.tags.get, - icon_class : 'tags' - })}); - return this.tagButton.render().$el; - }, - - // icon-button to load and display annotation html - //TODO: these should be a sub-MV - _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; - }, - - // ................................................................................ other elements - // render links to external genome display applications (igb, gbrowse, etc.) - //TODO: not a fan of the style on these - _render_displayApps : function(){ - if( !this.model.hasData() ){ return null; } - - var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); - if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ - //this.log( this + 'display_types:', this.model.get( 'urls' ).display_types ); - //TODO:?? does this ever get used? - displayAppsDiv.append( - HDAView.templates.displayApps({ displayApps : this.model.get( 'display_types' ) }) - ); - } - if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ - //this.log( this + 'display_apps:', this.model.get( 'urls' ).display_apps ); - displayAppsDiv.append( - HDAView.templates.displayApps({ displayApps : this.model.get( 'display_apps' ) }) - ); - } - return displayAppsDiv; - }, - - //TODO: into sub-MV - // render the area used to load tag display - _render_tagArea : function(){ - if( !this.urls.tags.set ){ return null; } - //TODO: move to mvc/tags.js - return $( HDAView.templates.tagArea( - _.extend( this.model.toJSON(), { urls: this.urls } ) - )); - }, - - //TODO: into sub-MV - // render the area used to load annotation display - _render_annotationArea : function(){ - if( !this.urls.annotation.get ){ return null; } - //TODO: move to mvc/annotations.js - return $( HDAView.templates.annotationArea( - _.extend( this.model.toJSON(), { urls: this.urls } ) - )); - }, - - // render the data peek - //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible - _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' ) ) - ); - }, - - // ................................................................................ state body renderers - // _render_body fns for the various states - //TODO: only render these on expansion (or already expanded) - _render_body_not_viewable : function( parent ){ - //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right - parent.append( $( '<div>You do not have permission to view dataset.</div>' ) ); - }, - - _render_body_uploading : function( parent ){ - parent.append( $( '<div>Dataset is uploading</div>' ) ); - }, - - _render_body_queued : function( parent ){ - parent.append( $( '<div>Job is waiting to run.</div>' ) ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_running : function( parent ){ - parent.append( '<div>Job is currently running.</div>' ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_error : function( parent ){ - if( !this.model.get( 'purged' ) ){ - parent.append( $( '<div>' + this.model.get( 'misc_blurb' ) + '</div>' ) ); - } - parent.append( ( 'An error occurred running this job: ' - + '<i>' + $.trim( this.model.get( 'misc_info' ) ) + '</i>' ) ); - parent.append( this._render_primaryActionButtons([ - this._render_downloadButton, - this._render_errButton, - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_discarded : function( parent ){ - parent.append( '<div>The job creating this dataset was cancelled before completion.</div>' ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_setting_metadata : function( parent ){ - parent.append( $( '<div>Metadata is being auto-detected.</div>' ) ); - }, - - _render_body_empty : function( parent ){ - //TODO: replace i with dataset-misc-info class - //?? why are we showing the file size when we know it's zero?? - parent.append( $( '<div>No data: <i>' + this.model.get( 'misc_blurb' ) + '</i></div>' ) ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_failed_metadata : function( parent ){ - //TODO: the css for this box is broken (unlike the others) - // add a message box about the failure at the top of the body... - parent.append( $( HDAView.templates.failedMetadata( this.model.toJSON() ) ) ); - //...then render the remaining body as STATES.OK (only diff between these states is the box above) - this._render_body_ok( parent ); - }, - - _render_body_ok : function( parent ){ - // most common state renderer and the most complicated - parent.append( this._render_hdaSummary() ); - - // return shortened form if del'd - //TODO: is this correct? maybe only on purged - if( this.model.isDeletedOrPurged() ){ - parent.append( this._render_primaryActionButtons([ - this._render_downloadButton, - this._render_showParamsButton, - this._render_rerunButton - ])); - return; - } - - //NOTE: change the order here - parent.append( this._render_primaryActionButtons([ - this._render_downloadButton, - this._render_errButton, - this._render_showParamsButton, - this._render_rerunButton, - this._render_visualizationsButton - ])); - parent.append( this._render_secondaryActionButtons([ - this._render_tagButton, - this._render_annotateButton - ])); - parent.append( '<div class="clear"/>' ); - - parent.append( this._render_tagArea() ); - parent.append( this._render_annotationArea() ); - - parent.append( this._render_displayApps() ); - parent.append( this._render_peek() ); - - //TODO??: still needed? - //// If Mozilla, hide scrollbars in hidden items since they cause animation bugs - //if ( $.browser.mozilla ) { - // $( "div.historyItemBody" ).each( function() { - // if ( !$(this).is(":visible") ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); } - // }); - //} - }, - - _render_body : function(){ - //this.log( this + '_render_body' ); - //this.log( 'state:', state, 'for_editing', for_editing ); - - //TODO: incorrect id (encoded - use hid?) - var body = $( '<div/>' ) - .attr( 'id', 'info-' + this.model.get( 'id' ) ) - .addClass( 'historyItemBody' ) - .attr( 'style', 'display: block' ); - - //TODO: not a fan of this dispatch - switch( this.model.get( 'state' ) ){ - case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : - this._render_body_not_viewable( body ); - break; - case HistoryDatasetAssociation.STATES.UPLOAD : - this._render_body_uploading( body ); - break; - case HistoryDatasetAssociation.STATES.QUEUED : - this._render_body_queued( body ); - break; - case HistoryDatasetAssociation.STATES.RUNNING : - this._render_body_running( body ); - break; - case HistoryDatasetAssociation.STATES.ERROR : - this._render_body_error( body ); - break; - case HistoryDatasetAssociation.STATES.DISCARDED : - this._render_body_discarded( body ); - break; - case HistoryDatasetAssociation.STATES.SETTING_METADATA : - this._render_body_setting_metadata( body ); - break; - case HistoryDatasetAssociation.STATES.EMPTY : - this._render_body_empty( body ); - break; - case HistoryDatasetAssociation.STATES.FAILED_METADATA : - this._render_body_failed_metadata( body ); - break; - case HistoryDatasetAssociation.STATES.OK : - this._render_body_ok( body ); - break; - default: - //??: no body? - body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) ); - } - body.append( '<div style="clear: both"></div>' ); - - if( this.expanded ){ - body.show(); - } else { - body.hide(); - } - return body; - }, - - // ................................................................................ EVENTS - events : { - 'click .historyItemTitle' : 'toggleBodyVisibility', - 'click a.icon-button.tags' : 'loadAndDisplayTags', - 'click a.icon-button.annotate' : 'loadAndDisplayAnnotation' - }, - - // ................................................................................ STATE CHANGES / MANIPULATION - // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide - //TODO: into sub-MV - loadAndDisplayTags : function( event ){ - //BUG: broken with latest - //TODO: this is a drop in from history.mako - should use MV as well - this.log( this + '.loadAndDisplayTags', event ); - var tagArea = this.$el.find( '.tag-area' ), - tagElt = tagArea.find( '.tag-elt' ); - - // Show or hide tag area; if showing tag area and it's empty, fill it. - if( tagArea.is( ":hidden" ) ){ - if( !jQuery.trim( tagElt.html() ) ){ - // Need to fill tag element. - $.ajax({ - //TODO: the html from this breaks a couple of times - url: this.urls.tags.get, - error: function() { alert( "Tagging failed" ); }, - success: function(tag_elt_html) { - tagElt.html(tag_elt_html); - tagElt.find(".tooltip").tooltip(); - tagArea.slideDown("fast"); - } - }); - } else { - // Tag element is filled; show. - tagArea.slideDown("fast"); - } - } else { - // Hide. - tagArea.slideUp("fast"); - } - return false; - }, - - // find the annotation area and, if initial: (via ajax) load the html for displaying it; otherwise, unhide/hide - //TODO: into sub-MV - loadAndDisplayAnnotation : function( event ){ - //TODO: this is a drop in from history.mako - should use MV as well - this.log( this + '.loadAndDisplayAnnotation', event ); - var annotationArea = this.$el.find( '.annotation-area' ), - annotationElem = annotationArea.find( '.annotation-elt' ), - setAnnotationUrl = this.urls.annotation.set; - - // Show or hide annotation area; if showing annotation area and it's empty, fill it. - if ( annotationArea.is( ":hidden" ) ){ - if( !jQuery.trim( annotationElem.html() ) ){ - // Need to fill annotation element. - $.ajax({ - url: this.urls.annotation.get, - error: function(){ alert( "Annotations failed" ); }, - success: function( htmlFromAjax ){ - if( htmlFromAjax === "" ){ - htmlFromAjax = "<em>Describe or add notes to dataset</em>"; - } - annotationElem.html( htmlFromAjax ); - annotationArea.find(".tooltip").tooltip(); - - async_save_text( - annotationElem.attr("id"), annotationElem.attr("id"), - setAnnotationUrl, - "new_annotation", 18, true, 4 - ); - annotationArea.slideDown("fast"); - } - }); - } else { - annotationArea.slideDown("fast"); - } - - } else { - // Hide. - annotationArea.slideUp("fast"); - } - return false; - }, - - // expand/collapse body - //side effect: trigger event - toggleBodyVisibility : function( event, expanded ){ - var $body = this.$el.find( '.historyItemBody' ); - expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); - //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); - - if( expanded ){ - $body.slideDown( 'fast' ); - } else { - $body.slideUp( 'fast' ); - } - this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), expanded ); - }, - - // ................................................................................ UTILTIY - toString : function(){ - var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HDAView(' + modelString + ')'; - } -}); - -//------------------------------------------------------------------------------ -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' ] -}; - -//============================================================================== -//TODO: these belong somewhere else - -//TODO: should be imported from scatterplot.js -//TODO: OR abstracted to 'load this in the galaxy_main frame' -function create_scatterplot_action_fn( url, params ){ - action = function() { - var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ), - final_url = url + '/scatterplot?' + $.param(params); - galaxy_main.attr( 'src', final_url ); - //TODO: this needs to go away - $( 'div.popmenu-wrapper' ).remove(); - return false; - }; - return action; -} - -// ----------------------------------------------------------------------------- -// Create trackster action function. -//TODO: should be imported from trackster.js -function create_trackster_action_fn(vis_url, dataset_params, dbkey) { - return function() { - var params = {}; - if (dbkey) { params.dbkey = dbkey; } - $.ajax({ - url: vis_url + '/list_tracks?f-' + $.param(params), - dataType: "html", - error: function() { alert( "Could not add this dataset to browser." ); }, - success: function(table_html) { - var parent = window.parent; - - parent.show_modal("View Data in a New or Saved Visualization", "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.show_modal("Add Data to Saved Visualization", table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - dataset_params.id = vis_id; - parent.location = vis_url + "/trackster?" + $.param(dataset_params); - }); - } - }); - }, - "View in new visualization": function() { - parent.location = vis_url + "/trackster?" + $.param(dataset_params); - } - }); - } - }); - return false; - }; -} - - -//============================================================================== -// view for the HDACollection (as per current right hand panel) -var HistoryView = BaseView.extend( LoggableMixin ).extend({ - - // uncomment this out see log messages - //logger : console, - - // direct attachment to existing element - el : 'body.historyPage', - - // init with the model, urlTemplates, set up storage, bind HDACollection events - //NOTE: this will create or load PersistantStorage keyed under 'HistoryView.<id>' - //pre: you'll need to pass in the urlTemplates (urlTemplates : { history : {...}, hda : {...} }) - initialize : function( attributes ){ - this.log( this + '.initialize:', attributes ); - - // set up url templates - //TODO: prob. better to put this in class scope (as the handlebars templates), but... - // they're added to GalaxyPaths on page load (after this file is loaded) - if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } - if( !attributes.urlTemplates.history ){ throw( 'HDAView needs urlTemplates.history on initialize' ); } - if( !attributes.urlTemplates.hda ){ throw( 'HDAView needs urlTemplates.hda on initialize' ); } - this.urlTemplates = attributes.urlTemplates.history; - this.hdaUrlTemplates = attributes.urlTemplates.hda; - - // 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 : {} } - ); - - // bind events from the model's hda collection - //this.model.bind( 'change', this.render, this ); - 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.bind( 'all', function(){ - // this.log( arguments ); - //}, this ); - - // set up instance vars - this.hdaViews = {}; - this.urls = {}; - }, - - add : function( hda ){ - //console.debug( 'add.' + this, hda ); - //TODO - }, - - addAll : function(){ - //console.debug( 'addAll.' + this ); - // re render when all hdas are reset - this.render(); - }, - - all : function( event ){ - //console.debug( 'allItemEvents.' + this, event ); - //...for which to do the debuggings - }, - - // render the urls for this view using urlTemplates and the model data - renderUrls : function( modelJson ){ - var historyView = this; - - historyView.urls = {}; - _.each( this.urlTemplates, function( urlTemplate, urlKey ){ - historyView.urls[ urlKey ] = _.template( urlTemplate, modelJson ); - }); - return historyView.urls; - }, - - // render urls, historyView body, and hdas (if any are shown), fade out, swap, fade in, set up behaviours - render : function(){ - var historyView = this, - setUpQueueName = historyView.toString() + '.set-up', - newRender = $( '<div/>' ), - modelJson = this.model.toJSON(), - initialRender = ( this.$el.children().size() === 0 ); - - //console.debug( this + '.render, initialRender:', initialRender ); - - // render the urls and add them to the model json - modelJson.urls = this.renderUrls( modelJson ); - - // render the main template, tooltips - //NOTE: this is done before the items, since item views should handle theirs themselves - newRender.append( HistoryView.templates.historyPanel( modelJson ) ); - newRender.find( '.tooltip' ).tooltip(); - - // render hda views (if any and any shown (show_deleted/hidden) - if( !this.model.hdas.length - || !this.renderItems( newRender.find( '#' + this.model.get( 'id' ) + '-datasets' ) ) ){ - // if history is empty or no hdas would be rendered, show the empty message - newRender.find( '#emptyHistoryMessage' ).show(); - } - - // fade out existing, swap with the new, fade in, set up behaviours - $( historyView ).queue( setUpQueueName, function( next ){ - historyView.$el.fadeOut( 'fast', function(){ next(); }); - }); - $( historyView ).queue( setUpQueueName, function( next ){ - // swap over from temp div newRender - historyView.$el.html( '' ); - historyView.$el.append( newRender.children() ); - - historyView.$el.fadeIn( 'fast', function(){ next(); }); - }); - $( historyView ).queue( setUpQueueName, function( next ){ - this.log( historyView + ' rendered:', historyView.$el ); - - //TODO: ideally, these would be set up before the fade in (can't because of async save text) - historyView.setUpBehaviours(); - - if( initialRender ){ - historyView.trigger( 'rendered:initial' ); - - } else { - historyView.trigger( 'rendered' ); - } - next(); - }); - $( historyView ).dequeue( setUpQueueName ); - return this; - }, - - // 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 ); - - // only render the shown hdas - _.each( visibleHdas, function( hda ){ - var hdaId = hda.get( 'id' ), - expanded = historyView.storage.get( 'expandedHdas' ).get( hdaId ); - historyView.hdaViews[ hdaId ] = new HDAView({ - model : hda, - expanded : expanded, - urlTemplates : historyView.hdaUrlTemplates - }); - historyView.setUpHdaListeners( historyView.hdaViews[ hdaId ] ); - // render it (NOTE: reverse order, newest on top (prepend)) - //TODO: by default send a reverse order list (although this may be more efficient - it's more confusing) - $whereTo.prepend( historyView.hdaViews[ hdaId ].render().$el ); - }); - return visibleHdas.length; - }, - - // set up HistoryView->HDAView listeners - setUpHdaListeners : function( hdaView ){ - var historyView = this; - - // use storage to maintain a list of hdas whose bodies are expanded - hdaView.bind( 'toggleBodyVisibility', function( id, visible ){ - if( visible ){ - historyView.storage.get( 'expandedHdas' ).set( id, true ); - } else { - historyView.storage.get( 'expandedHdas' ).deleteKey( id ); - } - }); - - // rendering listeners - hdaView.bind( 'rendered:ready', function(){ historyView.trigger( 'hda:rendered:ready' ); }); - }, - - // set up js/widget behaviours: tooltips, - //TODO: these should be either sub-MVs, or handled by events - setUpBehaviours : function(){ - // anon users shouldn't have access to any of these - if( !( this.model.get( 'user' ) && this.model.get( 'user' ).email ) ){ return; } - - // annotation slide down - var historyAnnotationArea = this.$( '#history-annotation-area' ); - this.$( '#history-annotate' ).click( function() { - if ( historyAnnotationArea.is( ":hidden" ) ) { - historyAnnotationArea.slideDown( "fast" ); - } else { - historyAnnotationArea.slideUp( "fast" ); - } - return false; - }); - - // title and annotation editable text - //NOTE: these use page scoped selectors - so these need to be in the page DOM before they're applicable - 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 ); - }, - - // update the history size display (curr. upper right of panel) - updateHistoryDiskSize : function(){ - this.$el.find( '#history-size' ).text( this.model.get( 'nice_size' ) ); - }, - - //TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here - showQuotaMessage : function( userData ){ - var msg = this.$el.find( '#quota-message-container' ); - //this.log( this + ' showing quota message:', msg, userData ); - if( msg.is( ':hidden' ) ){ msg.slideDown( 'fast' ); } - }, - - //TODO: this seems more like a per user message than a history message - hideQuotaMessage : function( userData ){ - var msg = this.$el.find( '#quota-message-container' ); - //this.log( this + ' hiding quota message:', msg, userData ); - if( !msg.is( ':hidden' ) ){ msg.slideUp( 'fast' ); } - }, - - events : { - 'click #history-collapse-all' : 'hideAllHdaBodies', - 'click #history-tag' : 'loadAndDisplayTags' - }, - - // collapse all hda bodies - hideAllHdaBodies : function(){ - _.each( this.hdaViews, function( item ){ - item.toggleBodyVisibility( null, false ); - }); - this.storage.set( 'expandedHdas', {} ); - }, - - // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide - //TODO: into sub-MV - loadAndDisplayTags : function( event ){ - this.log( this + '.loadAndDisplayTags', event ); - var tagArea = this.$el.find( '#history-tag-area' ), - tagElt = tagArea.find( '.tag-elt' ); - this.log( '\t tagArea', tagArea, ' tagElt', tagElt ); - - // Show or hide tag area; if showing tag area and it's empty, fill it - if( tagArea.is( ":hidden" ) ){ - if( !jQuery.trim( tagElt.html() ) ){ - var view = this; - // Need to fill tag element. - $.ajax({ - //TODO: the html from this breaks a couple of times - url: view.urls.tag, - error: function() { alert( "Tagging failed" ); }, - success: function(tag_elt_html) { - //view.log( view + ' tag elt html (ajax)', tag_elt_html ); - tagElt.html(tag_elt_html); - tagElt.find(".tooltip").tooltip(); - tagArea.slideDown("fast"); - } - }); - } else { - // Tag element already filled: show - tagArea.slideDown("fast"); - } - - } else { - // Currently shown: Hide - tagArea.slideUp("fast"); - } - return false; - }, - - toString : function(){ - var nameString = this.model.get( 'name' ) || ''; - return 'HistoryView(' + nameString + ')'; - } -}); -HistoryView.templates = { - historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] -}; - -//============================================================================== -//return { -// HistoryItem : HistoryItem, -// HDAView : HDAView, -// HistoryCollection : HistoryCollection, -// History : History, -// HistoryView : HistoryView -//};}); diff -r 3d27b35e1c1fa629ec4175f5e613b5a771152377 -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 static/scripts/mvc/history/history-model.js --- /dev/null +++ b/static/scripts/mvc/history/history-model.js @@ -0,0 +1,180 @@ +//define([ +// "../mvc/base-mvc" +//], function(){ +//============================================================================== +/** + * + */ +var History = BaseModel.extend( LoggableMixin ).extend({ + //TODO: bind change events from items and collection to this (itemLengths, states) + + // uncomment this out see log messages + //logger : console, + + // values from api (may need more) + defaults : { + id : '', + name : '', + state : '', + + //TODO: wire these to items (or this) + show_deleted : false, + show_hidden : false, + + diskSize : 0, + deleted : false, + + tags : [], + annotation : null, + + //TODO: quota msg and message? how to get those over the api? + message : null, + quotaMsg : false + }, + + url : function(){ + // api location of history resource + //TODO: hardcoded + return 'api/histories/' + this.get( 'id' ); + }, + + initialize : function( initialSettings, initialHdas ){ + this.log( this + ".initialize:", initialSettings, initialHdas ); + + this.hdas = new HDACollection(); + + // if we've got hdas passed in the constructor, load them and set up updates if needed + if( initialHdas && initialHdas.length ){ + this.hdas.reset( initialHdas ); + this.checkForUpdates(); + } + + //this.on( 'change', function( currModel, changedList ){ + // this.log( this + ' has changed:', currModel, changedList ); + //}); + //this.bind( 'all', function( event ){ + // this.log( this + '', arguments ); + //}); + }, + + // get data via the api (alternative to sending options,hdas to initialize) + loadFromApi : function( historyId, callback ){ + var history = this; + + // fetch the history AND the user (mainly to see if they're logged in at this point) + history.attributes.id = historyId; + //TODO:?? really? fetch user here? + jQuery.when( jQuery.ajax( 'api/users/current' ), history.fetch() + + ).then( function( userResponse, historyResponse ){ + //console.warn( 'fetched user, history: ', userResponse, historyResponse ); + history.attributes.user = userResponse[0]; //? meh. + history.log( history ); + + }).then( function(){ + // ...then the hdas (using contents?ids=...) + jQuery.ajax( history.url() + '/contents?' + jQuery.param({ + ids : history.itemIdsFromStateIds().join( ',' ) + + // reset the collection to the hdas returned + })).success( function( hdas ){ + //console.warn( 'fetched hdas' ); + history.hdas.reset( hdas ); + history.checkForUpdates(); + callback(); + }); + }); + }, + + // reduce the state_ids map of hda id lists -> a single list of ids + //...ugh - seems roundabout; necessary because the history doesn't have a straightforward list of ids + // (and history_contents/index curr returns a summary only) + hdaIdsFromStateIds : function(){ + return _.reduce( _.values( this.get( 'state_ids' ) ), function( reduction, currIdList ){ + return reduction.concat( currIdList ); + }); + }, + + // get the history's state from it's cummulative ds states, delay + update if needed + checkForUpdates : function( datasets ){ + // get overall History state from collection, run updater if History has running/queued hdas + // boiling it down on the client to running/not + if( this.hdas.running().length ){ + this.stateUpdater(); + } + return this; + }, + + // update this history, find any hda's running/queued, update ONLY those that have changed states, + // set up to run this again in some interval of time + stateUpdater : function(){ + var history = this, + oldState = this.get( 'state' ), + // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state + oldStateIds = this.get( 'state_ids' ); + + // pull from the history api + //TODO: fetch? + jQuery.ajax( 'api/histories/' + this.get( 'id' ) + + ).success( function( response ){ + //this.log( 'historyApiRequest, response:', response ); + history.set( response ); + history.log( 'current history state:', history.get( 'state' ), + '(was)', oldState, + 'new size:', history.get( 'nice_size' ) ); + + //TODO: revisit this - seems too elaborate, need something straightforward + // for each state, check for the difference between old dataset states and new + // the goal here is to check ONLY those datasets that have changed states (not all datasets) + var changedIds = []; + _.each( _.keys( response.state_ids ), function( state ){ + var diffIds = _.difference( response.state_ids[ state ], oldStateIds[ state ] ); + // aggregate those changed ids + changedIds = changedIds.concat( diffIds ); + }); + + // send the changed ids (if any) to dataset collection to have them fetch their own model changes + if( changedIds.length ){ + history.hdas.update( changedIds ); + } + + // set up to keep pulling if this history in run/queue state + //TODO: magic number here + if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + setTimeout( function(){ + history.stateUpdater(); + }, 4000 ); + } + + }).error( function( xhr, status, error ){ + if( console && console.warn ){ + console.warn( 'Error getting history updates from the server:', xhr, status, error ); + } + alert( 'Error getting history updates from the server.\n' + error ); + }); + }, + + toString : function(){ + var nameString = ( this.get( 'name' ) )? + ( ',' + this.get( 'name' ) ) : ( '' ); + return 'History(' + this.get( 'id' ) + nameString + ')'; + } +}); + +//============================================================================== +/** A collection of histories (per user or admin) + * (stub) currently unused + */ +var HistoryCollection = Backbone.Collection.extend( LoggableMixin ).extend({ + model : History, + urlRoot : 'api/histories', + logger : console +}); + +//============================================================================== +//return { +// History : History, +// HistoryCollection : HistoryCollection, +//};}); diff -r 3d27b35e1c1fa629ec4175f5e613b5a771152377 -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 static/scripts/mvc/history/history-panel.js --- /dev/null +++ b/static/scripts/mvc/history/history-panel.js @@ -0,0 +1,380 @@ +//define([ +// "../mvc/base-mvc" +//], function(){ +/* ============================================================================= +Backbone.js implementation of history panel + +TODO: + anon user, mako template init: + bug: rename url seems to be wrong url + + 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 + bug: quotaMeter bar rendering square in chrome + BUG: quotaMsg not showing when 100% (on load) + BUG: imported, shared history with unaccessible dataset errs in historycontents when getting history + (entire history is inaccessible) + ??: still happening? + + from loadFromApi: + BUG: not showing previous annotations + + fixed: + BUG: upload, history size, doesn't change + FIXED: using change:nice_size to trigger re-render of history size + BUG: delete uploading hda - now in state 'discarded'! ...new state to handle + FIXED: handled state + BUG: historyItem, error'd ds show display, download? + FIXED: removed + bug: loading hdas (alt_hist) + FIXED: added anon user api request ( trans.user == None and trans.history.id == requested id ) + bug: quota meter not updating on upload/tool run + FIXED: quotaMeter now listens for 'state:ready' from glx_history in alternate_history.mako + bug: use of new HDACollection with event listener in init doesn't die...keeps reporting + FIXED: change getVisible to return an array + BUG: history, broken intial hist state (running, updater, etc.) + ??: doesn't seem to happen anymore + BUG: collapse all should remove all expanded from storage + FIXED: hideAllItemBodies now resets storage.expandedItems + BUG: historyItem, shouldn't allow tag, annotate, peek on purged datasets + FIXED: ok state now shows only: info, rerun + BUG: history?, some ids aren't returning encoded... + FIXED:??? + BUG: history, showing deleted ds + FIXED + UGH: historyItems have to be decorated with history_ids (api/histories/:history_id/contents/:id) + FIXED by adding history_id to history_contents.show + BUG: history, if hist has err'd ds, hist has perm state 'error', updater on following ds's doesn't run + FIXED by reordering history state from ds' states here and histories + BUG: history, broken annotation on reload (can't get thru api (sets fine, tho)) + FIXED: get thru api for now + + replication: + show_deleted/hidden: + use storage + on/off ui + move histview fadein/out in render to app? + don't draw body until it's first expand event + localize all + ?: render url templates on init or render? + ?: history, annotation won't accept unicode + + RESTful: + move over webui functions available in api + delete, undelete + update? + currently, adding a dataset (via tool execute, etc.) creates a new dataset and refreshes the page + provide a means to update the panel via js + + hierarchy: + to relational model? + HDACollection, meta_files, display_apps, etc. + dataset -> hda + history -> historyForEditing, historyForViewing + display_structured? + + meta: + css/html class/id 'item' -> hda + add classes, ids on empty divs + events (local/ui and otherwise) + list in docs as well + require.js + convert function comments to jsDoc style, complete comments + move inline styles into base.less + watch the magic strings + watch your globals + + feature creep: + lineage + hide button + show permissions in info + show shared/sharing status on ds, history + maintain scroll position on refresh (storage?) + selection, multi-select (and actions common to selected (ugh)) + searching + sorting, re-shuffling + +============================================================================= */ +/** view for the HDACollection (as per current right hand panel) + * + */ +var HistoryPanel = BaseView.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + //logger : console, + + // direct attachment to existing element + el : 'body.historyPage', + + // init with the model, urlTemplates, set up storage, bind HDACollection events + //NOTE: this will create or load PersistantStorage keyed under 'HistoryView.<id>' + //pre: you'll need to pass in the urlTemplates (urlTemplates : { history : {...}, hda : {...} }) + initialize : function( attributes ){ + this.log( this + '.initialize:', attributes ); + + // set up url templates + //TODO: prob. better to put this in class scope (as the handlebars templates), but... + // they're added to GalaxyPaths on page load (after this file is loaded) + if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } + if( !attributes.urlTemplates.history ){ throw( 'HDAView needs urlTemplates.history on initialize' ); } + if( !attributes.urlTemplates.hda ){ throw( 'HDAView needs urlTemplates.hda on initialize' ); } + this.urlTemplates = attributes.urlTemplates.history; + this.hdaUrlTemplates = attributes.urlTemplates.hda; + + // 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 : {} } + ); + + // bind events from the model's hda collection + //this.model.bind( 'change', this.render, this ); + 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.bind( 'all', function(){ + // this.log( arguments ); + //}, this ); + + // set up instance vars + this.hdaViews = {}; + this.urls = {}; + }, + + add : function( hda ){ + //console.debug( 'add.' + this, hda ); + //TODO + }, + + addAll : function(){ + //console.debug( 'addAll.' + this ); + // re render when all hdas are reset + this.render(); + }, + + all : function( event ){ + //console.debug( 'allItemEvents.' + this, event ); + //...for which to do the debuggings + }, + + // render the urls for this view using urlTemplates and the model data + renderUrls : function( modelJson ){ + var historyView = this; + + historyView.urls = {}; + _.each( this.urlTemplates, function( urlTemplate, urlKey ){ + historyView.urls[ urlKey ] = _.template( urlTemplate, modelJson ); + }); + return historyView.urls; + }, + + // render urls, historyView body, and hdas (if any are shown), fade out, swap, fade in, set up behaviours + render : function(){ + var historyView = this, + setUpQueueName = historyView.toString() + '.set-up', + newRender = $( '<div/>' ), + modelJson = this.model.toJSON(), + initialRender = ( this.$el.children().size() === 0 ); + + //console.debug( this + '.render, initialRender:', initialRender ); + + // render the urls and add them to the model json + modelJson.urls = this.renderUrls( modelJson ); + + // 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(); + + // render hda views (if any and any shown (show_deleted/hidden) + if( !this.model.hdas.length + || !this.renderItems( newRender.find( '#' + this.model.get( 'id' ) + '-datasets' ) ) ){ + // if history is empty or no hdas would be rendered, show the empty message + newRender.find( '#emptyHistoryMessage' ).show(); + } + + // fade out existing, swap with the new, fade in, set up behaviours + $( historyView ).queue( setUpQueueName, function( next ){ + historyView.$el.fadeOut( 'fast', function(){ next(); }); + }); + $( historyView ).queue( setUpQueueName, function( next ){ + // swap over from temp div newRender + historyView.$el.html( '' ); + historyView.$el.append( newRender.children() ); + + historyView.$el.fadeIn( 'fast', function(){ next(); }); + }); + $( historyView ).queue( setUpQueueName, function( next ){ + this.log( historyView + ' rendered:', historyView.$el ); + + //TODO: ideally, these would be set up before the fade in (can't because of async save text) + historyView.setUpBehaviours(); + + if( initialRender ){ + historyView.trigger( 'rendered:initial' ); + + } else { + historyView.trigger( 'rendered' ); + } + next(); + }); + $( historyView ).dequeue( setUpQueueName ); + return this; + }, + + // 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 ); + + // only render the shown hdas + _.each( visibleHdas, function( hda ){ + var hdaId = hda.get( 'id' ), + expanded = historyView.storage.get( 'expandedHdas' ).get( hdaId ); + historyView.hdaViews[ hdaId ] = new HDAView({ + model : hda, + expanded : expanded, + urlTemplates : historyView.hdaUrlTemplates + }); + historyView.setUpHdaListeners( historyView.hdaViews[ hdaId ] ); + // render it (NOTE: reverse order, newest on top (prepend)) + //TODO: by default send a reverse order list (although this may be more efficient - it's more confusing) + $whereTo.prepend( historyView.hdaViews[ hdaId ].render().$el ); + }); + return visibleHdas.length; + }, + + // set up HistoryView->HDAView listeners + setUpHdaListeners : function( hdaView ){ + var historyView = this; + + // use storage to maintain a list of hdas whose bodies are expanded + hdaView.bind( 'toggleBodyVisibility', function( id, visible ){ + if( visible ){ + historyView.storage.get( 'expandedHdas' ).set( id, true ); + } else { + historyView.storage.get( 'expandedHdas' ).deleteKey( id ); + } + }); + + // rendering listeners + hdaView.bind( 'rendered:ready', function(){ historyView.trigger( 'hda:rendered:ready' ); }); + }, + + // set up js/widget behaviours: tooltips, + //TODO: these should be either sub-MVs, or handled by events + setUpBehaviours : function(){ + // anon users shouldn't have access to any of these + if( !( this.model.get( 'user' ) && this.model.get( 'user' ).email ) ){ return; } + + // annotation slide down + var historyAnnotationArea = this.$( '#history-annotation-area' ); + this.$( '#history-annotate' ).click( function() { + if ( historyAnnotationArea.is( ":hidden" ) ) { + historyAnnotationArea.slideDown( "fast" ); + } else { + historyAnnotationArea.slideUp( "fast" ); + } + return false; + }); + + // title and annotation editable text + //NOTE: these use page scoped selectors - so these need to be in the page DOM before they're applicable + 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 ); + }, + + // update the history size display (curr. upper right of panel) + updateHistoryDiskSize : function(){ + this.$el.find( '#history-size' ).text( this.model.get( 'nice_size' ) ); + }, + + //TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here + showQuotaMessage : function( userData ){ + var msg = this.$el.find( '#quota-message-container' ); + //this.log( this + ' showing quota message:', msg, userData ); + if( msg.is( ':hidden' ) ){ msg.slideDown( 'fast' ); } + }, + + //TODO: this seems more like a per user message than a history message + hideQuotaMessage : function( userData ){ + var msg = this.$el.find( '#quota-message-container' ); + //this.log( this + ' hiding quota message:', msg, userData ); + if( !msg.is( ':hidden' ) ){ msg.slideUp( 'fast' ); } + }, + + events : { + 'click #history-collapse-all' : 'hideAllHdaBodies', + 'click #history-tag' : 'loadAndDisplayTags' + }, + + // collapse all hda bodies + hideAllHdaBodies : function(){ + _.each( this.hdaViews, function( item ){ + item.toggleBodyVisibility( null, false ); + }); + this.storage.set( 'expandedHdas', {} ); + }, + + // find the tag area and, if initial: (via ajax) load the html for displaying them; otherwise, unhide/hide + //TODO: into sub-MV + loadAndDisplayTags : function( event ){ + this.log( this + '.loadAndDisplayTags', event ); + var tagArea = this.$el.find( '#history-tag-area' ), + tagElt = tagArea.find( '.tag-elt' ); + this.log( '\t tagArea', tagArea, ' tagElt', tagElt ); + + // Show or hide tag area; if showing tag area and it's empty, fill it + if( tagArea.is( ":hidden" ) ){ + if( !jQuery.trim( tagElt.html() ) ){ + var view = this; + // Need to fill tag element. + $.ajax({ + //TODO: the html from this breaks a couple of times + url: view.urls.tag, + error: function() { alert( "Tagging failed" ); }, + success: function(tag_elt_html) { + //view.log( view + ' tag elt html (ajax)', tag_elt_html ); + tagElt.html(tag_elt_html); + tagElt.find(".tooltip").tooltip(); + tagArea.slideDown("fast"); + } + }); + } else { + // Tag element already filled: show + tagArea.slideDown("fast"); + } + + } else { + // Currently shown: Hide + tagArea.slideUp("fast"); + } + return false; + }, + + toString : function(){ + var nameString = this.model.get( 'name' ) || ''; + return 'HistoryView(' + nameString + ')'; + } +}); + +//------------------------------------------------------------------------------ +HistoryPanel.templates = { + historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] +}; + +//============================================================================== +//return { +// HistoryPanel : HistoryPanel +//};}); diff -r 3d27b35e1c1fa629ec4175f5e613b5a771152377 -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -222,97 +222,127 @@ "template-user-quotaMeter-usage" )} -##TODO: fix: curr hasta be _after_ h.templates - move somehow +##TODO: fix: curr hasta be _after_ h.templates bc these use those templates - move somehow ${h.js( - "mvc/history", + "mvc/dataset/hda-model", "mvc/dataset/hda-edit", + "mvc/history/history-model", "mvc/history/history-panel", + ##"mvc/tags", "mvc/annotations", "mvc/user/user-model", "mvc/user/user-quotameter" )} <script type="text/javascript"> +function galaxyPageSetUp(){ + // moving global functions, objects into Galaxy namespace + top.Galaxy = top.Galaxy || {}; + + // bad idea from memleak standpoint? + top.Galaxy.mainWindow = top.Galaxy.mainWindow || top.frames.galaxy_main; + top.Galaxy.toolWindow = top.Galaxy.toolWindow || top.frames.galaxy_tools; + top.Galaxy.historyWindow = top.Galaxy.historyWindow || top.frames.galaxy_history; + + top.Galaxy.$masthead = top.Galaxy.$masthead || $( top.document ).find( 'div#masthead' ); + top.Galaxy.$messagebox = top.Galaxy.$messagebox || $( top.document ).find( 'div#messagebox' ); + top.Galaxy.$leftPanel = top.Galaxy.$leftPanel || $( top.document ).find( 'div#left' ); + top.Galaxy.$centerPanel = top.Galaxy.$centerPanel || $( top.document ).find( 'div#center' ); + top.Galaxy.$rightPanel = top.Galaxy.$rightPanel || $( top.document ).find( 'div#right' ); + + //modals + // other base functions + + // global backbone models + top.Galaxy.currUser = top.Galaxy.currUser; + top.Galaxy.currHistoryPanel = top.Galaxy.currHistoryPanel; + top.Galaxy.historyPanels = top.Galaxy.historyPanels || []; + + top.Galaxy.paths = galaxy_paths; + + window.Galaxy = top.Galaxy; +} + // set js localizable strings GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); // add needed controller urls to GalaxyPaths galaxy_paths.set( 'hda', ${get_hda_url_templates()} ); galaxy_paths.set( 'history', ${get_history_url_templates()} ); +//console.debug( 'galaxy_paths:', galaxy_paths ); $(function(){ + galaxyPageSetUp(); + Galaxy.historyFrame = window; // ostensibly, this is the App if( console && console.debug ){ //if( console.clear ){ console.clear(); } - console.debug( 'using backbone.js in history panel' ); console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); } + top.storage = jQuery.jStorage } - // load initial data in this page - since we're already sending it... + // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it... + // ...use mako to 'bootstrap' the models var user = ${ get_current_user() }, history = ${ get_history( history.id ) }, hdas = ${ get_hdas( history.id, datasets ) }; //console.debug( 'user:', user ); //console.debug( 'history:', history ); //console.debug( 'hdas:', hdas ); + var currUser = new User( user ); + if( !Galaxy.currUser ){ Galaxy.currUser = currUser; } - // i don't like this relationship, but user authentication changes views/behaviour + // 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' }; - //console.debug( 'galaxy_paths:', galaxy_paths ); - var glx_history = new History( history, hdas ); - glx_history.logger = console; - - var glx_history_view = new HistoryView({ - model: glx_history, + var historyPanel = new HistoryPanel({ + model : new History( history, hdas ), urlTemplates: galaxy_paths.attributes, - logger: console + logger : console }); - glx_history_view.render(); - - - // ...OR load from the api - //var glx_history = new History().setPaths( galaxy_paths ), - // glx_history_view = new HistoryView({ model: glx_history }); - //console.warn( 'fetching' ); - //glx_history.loadFromApi( pageData.history.id ); + historyPanel.render(); + if( !Galaxy.currHistoryPanel ){ Galaxy.currHistoryPanel = historyPanel; } + if( !( historyPanel in Galaxy.historyPanels ) ){ Galaxy.historyPanels.unshift( historyPanel ); } - // quota meter is a cross-frame ui element (meter in masthead, over quota message in history) + // ...or LOAD FROM THE API + //historyPanel = new HistoryView({ model: new History().setPaths( galaxy_paths ) }); + //historyPanel.loadFromApi( pageData.history.id ); + + + // 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) - window.currUser = new User( user ); + //TODO: this really belongs in the masthead + //window.currUser.logger = console; - window.quotaMeter = new UserQuotaMeter({ model: currUser, el: $( top.document ).find( '.quota-meter-container' ) }); - window.quotaMeter.render(); - //window.quotaMeter.logger = console; + var quotaMeter = new UserQuotaMeter({ + model : currUser, + el : $( top.document ).find( '.quota-meter-container' ) + }); + //quotaMeter.logger = console; window.quotaMeter = quotaMeter + quotaMeter.render(); // show/hide the 'over quota message' in the history when the meter tells it to - quotaMeter.bind( 'quota:over', glx_history_view.showQuotaMessage, glx_history_view ); - quotaMeter.bind( 'quota:under', glx_history_view.hideQuotaMessage, glx_history_view ); + quotaMeter.bind( 'quota:over', historyPanel.showQuotaMessage, historyPanel ); + quotaMeter.bind( 'quota:under', historyPanel.hideQuotaMessage, historyPanel ); // having to add this to handle re-render of hview while overquota (the above do not fire) - glx_history_view.on( 'rendered', function(){ - if( window.quotaMeter.isOverQuota() ){ - glx_history_view.showQuotaMessage(); + historyPanel.on( 'rendered', function(){ + if( quotaMeter.isOverQuota() ){ + historyPanel.showQuotaMessage(); } }); //TODO: this _is_ sent to the page (over_quota)... // update the quota meter when current history changes size - glx_history.bind( 'change:nice_size', function(){ - window.quotaMeter.update() - }, window.quotaMeter ); + historyPanel.model.bind( 'change:nice_size', function(){ + quotaMeter.update() + }, quotaMeter ); - if( console && console.debug ){ - window.user = top.user = user; - window._history = top._history = history; - window.hdas = top.hdas = hdas; - window.glx_history = top.glx_history = glx_history; - window.glx_history_view = top.glx_history_view = glx_history_view; - top.storage = jQuery.jStorage - } - return; }); </script> https://bitbucket.org/galaxy/galaxy-central/changeset/191126557331/ changeset: 191126557331 user: carlfeberhard date: 2012-11-06 21:58:25 summary: merge and pack scripts affected #: 8 files diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -400,7 +400,6 @@ # the state or whether the tool used exit codes and regular # expressions to do so. So we use # job.state == job.states.ERROR to replace this same test. - #elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and not context['stderr']: elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and job.states.ERROR != job.state: dataset._state = model.Dataset.states.FAILED_METADATA else: diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -183,8 +183,9 @@ def stop_job( self, job ): #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished - if job.get_external_output_metadata(): - pid = job.get_external_output_metadata()[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them + job_ext_output_metadata = job.get_external_output_metadata() + if job_ext_output_metadata: + pid = job_ext_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them else: pid = job.get_job_runner_external_id() if pid in [ None, '' ]: diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -18,7 +18,7 @@ from galaxy.model.item_attrs import UsesAnnotations, APIItem from sqlalchemy.orm import object_session from sqlalchemy.sql.expression import func -import sys, os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil +import os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil if sys.version_info[:2] < ( 2, 5 ): from sets import Set as set @@ -138,6 +138,12 @@ # TODO: Add accessors for members defined in SQL Alchemy for the Job table and # for the mapper defined to the Job table. + def get_external_output_metadata( self ): + """ + The external_output_metadata is currently a reference from Job to + JobExternalOutputMetadata. It exists for a job but not a task. + """ + return self.external_output_metadata def get_session_id( self ): return self.session_id def get_user_id( self ): @@ -370,6 +376,13 @@ # (e.g., for a session) or never use the member (e.g., external output # metdata). These can be filled in as needed. def get_external_output_metadata( self ): + """ + The external_output_metadata is currently a backref to + JobExternalOutputMetadata. It exists for a job but not a task, + and when a task is cancelled its corresponding parent Job will + be cancelled. So None is returned now, but that could be changed + to self.get_job().get_external_output_metadata(). + """ return None def get_job_runner_name( self ): """ diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py @@ -19,6 +19,14 @@ else: env_var_text = elem.text.replace( '$INSTALL_DIR', tool_shed_repository_install_dir ) return dict( name=env_var_name, action=env_var_action, value=env_var_text ) + if elem.text: + # Allow for environment variables that contain neither REPOSITORY_INSTALL_DIR nor INSTALL_DIR since there may be command line + # parameters that are tuned for a Galaxy instance. Allowing them to be set in one location rather than being hard coded into + # each tool config is the best approach. For example: + # <environment_variable name="GATK2_SITE_OPTIONS" action="set_to"> + # "--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD" + # </environment_variable> + return dict( name=env_var_name, action=env_var_action, value=elem.text) return None def create_or_update_env_shell_file( install_dir, env_var_dict ): env_var_name = env_var_dict[ 'name' ] diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1731,7 +1731,7 @@ callback( "", input, value[input.name] ) else: input.visit_inputs( "", value[input.name], callback ) - def handle_input( self, trans, incoming, history=None ): + def handle_input( self, trans, incoming, history=None, old_errors=None ): """ Process incoming parameters for this tool from the dict `incoming`, update the tool state (or create if none existed), and either return @@ -1766,7 +1766,7 @@ else: # Update state for all inputs on the current page taking new # values from `incoming`. - errors = self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming ) + errors = self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, old_errors=old_errors or {} ) # If the tool provides a `validate_input` hook, call it. validate_input = self.get_hook( 'validate_input' ) if validate_input: @@ -1895,7 +1895,10 @@ any_group_errors = True # Only need to find one that can't be removed due to size, since only # one removal is processed at # a time anyway - break + break + elif group_old_errors and group_old_errors[i]: + group_errors[i] = group_old_errors[i] + any_group_errors = True # Update state max_index = -1 for i, rep_state in enumerate( group_state ): @@ -1978,6 +1981,8 @@ update_only=update_only, old_errors=group_old_errors, item_callback=item_callback ) + if input.test_param.name in group_old_errors and not test_param_error: + test_param_error = group_old_errors[ input.test_param.name ] if test_param_error: group_errors[ input.test_param.name ] = test_param_error if group_errors: diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -94,3 +94,26 @@ value = params[key].value_from_basic( value, app, ignore_errors ) rval[ key ] = value return rval + +def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ): + """ + Given a tool's parameter definition (`inputs`) and a specific set of + parameter `input_values` objects, populate `incoming` with the html values. + + Useful for e.g. the rerun function. + """ + for input in inputs.itervalues(): + if isinstance( input, Repeat ) or isinstance( input, UploadDataset ): + for i, d in enumerate( input_values[ input.name ] ): + index = d['__index__'] + new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index ) + params_to_incoming( incoming, input.inputs, d, app, new_name_prefix ) + elif isinstance( input, Conditional ): + values = input_values[ input.name ] + current = values["__current_case__"] + new_name_prefix = name_prefix + input.name + "|" + 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 ) + diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1539,25 +1539,38 @@ if trans.workflow_building_mode: return None if not value: - raise ValueError( "History does not include a dataset of the required format / build" ) + raise ValueError( "History does not include a dataset of the required format / build" ) if value in [None, "None"]: return None if isinstance( value, list ): - return [ trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( v ) for v in value ] + rval = [ trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( v ) for v in value ] elif isinstance( value, trans.app.model.HistoryDatasetAssociation ): - return value + rval = value else: - return trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value ) + rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value ) + if isinstance( rval, list ): + values = rval + else: + values = [ rval ] + for v in values: + if v: + if v.deleted: + raise ValueError( "The previously selected dataset has been previously deleted" ) + if v.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: + raise ValueError( "The previously selected dataset has entered an unusable state" ) + return rval def to_string( self, value, app ): - if value is None or isinstance( value, str ): + if value is None or isinstance( value, basestring ): return value + elif isinstance( value, int ): + return str( value ) elif isinstance( value, DummyDataset ): return None elif isinstance( value, list) and len(value) > 0 and isinstance( value[0], DummyDataset): return None elif isinstance( value, list ): - return ",".join( [ val if isinstance( val, str ) else str(val.id) for val in value] ) + return ",".join( [ val if isinstance( val, basestring ) else str(val.id) for val in value] ) return value.id def to_python( self, value, app ): diff -r fdea658292c9d5d3b42aaac5dc982708ecacabf9 -r 1911265573315cf71962ac1ae5ca6ba513d051b2 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -6,6 +6,7 @@ from galaxy.util.bunch import Bunch from galaxy.tools import DefaultToolState from galaxy.tools.parameters.basic import UnvalidatedValue +from galaxy.tools.parameters import params_to_incoming from galaxy.tools.actions import upload_common import logging @@ -192,25 +193,29 @@ if isinstance(value,list): values = [] for val in value: - if val not in history.datasets and val in hda_source_dict: + if val in history.datasets: + values.append( val ) + elif val in hda_source_dict: values.append( hda_source_dict[ val ]) return values if value not in history.datasets and value in hda_source_dict: return hda_source_dict[ value ] visit_input_values( tool.inputs, params_objects, rerun_callback ) - # Create a fake tool_state for the tool, with the parameters values + # Create a fake tool_state for the tool, with the parameters values state = tool.new_state( trans ) state.inputs = params_objects - tool_state_string = util.object_to_string(state.encode(tool, trans.app)) - # Setup context for template - vars = dict( tool_state=state, errors = upgrade_messages ) + #create an incoming object from the original job's dataset-modified param objects + incoming = {} + params_to_incoming( incoming, tool.inputs, params_objects, trans.app ) + incoming[ "tool_state" ] = util.object_to_string( state.encode( tool, trans.app ) ) + template, vars = tool.handle_input( trans, incoming, old_errors=upgrade_messages ) #update new state with old parameters # Is the "add frame" stuff neccesary here? add_frame = AddFrameData() add_frame.debug = trans.debug if from_noframe is not None: add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True - return trans.fill_template( "tool_form.mako", + return trans.fill_template( template, history=history, toolbox=self.get_toolbox(), tool_version_select_field=tool_version_select_field, 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.