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

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9beb21b505e9/ changeset: 9beb21b505e9 user: carlfeberhard date: 2012-08-31 17:53:46 summary: (WIP) history panel, backbone.js conversion (includes alternate_history.mako as a temporary transition template) affected #: 3 files diff -r 01ed2f462dd7709876458b031d786d277d1f72f3 -r 9beb21b505e9485e27902d75bf342beea80c6b7e lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -119,7 +119,11 @@ show_deleted = show_purged = util.string_as_bool( show_deleted ) show_hidden = util.string_as_bool( show_hidden ) datasets = self.get_history_datasets( trans, history, show_deleted, show_hidden, show_purged ) - return trans.stream_template_mako( "root/history.mako", + + # history panel -> backbone + history_panel_template = "root/history.mako" + #history_panel_template = "root/alternate_history.mako" + return trans.stream_template_mako( history_panel_template, history = history, annotation = self.get_item_annotation_str( trans.sa_session, trans.user, history ), datasets = datasets, @@ -508,3 +512,85 @@ @web.expose def generate_error( self, trans ): raise Exception( "Fake error!" ) + + + +""" +import galaxy.web.framework.helpers as web_helpers +from functools import wraps +def debug_mako_template( template_fn ): + # Wrap a function that produces a mako template for better debugging + + # http://stackoverflow.com/questions/390409/how-do-you-debug-mako-templates + @wraps( template_fn ) + def wrapper( *args, **kwargs ): + try: + log.debug( 'rendering template' ) + return template_fn( *args, **kwargs ) + log.debug( 'done rendering template' ) + except Exception, ex: + log.error( "Mako Exception: " + str( ex ), exc_info=True ) + return exceptions.html_error_template().render() + return wrapper + +def prep_dataset( hda, trans ): + states = trans.app.model.Dataset.states + print states + STATES_INTERPRETED_AS_QUEUED = [ 'no state', '', None ] + ## dataset is actually a HistoryDatasetAssociation + #ported mostly from history_common + #post: return dictionary form + #??: move out of templates? + #??: gather data from model? + + + #TODO: clean up magic strings + + hda_dict = hda.get_api_value() + #TODO: use hda_dict.update to add these (instead of localvars) + def add_to_hda( **kwargs ): + hda_dict.update( kwargs ) + + # trans + encoded_hda_id = trans.security.encode_id( hda.id ) + add_to_hda( id=encoded_hda_id ) + + add_to_hda( state=hda.state ) + if hda.state in STATES_INTERPRETED_AS_QUEUED: + #TODO: magic string + add_to_hda( state='queued' ) + + # trans + current_user_roles = trans.get_current_user_roles() + add_to_hda( can_edit=( not ( hda.deleted or hda.purged ) ) ) + + # considered accessible if user can access or user isn't admin + # trans + accessible = trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset ) + accessible = trans.user_is_admin() or accessible + add_to_hda( accessible=accessible ) + + #TODO: move urls into js galaxy_paths (decorate) + deleted = hda.deleted + purged = hda.purged + dataset_purged = hda.dataset.purged + if not ( dataset_purged or purged ) and for_editing: + undelete_url = web_helpers.url_for( controller='dataset', action='undelete', dataset_id=encoded_hda_id ) + # trans + if trans.app.config.allow_user_dataset_purge: + purge_url = web_helpers.url_for( controller='dataset', action='purge', dataset_id=encoded_hda_id ) + + if not hda.visible: + unhide_url = web_helpers.url_for( controller='dataset', action='unhide', dataset_id=encoded_hda_id ) + + + print 'dataset:', dataset + + undelete_url = web_helpers.url_for( controller='dataset', action='undelete', dataset_id=encoded_hda_id ) + purge_url = web_helpers.url_for( controller='dataset', action='purge', dataset_id=encoded_hda_id ) + unhide_url = web_helpers.url_for( controller='dataset', action='unhide', dataset_id=encoded_hda_id ) + print 'urls:', '\n'.join( undelete_url, purge_url, unhide_url ) + + return hda_dict + +""" \ No newline at end of file diff -r 01ed2f462dd7709876458b031d786d277d1f72f3 -r 9beb21b505e9485e27902d75bf342beea80c6b7e static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -1,145 +1,1060 @@ /* -TODO: +Backbone.js implementation of history panel + +TODO: + replicate then refactor (could be the wrong order) + History meta controls (rename, annotate, etc. - see history.js.120823.bak) + choose a templating system and use it consistently + HIview state transitions (eg. upload -> ok), curr: build new, delete old, place new (in render) + events (local/ui and otherwise) + widget building (popupmenu, etc.) + localization + incorporate relations + convert function comments to /** style + complete comments + as always: where does the model end and the view begin? HistoryPanel - HistoryCollection: (collection of histories: 'Saved Histories') + HistoryCollection: (collection of History: 'Saved Histories') -CASES: - logged-in/NOT + CASES: + logged-in/NOT + show-deleted/DONT + + ?? anyway to _clone_ base HistoryItemView instead of creating a new one each time? + + move inline styles into base.less + add classes, ids on empty divs + localized text from template + watch the magic strings + + poly HistoryItemView on: can/cant_edit */ +_ = _; + //============================================================================== -var HistoryItem = BaseModel.extend({ - // a single history structure - // from: http://localhost:8080/api/histories/f2db41e1fa331b3e/contents/f2db41e1fa331b... - /* - { - "data_type": "fastq", - "deleted": false, - "download_url": "/datasets/f2db41e1fa331b3e/display?to_ext=fastq", - "file_size": 226297533, - "genome_build": "?", - "id": "f2db41e1fa331b3e", - "metadata_data_lines": null, - "metadata_dbkey": "?", - "metadata_sequences": null, - "misc_blurb": "215.8 MB", - "misc_info": "uploaded fastq file", - "model_class": "HistoryDatasetAssociation", - "name": "LTCF-2-19_GTGAAA_L001_R1_001.fastq", - "state": "ok", - "visible": true +var Loggable = { + // replace null with console (if available) to see all logs + logger : null, + + log : function(){ + return ( this.logger )?( this.logger.debug.apply( this, arguments ) ) + :( undefined ); } - */ +}; +var LoggingModel = BaseModel.extend( Loggable ); +var LoggingView = BaseView.extend( Loggable ); + +//============================================================================== +//TODO: move to Galaxy obj./namespace, decorate for current page (as GalaxyPaths) +var Localizable = { + localizedStrings : {}, + setLocalizedString : function( str, localizedString ){ + this.localizedStrings[ str ] = localizedString; + }, + localize : function( str ){ + if( str in this.localizedStrings ){ return this.localizedStrings[ str ]; } + return str; + } +}; +var LocalizableView = LoggingView.extend( Localizable ); +//TODO: wire up to views + +//============================================================================== +// jq plugin? +//?? into template? I dunno: need to handle variadic keys, remove empty attrs (href="") +//TODO: not happy with this (a 4th rendering/templating system!?) or it being global +function linkHTMLTemplate( config, tag ){ + // Create an anchor (or any tag) using any config params passed in + //NOTE!: send class attr as 'classes' to avoid res. keyword collision (jsLint) + if( !config ){ return '<a></a>'; } + tag = tag || 'a'; - display : function(){}, - edit_attr : function(){}, - delete : function(){}, - download : function(){}, - details : function(){}, - rerun : function(){}, - tags : function(){}, - annotations : function(){}, - peek : function(){}, + var template = [ '<' + tag ]; + for( key in config ){ + var val = config[ key ]; + if( val === '' ){ continue; } + switch( key ){ + case 'text': continue; + case 'classes': + // handle keyword class which is also an HTML attr name + key = 'class'; + val = ( config.classes.join )?( config.classes.join( ' ' ) ):( config.classes ); + //note: lack of break (fall through) + default: + template.push( [ ' ', key, '="', val, '"' ].join( '' ) ); + } + } + template.push( '>' ); + if( 'text' in config ){ template.push( config.text ); } + template.push( '</' + tag + '>' ); + + return template.join( '' ); +} + +//============================================================================== +var HistoryItem = LoggingModel.extend({ + // a single HDA model + + // uncomment this out see log messages + //logger : console, + + defaults : { + + id : null, + name : '', + data_type : null, + file_size : 0, + genome_build : null, + metadata_data_lines : 0, + metadata_dbkey : null, + metadata_sequences : 0, + misc_blurb : '', + misc_info : '', + model_class : '', + state : '', + deleted : false, + purged : false, + + // clash with BaseModel here? + visible : true, + + for_editing : true, + // additional urls will be passed and added, if permissions allow their use + + bodyIsShown : false + }, + + initialize : function(){ + this.log( this + '.initialize', this.attributes ); + this.log( '\tparent history_id: ' + this.get( 'history_id' ) ); + }, + + isEditable : function(){ + // roughly can_edit from history_common.mako + return ( !( this.get( 'deleted' ) || this.get( 'purged' ) ) ); + }, + + hasData : function(){ + //TODO:?? is this equivalent to all possible hda.has_data calls? + return ( this.get( 'file_size' ) > 0 ); + }, + + toString : function(){ + return 'HistoryItem(' + ( this.get( 'name' ) || this.get( 'id' ) || '' ) + ')'; + } }); -//.............................................................................. -var HistoryItemView = BaseView.extend({ - // view for History model used in HistoryPanelView +//------------------------------------------------------------------------------ +HistoryItem.STATES = { + NEW : 'new', + UPLOAD : 'upload', + QUEUED : 'queued', + RUNNING : 'running', + OK : 'ok', + EMPTY : 'empty', + ERROR : 'error', + DISCARDED : 'discarded', + SETTING_METADATA : 'setting_metadata', + FAILED_METADATA : 'failed_metadata' +}; + + +//============================================================================== +var HistoryItemView = LoggingView.extend({ + // view for HistoryItem model above + + // uncomment this out see log messages + logger : console, + tagName : "div", className : "historyItemContainer", - icons : { - display : 'path to icon', - edit_attr : 'path to icon', - delete : 'path to icon', - download : 'path to icon', - details : 'path to icon', - rerun : 'path to icon', - tags : 'path to icon', - annotations : 'path to icon', + + // ................................................................................ SET UP + initialize : function(){ + this.log( this + '.initialize:', this, this.model ); + return this; + }, + + // ................................................................................ RENDER MAIN + //??: this style builds an entire, new DOM tree - is that what we want?? + render : function(){ + this.log( this + '.model:', this.model ); + var id = this.model.get( 'id' ), + state = this.model.get( 'state' ); + + this.$el.attr( 'id', 'historyItemContainer-' + id ); + + var itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ) + .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) + .addClass( 'historyItem-' + state ); + + itemWrapper.append( this._render_purgedWarning() ); + itemWrapper.append( this._render_deletionWarning() ); + itemWrapper.append( this._render_visibleWarning() ); + + itemWrapper.append( this._render_titleBar() ); + + this.body = $( this._render_body() ); + itemWrapper.append( this.body ); + + // set up canned behavior (bootstrap, popupmenus, editable_text, etc.) + itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); + + //TODO: broken + var popupmenus = itemWrapper.find( '[popupmenu]' ); + popupmenus.each( function( i, menu ){ + menu = $( menu ); + make_popupmenu( menu ); + }); + + //TODO: better transition/method than this... + this.$el.children().remove(); + return this.$el.append( itemWrapper ); + }, + + // ................................................................................ RENDER WARNINGS + //TODO: refactor into generalized warning widget/view + //TODO: refactor the three following - too much common ground + _render_purgedWarning : function(){ + // Render warnings for purged + //this.log( this + '_render_purgedWarning' ); + var warning = null; + if( this.model.get( 'purged' ) ){ + warning = $( HistoryItemView.STRINGS.purgedMsg ); + } + //this.log( 'warning:', warning ); + return warning; + }, + + _render_deletionWarning : function(){ + //this.log( this + '_render_deletionWarning' ); + // Render warnings for deleted items (and links: undelete and purge) + //pre: this.model.purge_url will be undefined if trans.app.config.allow_user_dataset_purge=False + var warningElem = null; + if( this.model.get( 'deleted' ) ){ + var warning = ''; + + if( this.model.get( 'undelete_url' ) ){ + warning += HistoryItemView.TEMPLATES.undeleteLink( this.model.attributes ); + } + if( this.model.get( 'purge_url' ) ){ + warning += HistoryItemView.TEMPLATES.purgeLink( this.model.attributes ); + } + // wrap it in the standard warning msg + warningElem = $( HistoryItemView.TEMPLATES.warningMsg({ warning: warning }) ); + } + //this.log( 'warning:', warning ); + return warningElem; + }, + + _render_visibleWarning : function(){ + //this.log( this + '_render_visibleWarning' ); + // Render warnings for hidden items (and link: unhide) + var warningElem = null; + if( !this.model.get( 'visible' ) && this.model.get( 'unhide_url' ) ){ + var warning = HistoryItemView.TEMPLATES.hiddenMsg( this.model.attributes ); + + // wrap it in the standard warning msg + warningElem = $( HistoryItemView.TEMPLATES.warningMsg({ warning: warning }) ); + } + //this.log( 'warning:', warning ); + return warningElem; + }, + + // ................................................................................ RENDER TITLEBAR + _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 + _render_titleButtons : function(){ + // render the display, edit attr and delete icon-buttons + var buttonDiv = $( '<div class="historyItemButtons"></div>' ), + for_editing = this.model.get( 'for_editing' ); + + // don't show display, edit while uploading + if( this.model.get( 'state' ) !== HistoryItem.STATES.UPLOAD ){ + buttonDiv.append( this._render_displayButton() ); + + if( for_editing ){ buttonDiv.append( this._render_editButton() ); } + } + if( for_editing ){ buttonDiv.append( this._render_deleteButton() ); } + return buttonDiv; + }, + + //TODO: refactor the following three - use extend for new href (with model data or something else) + //TODO: move other data (non-href) into {} in view definition, cycle over those keys in _titlebuttons + //TODO: move disabled span data into view def, move logic into _titlebuttons + _render_displayButton : function(){ + // render the display icon-button + // show a disabled display if the data's been purged + if( this.model.get( 'purged' ) ){ + return $( '<span class="icon-button display_disabled tooltip" ' + + 'title="Cannot display datasets removed from disk"></span>' ); + } + var id = this.model.get( 'id' ), + displayBtnData = { + //TODO: localized title + title : 'Display data in browser', + //TODO: need generated url here + href : '/datasets/' + id + '/display/?preview=True', + target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( '' ), + classes : [ 'icon-button', 'tooltip', 'display' ], + dataset_id : id + }; + return $( linkHTMLTemplate( displayBtnData ) ); + }, + + _render_editButton : function(){ + // render the edit attr icon-button + var id = this.model.get( 'id' ), + purged = this.model.get( 'purged' ), + deleted = this.model.get( 'deleted' ); + + if( deleted || purged ){ + if( !purged ){ + return $( '<span class="icon-button edit_disabled tooltip" ' + + 'title="Undelete dataset to edit attributes"></span>' ); + } else { + return $( '<span class="icon-button edit_disabled tooltip" ' + + 'title="Cannot edit attributes of datasets removed from disk"></span>' ); + } + } + return $( linkHTMLTemplate({ + title : 'Edit attributes', + //TODO: need generated url here + href : '/datasets/' + id + '/edit', + target : 'galaxy_main', + classes : [ 'icon-button', 'tooltip', 'edit' ] + }) ); + }, + + _render_deleteButton : function(){ + // render the delete icon-button + var id = this.model.get( 'id' ), + purged = this.model.get( 'purged' ), + deleted = this.model.get( 'deleted' ); + + //??: WHAAAA? can_edit == deleted?? + // yes! : (history_common.mako) can_edit=( not ( data.deleted or data.purged ) ) + if( purged || deleted ){ + return $( '<span title="Dataset is already deleted" ' + + 'class="icon-button delete_disabled tooltip"></span>' ); + } + return $( linkHTMLTemplate({ + title : 'Delete', + //TODO: need generated url here + href : '/datasets/' + id + '/delete?show_deleted_on_refresh=False', + target : 'galaxy_main', + id : 'historyItemDeleter-' + id, + classes : [ 'icon-button', 'tooltip', 'delete' ] + })); + }, + + _render_titleLink : function(){ + // render the title (hda name) + var h_name = this.model.get( 'name' ), + hid = this.model.get( 'hid' ); + title = ( hid + ': ' + h_name ); + return $( linkHTMLTemplate({ + href : 'javascript:void(0);', + text : '<span class="historyItemTitle">' + title + '</span>' + })); + }, + + // ................................................................................ RENDER BODY + // _render_body fns for the various states + _render_body_not_viewable : function( parent ){ + 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_showParamsAndRerun() ); + }, + + _render_body_running : function( parent ){ + parent.append( '<div>Job is currently running.</div>' ); + parent.append( this._render_showParamsAndRerun() ); + }, + + _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>' ) ); + + var actionBtnDiv = $( this._render_showParamsAndRerun() ); + // bug report button + //NOTE: these are shown _before_ info, rerun so use _prepend_ + if( this.model.get( 'for_editing' ) ){ + actionBtnDiv.prepend( $( linkHTMLTemplate({ + title : 'View or report this error', + href : this.model.get( 'report_errors_url' ), + target : 'galaxy_main', + classes : [ 'icon-button', 'tooltip', 'bug' ] + }))); + } + if( this.model.hasData() ){ + //TODO: render_download_links( data, dataset_id ) + // download dropdown + actionBtnDiv.prepend( this._render_downloadLinks() ); + } + parent.append( actionBtnDiv ); + }, + + _render_body_discarded : function( parent ){ + parent.append( '<div>The job creating this dataset was cancelled before completion.</div>' ); + parent.append( this._render_showParamsAndRerun() ); + }, + + _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_showParamsAndRerun() ); + }, + + _render_body_failed_metadata : function( parent ){ + // add a message box about the failure at the top of the body, then... + var warningMsgText = 'An error occurred setting the metadata for this dataset.'; + if( this.model.isEditable() ){ + var editLink = linkHTMLTemplate({ + text : 'set it manually or retry auto-detection', + href : this.model.get( 'edit_url' ), + target : 'galaxy_main' + }); + warningMsgText += 'You may be able to ' + editLink + '.'; + } + parent.append( $( HistoryItemView.TEMPLATES.warningMsg({ warning: warningMsgText }) ) ); + + //...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 + + // build the summary info (using template and dbkey data) + parent.append( this._render_hdaSummary() ); + + if( this.model.get( 'misc_info' ) ){ + parent.append( $( '<div class="info">Info: ' + this.model.get( 'misc_info' ) + '</div>' ) ); + } + + // hasData + if( this.model.hasData() ){ + var actionBtnDiv = $( '<div/>' ); + + // render download links, show_params + actionBtnDiv.append( this._render_downloadLinks() ); + actionBtnDiv.append( $( linkHTMLTemplate({ + title : 'View details', + href : this.model.get( 'show_params_url' ), + target : 'galaxy_main', + classes : [ 'icon-button', 'tooltip', 'information' ] + }))); + + // if for_editing + if( this.model.get( 'for_editing' ) ){ + + // rerun + actionBtnDiv.append( $( linkHTMLTemplate({ + title : 'Run this job again', + href : this.model.get( 'rerun_url' ), + target : 'galaxy_main', + classes : [ 'icon-button', 'tooltip', 'arrow-circle' ] + }))); + + if( this.model.get( 'trackster_urls' ) ){ + // link to trackster + var trackster_urls = this.model.get( 'trackster_urls' ); + actionBtnDiv.append( $( linkHTMLTemplate({ + title : 'View in Trackster', + href : "javascript:void(0)", + classes : [ 'icon-button', 'tooltip', 'chart_curve', 'trackster-add' ], + // prob just _.extend + 'data-url' : trackster_urls[ 'data-url' ], + 'action-url': trackster_urls[ 'action-url' ], + 'new-url' : trackster_urls[ 'new-url' ] + }))); + } + + // if trans.user + if( this.model.get( 'retag_url' ) && this.model.get( 'annotate_url' ) ){ + // tags, annotation buttons and display areas + var tagsAnnotationsBtns = $( '<div style="float: right;"></div>' ); + tagsAnnotationsBtns.append( $( linkHTMLTemplate({ + title : 'Edit dataset tags', + target : 'galaxy_main', + href : this.model.get( 'retag_url' ), + classes : [ 'icon-button', 'tooltip', 'tags' ] + }))); + tagsAnnotationsBtns.append( $( linkHTMLTemplate({ + title : 'Edit dataset annotation', + target : 'galaxy_main', + href : this.model.get( 'annotation_url' ), + classes : [ 'icon-button', 'tooltip', 'annotate' ] + }))); + actionBtnDiv.append( tagsAnnotationsBtns ); + actionBtnDiv.append( '<div style="clear: both"></div>' ); + + var tagArea = $( '<div class="tag-area" style="display: none">' ); + tagArea.append( '<strong>Tags:</strong>' ); + tagArea.append( '<div class="tag-elt"></div>' ); + actionBtnDiv.append( tagArea ); + + var annotationArea = $( ( '<div id="${dataset_id}-annotation-area"' + + ' class="annotation-area" style="display: none">' ) ); + annotationArea.append( '<strong>Annotation:</strong>' ); + annotationArea.append( ( '<div id="${dataset_id}-annotation-elt" ' + + 'style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" ' + + 'title="Edit dataset annotation"></div>' ) ); + actionBtnDiv.append( annotationArea ); + } + } + // clear div + actionBtnDiv.append( '<div style="clear: both;"></div>' ); + parent.append( actionBtnDiv ); + + var display_appsDiv = $( '<div/>' ); + if( this.model.get( 'display_apps' ) ){ + var display_apps = this.model.get( 'display_apps' ), + display_app_span = $( '<span/>' ); + + //TODO: grrr...somethings not in the right scope here + for( app_name in display_apps ){ + //TODO: to template + var display_app = display_apps[ app_name ], + display_app_HTML = app_name + ' '; + for( location_name in display_app ){ + display_app_HTML += linkHTMLTemplate({ + text : location_name, + href : display_app[ location_name ].url, + target : display_app[ location_name ].target + }) + ' '; + } + display_app_span.append( display_app_HTML ); + } + display_appsDiv.append( display_app_span ); + } + //display_appsDiv.append( '<br />' ); + parent.append( display_appsDiv ); + + } else if( this.model.get( 'for_editing' ) ){ + parent.append( this._render_showParamsAndRerun() ); + } + + parent.append( this._render_peek() ); + }, + + _render_body : function(){ + this.log( this + '_render_body' ); + var state = this.model.get( 'state' ), + for_editing = this.model.get( 'for_editing' ); + 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' ); + + switch( state ){ + case HistoryItem.STATES.NOT_VIEWABLE : + this._render_body_not_viewable( body ); + break; + case HistoryItem.STATES.UPLOAD : + this._render_body_uploading( body ); + break; + case HistoryItem.STATES.QUEUED : + this._render_body_queued( body ); + break; + case HistoryItem.STATES.RUNNING : + this._render_body_running( body ); + break; + case HistoryItem.STATES.ERROR : + this._render_body_error( body ); + break; + case HistoryItem.STATES.DISCARDED : + this._render_body_discarded( body ); + break; + case HistoryItem.STATES.SETTING_METADATA : + this._render_body_setting_metadata( body ); + break; + case HistoryItem.STATES.EMPTY : + this._render_body_empty( body ); + break; + case HistoryItem.STATES.FAILED_METADATA : + this._render_body_failed_metadata( body ); + break; + case HistoryItem.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.model.get( 'bodyIsShown' ) === false ){ + body.hide(); + } + return body; + }, + + _render_hdaSummary : function(){ + // default span rendering + var dbkeyHTML = _.template( '<span class="<%= dbkey %>"><%= dbkey %></span>', + { dbkey: this.model.get( 'metadata_dbkey' ) } ); + // if there's no dbkey and it's editable : render a link to editing in the '?' + if( this.model.get( 'metadata_dbkey' ) === '?' && this.model.isEditable() ){ + dbkeyHTML = linkHTMLTemplate({ + text : this.model.get( 'metadata_dbkey' ), + href : this.model.get( 'edit_url' ), + target : 'galaxy_main' + }); + } + return ( HistoryItemView.TEMPLATES.hdaSummary( + _.extend({ dbkeyHTML: dbkeyHTML }, this.model.attributes ) ) ); + }, + + _render_showParamsAndRerun : function(){ + //TODO??: generalize to _render_actionButtons, pass in list of 'buttons' to render, default to these two + var actionBtnDiv = $( '<div/>' ); + actionBtnDiv.append( $( linkHTMLTemplate({ + title : 'View details', + href : this.model.get( 'show_params_url' ), + target : 'galaxy_main', + classes : [ 'icon-button', 'tooltip', 'information' ] + }))); + if( this.model.get( 'for_editing' ) ){ + actionBtnDiv.append( $( linkHTMLTemplate({ + title : 'Run this job again', + href : this.model.get( 'rerun_url' ), + target : 'galaxy_main', + classes : [ 'icon-button', 'tooltip', 'arrow-circle' ] + }))); + } + return actionBtnDiv; + }, + + _render_downloadLinks : function(){ + // 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) + + // don't show anything if the data's been purged + if( this.model.get( 'purged' ) ){ return null; } + + var downloadLink = linkHTMLTemplate({ + title : 'Download', + href : this.model.get( 'download_url' ), + classes : [ 'icon-button', 'tooltip', 'disk' ] + }); + + // if no metafiles, return only the main download link + var download_meta_urls = this.model.get( 'download_meta_urls' ); + if( !download_meta_urls ){ + return downloadLink; + } + + // build the popupmenu for downloading main, meta files + var popupmenu = $( '<div popupmenu="dataset-' + this.model.get( 'id' ) + '-popup"></div>' ); + popupmenu.append( linkHTMLTemplate({ + text : 'Download Dataset', + title : 'Download', + href : this.model.get( 'download_url' ), + classes : [ 'icon-button', 'tooltip', 'disk' ] + })); + popupmenu.append( '<a>Additional Files</a>' ); + for( file_type in download_meta_urls ){ + popupmenu.append( linkHTMLTemplate({ + text : 'Download ' + file_type, + href : download_meta_urls[ file_type ], + classes : [ 'action-button' ] + })); + } + var menuButton = $( ( '<div style="float:left;" class="menubutton split popup"' + + ' id="dataset-${dataset_id}-popup"></div>' ) ); + menuButton.append( downloadLink ); + popupmenu.append( menuButton ); + return popupmenu; + }, + + _render_peek : function(){ + if( !this.model.get( 'peek' ) ){ return null; } + return $( '<div/>' ).append( + $( '<pre/>' ) + .attr( 'id', 'peek' + this.model.get( 'id' ) ) + .addClass( 'peek' ) + .append( this.model.get( 'peek' ) ) + ); + }, + + // ................................................................................ EVENTS + events : { + 'click .historyItemTitle' : 'toggleBodyVisibility' + }, + + // ................................................................................ STATE CHANGES / MANIPULATION + toggleBodyVisibility : function(){ + this.log( this + '.toggleBodyVisibility' ); + this.$el.find( '.historyItemBody' ).toggle(); + }, + + // ................................................................................ UTILTIY + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '' ); + return 'HistoryItemView(' + modelString + ')'; + } +}); + +//------------------------------------------------------------------------------ +HistoryItemView.TEMPLATES = {}; + +//TODO: move next one out - doesn't belong +HistoryItemView.TEMPLATES.warningMsg = + _.template( '<div class=warningmessagesmall><strong><%= warning %></strong></div>' ); + + +//??TODO: move into functions? +HistoryItemView.TEMPLATES.undeleteLink = _.template( + 'This dataset has been deleted. ' + + 'Click <a href="<%= undelete_url %>" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" ' + + ' target="galaxy_history">here</a> to undelete it.' ); + +HistoryItemView.TEMPLATES.purgeLink = _.template( + ' or <a href="<%= purge_url %>" class="historyItemPurge" id="historyItemPurger-{{ id }}"' + + ' target="galaxy_history">here</a> to immediately remove it from disk.' ); + +HistoryItemView.TEMPLATES.hiddenMsg = _.template( + 'This dataset has been hidden. ' + + 'Click <a href="<%= unhide_url %>" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" ' + + ' target="galaxy_history">here</a> to unhide it.' ); + +//TODO: contains localized strings +HistoryItemView.TEMPLATES.hdaSummary = _.template([ + '<%= misc_blurb %><br />', + 'format: <span class="<%= data_type %>"><%= data_type %></span>, ', + 'database: <%= dbkeyHTML %>' +].join( '' )); + + +//------------------------------------------------------------------------------ +HistoryItemView.STRINGS = {}; + +HistoryItemView.STRINGS.purgedMsg = HistoryItemView.TEMPLATES.warningMsg( + { warning: 'This dataset has been deleted and removed from disk.' }); + + +//============================================================================== +var HistoryCollection = Backbone.Collection.extend({ + model : HistoryItem, + + toString : function(){ + return ( 'HistoryCollection()' ); + } +}); + + +//============================================================================== +var History = LoggingModel.extend({ + + // uncomment this out see log messages + logger : console, + + // values from api (may need more) + defaults : { + id : '', + name : '', + state : '', + state_details : { + discarded : 0, + empty : 0, + error : 0, + failed_metadata : 0, + ok : 0, + queued : 0, + running : 0, + setting_metadata: 0, + upload : 0 + } + }, + + initialize : function( data, history_datasets ){ + this.log( this + '.initialize', data, history_datasets ); + this.items = new HistoryCollection(); + }, + + loadDatasetsAsHistoryItems : function( datasets ){ + // adds the given dataset/Item data to historyItems + // and updates this.state based on their states + //pre: datasets is a list of objs + //this.log( this + '.loadDatasets', datasets ); + var self = this, + selfID = this.get( 'id' ), + stateDetails = this.get( 'state_details' ); + + _.each( datasets, function( dataset, index ){ + self.log( 'loading dataset: ', dataset, index ); + + // create an item sending along the history_id as well + var historyItem = new HistoryItem( + _.extend( dataset, { history_id: selfID } ) ); + self.log( 'as History:', historyItem ); + self.items.add( historyItem ); + + // add item's state to running totals in stateDetails + var itemState = dataset.state; + stateDetails[ itemState ] += 1; + }); + + // get overall History state from totals + this.set( 'state_details', stateDetails ); + this._stateFromStateDetails(); + return this; + }, + + _stateFromStateDetails : function(){ + // sets this.state based on current historyItems' states + // ported from api/histories.traverse + //pre: state_details is current counts of dataset/item states + this.set( 'state', '' ); + var stateDetails = this.get( 'state_details' ); + + //TODO: make this more concise + if( ( stateDetails.error > 0 ) + || ( stateDetails.failed_metadata > 0 ) ){ + this.set( 'state', HistoryItem.STATES.ERROR ); + + } else if( ( stateDetails.running > 0 ) + || ( stateDetails.setting_metadata > 0 ) ){ + this.set( 'state', HistoryItem.STATES.RUNNING ); + + } else if( stateDetails.queued > 0 ){ + this.set( 'state', HistoryItem.STATES.QUEUED ); + + } else if( stateDetails.ok === this.items.length ){ + this.set( 'state', HistoryItem.STATES.OK ); + + } else { + throw( '_stateFromStateDetails: unable to determine ' + + 'history state from state details: ' + this.state_details ); + } + return this; + }, + + toString : function(){ + var nameString = ( this.get( 'name' ) )? + ( ',' + this.get( 'name' ) ) : ( '' ); + return 'History(' + this.get( 'id' ) + nameString + ')'; + } +}); + +//------------------------------------------------------------------------------ +var HistoryView = LoggingView.extend({ + // view for the HistoryCollection (as per current right hand panel) + + // uncomment this out see log messages + logger : console, + + // direct attachment to existing element + el : 'body.historyPage', + + initialize : function(){ + this.log( this + '.initialize' ); + this.itemViews = []; + var parent = this; + this.model.items.each( function( item ){ + var itemView = new HistoryItemView({ model: item }); + parent.itemViews.push( itemView ); + }); + //itemViews.reverse(); }, render : function(){ - this.$el.append( 'div' ) + this.log( this + '.render' ); + + // render to temp, move all at once, remove temp holder + //NOTE!: render in reverse (newest on top) via prepend (instead of append) + var tempDiv = $( '<div/>' ); + _.each( this.itemViews, function( view ){ + tempDiv.prepend( view.render() ); + }); + this.$el.append( tempDiv.children() ); + tempDiv.remove(); }, + toString : function(){ + var nameString = this.model.get( 'name' ) || ''; + return 'HistoryView(' + nameString + ')'; + } }); +//============================================================================== +//USE_MOCK_DATA = true; +if( window.USE_MOCK_DATA ){ + mockHistory = {}; + mockHistory.data = { + + template : { + id : 'a799d38679e985db', + name : 'template', + data_type : 'fastq', + file_size : 226297533, + genome_build : '?', + metadata_data_lines : 0, + metadata_dbkey : '?', + metadata_sequences : 0, + misc_blurb : '215.8 MB', + misc_info : 'uploaded fastq file', + model_class : 'HistoryDatasetAssociation', + download_url : '', + state : 'ok', + visible : true, + deleted : false, + purged : false, + + hid : 0, + //TODO: move to history + for_editing : true, + //for_editing : false, + + //?? not needed + //can_edit : true, + //can_edit : false, + + //TODO: move into model functions (build there (and cache?)) + //!! be careful with adding these accrd. to permissions + //!! IOW, don't send them via template/API if the user doesn't have perms to use + //!! (even if they don't show up) + undelete_url : 'example.com/undelete', + purge_url : 'example.com/purge', + unhide_url : 'example.com/unhide', + + display_url : 'example.com/display', + edit_url : 'example.com/edit', + delete_url : 'example.com/delete', + + show_params_url : 'example.com/show_params', + rerun_url : 'example.com/rerun', + + retag_url : 'example.com/retag', + annotate_url : 'example.com/annotate', + + peek : [ + '<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>', + '<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>', + '<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>', + '<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>', + '<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>', + '<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>', + '<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>', + '</table>' + ].join( '' ) + } + + }; + _.extend( mockHistory.data, { + + //deleted, purged, visible + deleted : + _.extend( _.clone( mockHistory.data.template ), + { deleted : true }), + //purged : + // _.extend( _.clone( mockHistory.data.template ), + // { purged : true, deleted : true }), + purgedNotDeleted : + _.extend( _.clone( mockHistory.data.template ), + { purged : true }), + notvisible : + _.extend( _.clone( mockHistory.data.template ), + { visible : false }), + hasDisplayApps : + _.extend( _.clone( mockHistory.data.template ), + { display_apps : { + 'display in IGB' : { + Web: "/display_application/63cd3858d057a6d1/igb_bam/Web", + Local: "/display_application/63cd3858d057a6d1/igb_bam/Local" + } + } + } + ), + canTrackster : + _.extend( _.clone( mockHistory.data.template ), + { trackster_urls : { + 'data-url' : "example.com/trackster-data", + 'action-url' : "example.com/trackster-action", + 'new-url' : "example.com/trackster-new" + } + } + ), + zeroSize : + _.extend( _.clone( mockHistory.data.template ), + { file_size : 0 }), + + hasMetafiles : + _.extend( _.clone( mockHistory.data.template ), { + download_meta_urls : { + 'bam_index' : "example.com/bam-index" + } + }), + + //states + upload : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.UPLOAD }), + queued : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.QUEUED }), + running : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.RUNNING }), + empty : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.EMPTY }), + error : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.ERROR }), + discarded : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.DISCARDED }), + setting_metadata : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.SETTING_METADATA }), + failed_metadata : + _.extend( _.clone( mockHistory.data.template ), + { state : HistoryItem.STATES.FAILED_METADATA }) + + }); + + $( document ).ready( function(){ + //mockHistory.views.deleted.logger = console; + mockHistory.items = {}; + mockHistory.views = {}; + for( key in mockHistory.data ){ + mockHistory.items[ key ] = new HistoryItem( mockHistory.data[ key ] ); + mockHistory.items[ key ].set( 'name', key ); + mockHistory.views[ key ] = new HistoryItemView({ model : mockHistory.items[ key ] }); + //console.debug( 'view: ', mockHistory.views[ key ] ); + $( 'body' ).append( mockHistory.views[ key ].render() ); + } + }); +} -//============================================================================== -var History = Backbone.Collection.extend({ - // a collection of HistoryItems - - // from: http://localhost:8080/api/histories/f2db41e1fa331b3e - /* - { - "contents_url": "/api/histories/f2db41e1fa331b3e/contents", - "id": "f2db41e1fa331b3e", - "name": "one", - "state": "ok", - "state_details": { - "discarded": 0, - "empty": 0, - "error": 0, - "failed_metadata": 0, - "new": 0, - "ok": 4, - "queued": 0, - "running": 0, - "setting_metadata": 0, - "upload": 0 - } - } - */ - - // from: http://localhost:8080/api/histories/f2db41e1fa331b3e/contents - // (most are replicated in HistoryItem) - /* - [ - { - "id": "f2db41e1fa331b3e", - "name": "LTCF-2-19_GTGAAA_L001_R1_001.fastq", - "type": "file", - "url": "/api/histories/f2db41e1fa331b3e/contents/f2db41e1fa331b3e" - }, - { - "id": "f597429621d6eb2b", - "name": "LTCF-2-19_GTGAAA_L001_R2_001.fastq", - "type": "file", - "url": "/api/histories/f2db41e1fa331b3e/contents/f597429621d6eb2b" - }, - { - "id": "1cd8e2f6b131e891", - "name": "FASTQ Groomer on data 1", - "type": "file", - "url": "/api/histories/f2db41e1fa331b3e/contents/1cd8e2f6b131e891" - }, - { - "id": "ebfb8f50c6abde6d", - "name": "FASTQ Groomer on data 2", - "type": "file", - "url": "/api/histories/f2db41e1fa331b3e/contents/ebfb8f50c6abde6d" - }, - { - "id": "33b43b4e7093c91f", - "name": "Sa.04-02981.fasta", - "type": "file", - "url": "/api/histories/f2db41e1fa331b3e/contents/33b43b4e7093c91f" - } - ] - */ -}); - -//.............................................................................. -var HistoryCollectionView = BaseView.extend({ - // view for the HistoryCollection (as per current right hand panel) - tagName : "body", - className : "historyCollection", - - render : function(){ - - }, - -}); - diff -r 01ed2f462dd7709876458b031d786d277d1f72f3 -r 9beb21b505e9485e27902d75bf342beea80c6b7e templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -104,6 +104,8 @@ %endif ></a> %endif + + ## edit attr button %if for_editing: %if data.deleted and not data.purged: <span title="Undelete dataset to edit attributes" class="icon-button edit_disabled tooltip"></span> @@ -113,7 +115,10 @@ <a class="icon-button edit tooltip" title='${_("Edit attributes")}' href="${h.url_for( controller='dataset', action='edit', dataset_id=dataset_id )}" target="galaxy_main"></a> %endif %endif + %endif + + ## delete button %if for_editing: %if can_edit: <a class="icon-button delete tooltip" title='${_("Delete")}' href="${h.url_for( controller='dataset', action='delete', dataset_id=dataset_id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${dataset_id}"></a> https://bitbucket.org/galaxy/galaxy-central/changeset/b822f138cd97/ changeset: b822f138cd97 user: carlfeberhard date: 2012-08-31 18:12:28 summary: merge; add temporary template to commit affected #: 310 files Diff too large to display. 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.