[galaxy-commits] commit/galaxy-central: carlfeberhard: base/_panels.mako: IE console protection; history panel: move hda updater into history-model (from HDACollection), handle new hdas more gracefully, handle hidden hdas that move into the ready states.

4 Dec 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/e40fdd5f6e89/
changeset:   e40fdd5f6e89
user:        carlfeberhard
date:        2012-12-04 20:43:49
summary:     base/_panels.mako: IE console protection; history panel: move hda updater into history-model (from HDACollection), handle new hdas more gracefully, handle hidden hdas that move into the ready states.
affected #:  8 files

diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/dataset/hda-base.js

--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -72,7 +72,13 @@
                 if( urlKey === 'meta_download' ){
                     urls[ urlKey ] = hdaView._renderMetaDownloadUrls( urlTemplateOrObj, modelJson );
                 } else {
-                    urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson );
+                    try {
+                        urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson );
+                    } catch( Error ){
+                        throw( hdaView + '._renderUrls error: ' + Error +
+                               '\n rendering:' + urlTemplateOrObj +
+                               '\n with ' + JSON.stringify( modelJson ) );
+                    }
                 }
             }
         });
@@ -109,7 +115,6 @@
             itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ),
             initialRender = ( this.$el.children().size() === 0 );
 
-        //console.debug( this + '.render, initial?:', initialRender );
         this.$el.attr( 'id', 'historyItemContainer-' + id );
         
         itemWrapper
@@ -362,7 +367,7 @@
                 break;
             default:
                 //??: no body?
-                body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) );
+                body.append( $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ) );
         }
         body.append( '<div style="clear: both"></div>' );
 
@@ -520,6 +525,11 @@
         }
     },
 
+
+    remove : function(){
+
+    },
+
     // ......................................................................... MISC
     toString : function(){
         var modelString = ( this.model )?( this.model + '' ):( '(no model)' );


diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/dataset/hda-edit.js
--- a/static/scripts/mvc/dataset/hda-edit.js
+++ b/static/scripts/mvc/dataset/hda-edit.js
@@ -193,7 +193,6 @@
         if( !( this.model.hasData() )
         ||  !( visualizations && visualizations.length )
         ||  !( visualization_url ) ){
-            //console.warn( 'NOT rendering visualization icon' )
             this.visualizationsButton = null;
             return null;
         }


diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/dataset/hda-model.js
--- a/static/scripts/mvc/dataset/hda-model.js
+++ b/static/scripts/mvc/dataset/hda-model.js
@@ -32,13 +32,14 @@
         // ---whereas these are Dataset related/inherited
 
         id                  : null, 
-        name                : '',
+        name                : '(unnamed dataset)',
         // one of HistoryDatasetAssociation.STATES
-        state               : '',
+        state               : 'ok',
         // sniffed datatype (sam, tabular, bed, etc.)
         data_type           : null,
         // size in bytes
         file_size           : 0,
+        file_ext            : '',
 
         // array of associated file types (eg. [ 'bam_index', ... ])
         meta_files          : [],
@@ -48,10 +49,10 @@
 
         deleted             : false, 
         purged              : false,
-        // aka. !hidden
+        // aka. !hidden (start hidden)
         visible             : false,
         // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset ))
-        accessible          : false
+        accessible          : true
     },
 
     /** fetch location of this history in the api */
@@ -59,6 +60,7 @@
     url : function(){
         //TODO: get this via url router
         return 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );
+        //TODO: this breaks on save()
     },
     
     /** Set up the model, determine if accessible, bind listeners
@@ -222,6 +224,34 @@
         return this.map( function( item ){ return item.id; });
     },
 
+    /** If the given hid is in the collection, return it's index. If not, return the insertion point it would need.
+     *      NOTE: assumes hids are unique and valid
+     *  @param {Int} hid the hid to find or create. If hid is 0, null, undefined: return the last hid + 1
+     *  @returns the collection index of the existing hda or an insertion point if it doesn't exist
+     */
+    hidToCollectionIndex : function( hid ){
+        // if the hid is 0, null, undefined: assume a request for a new hid (return the last index)
+        if( !hid ){
+            return this.models.length;
+        }
+
+        var endingIndex = this.models.length - 1;
+        //TODO: prob. more efficient to cycle backwards through these (assuming ordered by hid)
+        for( var i=endingIndex; i>=0; i-- ){
+            var hdaHid = this.at( i ).get( 'hid' );
+            //this.log( i, 'hdaHid:', hdaHid );
+            if( hdaHid == hid ){
+                //this.log( '\t match:', hdaHid, hid, ' returning:', i );
+                return i;
+            }
+            if( hdaHid < hid ){
+                //this.log( '\t past it, returning:', ( i + 1 ) );
+                return i + 1;
+            }
+        }
+        return null;
+    },
+
     /** Get every 'shown' hda in this collection based on show_deleted/hidden
      *  @param {Boolean} show_deleted are we showing deleted hdas?
      *  @param {Boolean} show_hidden are we showing hidden hdas?
@@ -263,24 +293,31 @@
     },
 
     /** Update (fetch) the data of the hdas with the given ids.
+     *  @param {String} historyId the id of the history containing this collection
      *  @param {String[]} ids an array of hda ids to update
+     *  @returns {HistoryDatasetAssociation[]} hda models that were updated
      *  @see HistoryDatasetAssociation#fetch
      */
     update : function( ids ){
         this.log( this + 'update:', ids );
 
-        if( !( ids && ids.length ) ){ return; }
+        if( !( ids && ids.length ) ){ return []; }
 
-        var collection = this;
+        var collection = this,
+            updatedHdas = null;
         _.each( ids, function( id, index ){
-            var historyItem = collection.get( id );
-            historyItem.fetch();
+            var hda = collection.get( id );
+            if( hda ){
+                hda.fetch();
+                updatedHdas.push( hda );
+            }
         });
+        return updatedHdas;
     },
 
     /** String representation. */
     toString : function(){
-         return ( 'HDACollection(' + this.ids().join(',') + ')' );
+         return ( 'HDACollection()' );
     }
 });
 


diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/history/history-model.js
--- a/static/scripts/mvc/history/history-model.js
+++ b/static/scripts/mvc/history/history-model.js
@@ -88,8 +88,6 @@
                 history.fetch()
 
             ).then( function( userResponse, historyResponse ){
-                //console.warn( 'fetched user: ', userResponse[0] );
-                //console.warn( 'fetched history: ', historyResponse[0] );
                 history.attributes.user = userResponse[0]; //? meh.
 
                 history.trigger( 'loaded:user', userResponse[0] );
@@ -102,7 +100,6 @@
 
                 // reset the collection to the hdas returned
                 })).success( function( hdas ){
-                    //console.warn( 'fetched hdas', hdas );
                     history.hdas.reset( hdas );
                     history.checkForUpdates();
 
@@ -167,7 +164,7 @@
 
             // send the changed ids (if any) to dataset collection to have them fetch their own model changes
             if( changedIds.length ){
-                history.hdas.update( changedIds );
+                history.updateHdas( changedIds );
             }
 
             // set up to keep pulling if this history in run/queue state
@@ -176,7 +173,7 @@
             ||  ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){
                 setTimeout( function(){
                     history.stateUpdater();
-                }, 4000 );
+                }, History.UPDATE_DELAY );
 
             // otherwise, we're now in a 'ready' state (no hdas running)
             } else {
@@ -187,14 +184,70 @@
             // if not interruption by iframe reload
             //TODO: remove when iframes are removed
             if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){
-                //if( console && console.warn ){
-                //    console.warn( 'Error getting history updates from the server:', xhr, status, error );
-                //}
                 alert( _l( 'Error getting history updates from the server.' ) + '\n' + error );
             }
         });
     },
 
+    /** Update the models in the hdas collection that match the ids given by getting their data
+     *      via the api/AJAX. If a model exists in the collection, set will be used with the new data.
+     *      If it's not in the collection, addHdas will be used to create it.
+     *  @param {String[]} hdaIds an array of the encoded ids of the hdas to get from the server.
+     */
+    updateHdas : function( hdaIds ){
+        //TODO:?? move to collection? still need proper url
+        var history = this;
+        jQuery.ajax({
+            url     : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }),
+
+            error   : function( xhr, status, error ){
+                var msg = 'ERROR updating hdas from api history contents:';
+                history.log( msg, hdaIds, xhr, status, error );
+                alert( msg + hdaIds.join(',') );
+            },
+
+            /** when the proper models for the requested ids are returned,
+             *      either update existing or create new entries in the hdas collection
+             *  @inner
+             */
+            success : function( hdaDataList, status, xhr ){
+                history.log( history + '.updateHdas, success:', hdaDataList, status, xhr );
+                //TODO: compile new models to be added in one go
+                var hdasToAdd = [];
+
+                _.each( hdaDataList, function( hdaData, index ){
+                    var existingModel = history.hdas.get( hdaData.id );
+                    // if this model exists already, update it
+                    if( existingModel ){
+                        history.log( 'found existing model in list for id ' + hdaData.id + ', updating...:' );
+                        existingModel.set( hdaData );
+
+                    // if this model is new and isn't in the hda collection, cache it to be created
+                    } else {
+                        history.log( 'NO existing model for id ' + hdaData.id + ', creating...:' );
+                        modelsToAdd.push( hdaData );
+                    }
+                });
+                if( hdasToAdd.length ){
+                    history.addHdas( hdasToAdd );
+                }
+            }
+        });
+    },
+
+    /** Add multiple hda models to the hdas collection from an array of hda data.
+     */
+    addHdas : function( hdaDataList ){
+        //TODO: this is all probably easier if hdas is a relation
+        var history = this;
+        //TODO:?? what about hidden? deleted?
+        _.each( hdaDataList, function( hdaData, index ){
+            var indexFromHid = history.hdas.hidToCollectionIndex( hdaData.hid );
+            hdaData.history_id = history.get( 'id' );
+            history.hdas.add( new HistoryDatasetAssociation( hdaData ), { at: indexFromHid });
+        });
+    },
+
     toString : function(){
         var nameString = ( this.get( 'name' ) )?
             ( ',' + this.get( 'name' ) ) : ( '' );
@@ -202,6 +255,13 @@
     }
 });
 
+//------------------------------------------------------------------------------ CLASS VARS
+/** When the history has running hdas,
+ *  this is the amount of time between update checks from the server
+ */
+History.UPDATE_DELAY = 4000;
+
+
 //==============================================================================
 /** @class A collection of histories (per user).
  *      (stub) currently unused.


diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -160,6 +160,20 @@
         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 );
+
+        // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state,
+        //  then: remove it from the collection if the panel is set to NOT show hidden datasets
+        this.model.hdas.bind( 'change:state',
+            function( hda, newState, changedList ){
+                //TODO: magic string here - somehow use HDA.states
+                if( ( hda.inReadyState() )
+                &&  ( !hda.get( 'visible' ) )
+                &&  ( !this.storage.get( 'show_hidden' ) ) ){
+                    this.removeHda( hda );
+                }
+            },
+        this );
+
         //this.bind( 'all', function(){
         //    this.log( arguments );
         //}, this );
@@ -178,6 +192,8 @@
      *  @see PersistantStorage
      */
     _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){
+        //this.log( '_setUpWebStorage, initiallyExpanded:', initiallyExpanded,
+        //    'show_deleted:', show_deleted, 'show_hidden', show_hidden );
 
         // data that needs to be persistant over page refreshes
         //  (note the key function which uses the history id as well)
@@ -197,7 +213,6 @@
 
         // get the show_deleted/hidden settings giving priority to values passed in,
         //  using web storage otherwise
-        //this.log( 'show_deleted:', show_deleted, 'show_hidden', show_hidden );
         // if the page has specifically requested show_deleted/hidden, these will be either true or false
         //  (as opposed to undefined, null) - and we give priority to that setting
         if( ( show_deleted === true ) || ( show_deleted === false ) ){
@@ -218,18 +233,31 @@
      *  @param {HistoryDatasetAssociation} hda hda to add to the collection
      */
     add : function( hda ){
-        //console.debug( 'add.' + this, hda );
-        //TODO
+        //this.log( 'add.' + this, hda );
+        //KISS: just re-render the entire thing when adding
+        this.render();
     },
 
     /** Event hander to respond when hdas are reset
      */
     addAll : function(){
-        //console.debug( 'addAll.' + this );
+        //this.log( 'addAll.' + this );
         // re render when all hdas are reset
         this.render();
     },
 
+    /** Remove a view from the panel and the assoc. model from the collection
+     *  @param {HistoryDataAssociation} the hda to remove
+     */
+    removeHda : function( hdaModel, callback ){
+        var hdaView = this.hdaViews[ hdaModel.get( 'id' ) ];
+        hdaView.$el.fadeOut( 'fast', function(){
+            hdaView.$el.remove();
+            if( callback ){ callback(); }
+        });
+        this.model.hdas.remove( hdaModel );
+    },
+
     // ......................................................................... RENDERING
     /** Render urls, historyPanel body, and hdas (if any are shown)
      *  @see Backbone.View#render
@@ -243,8 +271,6 @@
             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 );
 
@@ -466,7 +492,7 @@
         }
         return false;
     },
-    
+
     // ......................................................................... MISC
     /** Return a string rep of the history
      */


diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee templates/base.mako
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -23,29 +23,39 @@
 
 ## Default javascripts
 <%def name="javascripts()">
-  ## <!--[if lt IE 7]>
-  ## <script type='text/javascript' src="/static/scripts/libs/IE/IE7.js"></script>
-  ## <![endif]-->
-  
-  ${h.js(
-    "libs/jquery/jquery",
-    "libs/json2",
-    "libs/bootstrap",
-    "galaxy.base",
-    "libs/underscore",
-    "libs/backbone/backbone",
-    "libs/backbone/backbone-relational",
-    "libs/handlebars.runtime",
-    "mvc/ui"
-  )}
-  
-  <script type="text/javascript">
-      // Set up needed paths.
-      var galaxy_paths = new GalaxyPaths({
-          root_path: '${h.url_for( "/" )}',
-          image_path: '${h.url_for( "/static/images" )}'
-      });
-  </script>
+    ## <!--[if lt IE 7]>
+    ## <script type='text/javascript' src="/static/scripts/libs/IE/IE7.js"></script>
+    ## <![endif]-->
+    
+    ${h.js(
+        "libs/jquery/jquery",
+        "libs/json2",
+        "libs/bootstrap",
+        "galaxy.base",
+        "libs/underscore",
+        "libs/backbone/backbone",
+        "libs/backbone/backbone-relational",
+        "libs/handlebars.runtime",
+        "mvc/ui"
+    )}
+    
+    <script type="text/javascript">
+        // console protection
+        window.console = window.console || {
+            log     : function(){},
+            debug   : function(){},
+            info    : function(){},
+            warn    : function(){},
+            error   : function(){},
+            assert  : function(){},
+        };
+      
+        // Set up needed paths.
+        var galaxy_paths = new GalaxyPaths({
+            root_path: '${h.url_for( "/" )}',
+            image_path: '${h.url_for( "/static/images" )}'
+        });
+    </script></%def>
 
 ## Additional metas can be defined by templates inheriting from this one.


diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee templates/base/base_panels.mako
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -60,6 +60,16 @@
         'galaxy.base'
     )}
     <script type="text/javascript">
+        // console protection
+        window.console = window.console || {
+            log     : function(){},
+            debug   : function(){},
+            info    : function(){},
+            warn    : function(){},
+            error   : function(){},
+            assert  : function(){},
+        };
+
         // Set up needed paths.
         var galaxy_paths = new GalaxyPaths({
             root_path: '${h.url_for( "/" )}',


diff -r b175274d13e0be88c4504d51aa0f49d0802cc42b -r e40fdd5f6e8936f936f7118b0b9521f7379972ee templates/root/alternate_history.mako
--- a/templates/root/alternate_history.mako
+++ b/templates/root/alternate_history.mako
@@ -297,14 +297,13 @@
 // 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( window.console && console.debug ){
     //    //if( console.clear ){ console.clear(); }
     //    console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); }
     //    top.storage = jQuery.jStorage
@@ -315,9 +314,6 @@
     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; }

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: carlfeberhard: base/_panels.mako: IE console protection; history panel: move hda updater into history-model (from HDACollection), handle new hdas more gracefully, handle hidden hdas that move into the ready states.

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