Merge branch 'dev' into fix_refresh_trigger

client/galaxy/scripts/mvc/collection/collection-view-edit.js

@@ -3,9 +3,11 @@ define([
     "mvc/collection/collection-model",
     "mvc/collection/collection-li-edit",
     "mvc/base-mvc",
+    "mvc/tag",
+    "ui/fa-icon-button",
     "utils/localization",
     "ui/editable-text",
-], function( DC_VIEW, DC_MODEL, DC_EDIT, BASE_MVC, _l ){
+], function( DC_VIEW, DC_MODEL, DC_EDIT, BASE_MVC, TAGS, faIconButton, _l ){
 
 'use strict';
 /* =============================================================================
@@ -47,6 +49,8 @@ var CollectionViewEdit = _super.extend(
             return;
         }
 
+        this.tagsEditorShown = true;
+
         //TODO: extract
         var panel = this,
             nameSelector = '> .controls .name';
@@ -67,6 +71,13 @@ var CollectionViewEdit = _super.extend(
                     }
                 }
             });
+        this.tagsEditor = new TAGS.TagsEditor({
+            model           : this.model,
+            el              : $where.find( '.tags-display' ),
+            onshowFirstTime : function(){ this.render(); },
+            usePrompt       : false
+        });
+        this.tagsEditor.toggle( true );
     },
 
     // ........................................................................ misc

client/galaxy/scripts/mvc/collection/collection-view.js

@@ -169,6 +169,8 @@ CollectionView.prototype.templates = (function(){
                     '<% } %>',
                 '</div>',
             '</div>',
+
+            '<div class="tags-display"></div>',
         '</div>'
     ], 'collection' );
 

client/galaxy/scripts/mvc/dataset/dataset-li.js

@@ -59,7 +59,14 @@ var DatasetListItemView = _super.extend(
                         .done( function(){ self.render(); });
 
                 } else {
-                    self.render();
+                    if( _.has( model.changed, 'tags' ) && _.keys( model.changed ).length === 1 ){
+                        // If only the tags have changed, rerender specifically
+                        // the titlebar region.  Otherwise default to the full
+                        // render.
+                        this.$( '> .title-bar' ).replaceWith( this._renderTitleBar() );
+                    } else {
+                        self.render();
+                    }
                 }
             }
         });

client/galaxy/scripts/mvc/history/hda-li.js

@@ -45,8 +45,10 @@ HDAListItemView.prototype.templates = (function(){
             '</div>',
             '</br>',
             '<span class="nametags">',
-                '<% _.each(dataset.nametags, function(tag){ %>',
-                    '<span class="label label-info"><%- tag %></span>',
+                '<% _.each(dataset.tags, function(tag){ %>',
+                    '<% if (tag.indexOf("name:") == 0){ %>',
+                        '<span class="label label-info"><%- tag.slice(5) %></span>',
+                    '<% } %>',
                 '<% }); %>',
             '</span>',
         '</div>'

client/galaxy/scripts/mvc/history/hdca-li.js

@@ -20,9 +20,8 @@ var HDCAListItemView = _super.extend(
     /** event listeners */
     _setUpListeners : function(){
         _super.prototype._setUpListeners.call( this );
-
         this.listenTo( this.model, {
-            'change:populated change:visible' : function( model, options ){ this.render(); },
+            'change:tags change:populated change:visible' : function( model, options ){ this.render(); },
         });
     },
 
@@ -85,6 +84,13 @@ HDCAListItemView.prototype.templates = (function(){
                 '<span class="name"><%- collection.name %></span>',
             '</div>',
             '<div class="subtitle"></div>',
+            '<span class="nametags">',
+                '<% _.each(collection.tags, function(tag){ %>',
+                    '<% if (tag.indexOf("name:") == 0){ %>',
+                        '<span class="label label-info"><%- tag.slice(5) %></span>',
+                    '<% } %>',
+                '<% }); %>',
+            '</span>',
         '</div>'
     ], 'collection' );
 

client/galaxy/scripts/mvc/tag.js

@@ -18,23 +18,25 @@ var TagsEditor = Backbone.View
     initialize : function( options ){
         //console.debug( this, options );
         // only listen to the model only for changes to tags - re-render
-        this.listenTo( this.model, 'change:tags', function(){
-            this.render();
-        });
+        if (options.usePrompt === false) {
+            this.label = '';
+        } else {
+            this.label = '<label class="prompt">' + _l( 'Tags' ) + '</label>';
+        }
         this.hiddenUntilActivated( options.$activator, options );
     },
 
     /** Build the DOM elements, call select to on the created input, and set up behaviors */
     render : function(){
-        var view = this;
+        var self = this;
         this.$el.html( this._template() );
 
         this.$input().select2({
             placeholder : 'Add tags',
             width       : '100%',
             tags : function(){
                 // initialize possible tags in the dropdown based on all the tags the user has used so far
-                return view._getTagsUsed();
+                return self._getTagsUsed();
             }
         });
 
@@ -45,8 +47,7 @@ var TagsEditor = Backbone.View
     /** @returns {String} the html text used to build the view's DOM */
     _template : function(){
         return [
-            //TODO: make prompt optional
-            '<label class="prompt">', _l( 'Tags' ), '</label>',
+            this.label,
             // set up initial tags by adding as CSV to input vals (necc. to init select2)
             '<input class="tags-input" value="', this.tagsToCSV(), '" />'
         ].join( '' );
@@ -79,7 +80,7 @@ var TagsEditor = Backbone.View
         var view = this;
         this.$input().on( 'change', function( event ){
             // save the model's tags in either remove or added event
-            view.model.save({ tags: event.val }, { silent: true });
+            view.model.save({ tags: event.val });
             // if it's new, add the tag to the users tags
             if( event.added ){
                 //??: solve weird behavior in FF on test.galaxyproject.org where

client/package.json

@@ -5,12 +5,15 @@
   "keywords": [
     "galaxy"
   ],
-  "repository": { "type": "git",
-                  "url": "https://github.com/galaxyproject/galaxy.git"
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/galaxyproject/galaxy.git"
   },
   "license": "AFL-3.0",
   "dependencies": {
     "amdi18n-loader": "^0.2.0",
+    "babel-core": "^6.24.0",
+    "babel-loader": "^6.4.1",
     "grunt": "^0.4.5",
     "grunt-bower-install-simple": "^1.1.0",
     "grunt-check-modules": "^1.0.0",

client/webpack.config.js

@@ -54,6 +54,10 @@ module.exports = {
     },
     module : {
         loaders : [
+            { test: /\.js$/,
+              exclude: /node_modules/,
+              loader: 'babel-loader',
+              query: { compact: false } },
         ],
     },
     resolveLoader : {

lib/galaxy/managers/collections.py

@@ -36,24 +36,15 @@ def __init__( self, app ):
 
         self.hda_manager = hdas.HDAManager( app )
         self.history_manager = histories.HistoryManager( app )
-        self.tag_manager = tags.TagManager( app )
+        self.tag_manager = tags.GalaxyTagManager( app )
         self.ldda_manager = lddas.LDDAManager( app )
 
-    def create(
-        self,
-        trans,
-        parent,
-        # PRECONDITION: security checks on ability to add to parent
-        # occurred during load.
-        name,
-        collection_type,
-        element_identifiers=None,
-        elements=None,
-        implicit_collection_info=None,
-        trusted_identifiers=None,  # Trust preloaded element objects
-        hide_source_items=False,
-    ):
+    def create( self, trans, parent, name, collection_type, element_identifiers=None,
+                elements=None, implicit_collection_info=None, trusted_identifiers=None,
+                hide_source_items=False, tags=None):
         """
+        PRECONDITION: security checks on ability to add to parent
+        occurred during load.
         """
         # Trust embedded, newly created objects created by tool subsystem.
         if trusted_identifiers is None:
@@ -107,17 +98,17 @@ def create(
             message = "Internal logic error - create called with unknown parent type %s" % type( parent )
             log.exception( message )
             raise MessageException( message )
+        tags = tags or []
+        if implicit_collection_info:
+            for k, v in implicit_collection_info.get('implicit_inputs', []):
+                tags.extend(v.tags)
+        for tag in tags:
+            dataset_collection_instance.tags.append(tag.copy())
 
         return self.__persist( dataset_collection_instance )
 
-    def create_dataset_collection(
-        self,
-        trans,
-        collection_type,
-        element_identifiers=None,
-        elements=None,
-        hide_source_items=False,
-    ):
+    def create_dataset_collection( self, trans, collection_type, element_identifiers=None, elements=None,
+                                   hide_source_items=None ):
         if element_identifiers is None and elements is None:
             raise RequestParameterInvalidException( ERROR_INVALID_ELEMENTS_SPECIFICATION )
         if not collection_type:
@@ -188,15 +179,11 @@ def update( self, trans, instance_type, id, payload ):
         changed = self._set_from_dict( trans, dataset_collection_instance, payload )
         return changed
 
-    def copy(
-        self,
-        trans,
-        parent,
-        # PRECONDITION: security checks on ability to add to parent
-        # occurred during load.
-        source,
-        encoded_source_id,
-    ):
+    def copy( self, trans, parent, source, encoded_source_id ):
+        """
+        PRECONDITION: security checks on ability to add to parent occurred
+        during load.
+        """
         assert source == "hdca"  # for now
         source_hdca = self.__get_history_collection_instance( trans, encoded_source_id )
         new_hdca = source_hdca.copy()
@@ -213,6 +200,7 @@ def _set_from_dict( self, trans, dataset_collection_instance, new_data ):
             dataset_collection_instance.add_item_annotation( trans.sa_session, trans.get_user(), dataset_collection_instance, new_data[ 'annotation' ] )
             changed[ 'annotation' ] = new_data[ 'annotation' ]
         if 'tags' in new_data.keys() and trans.get_user():
+            # set_tags_from_list will flush on its own, no need to add to 'changed' here and incur a second flush.
             self.tag_manager.set_tags_from_list( trans.get_user(), dataset_collection_instance, new_data[ 'tags' ] )
 
         if changed.keys():

lib/galaxy/managers/hdas.py

@@ -261,7 +261,7 @@ def __init__( self, app ):
             'state',
             'extension',
             'deleted', 'purged', 'visible',
-            'nametags',
+            'tags',
             'type',
             'url',
             'create_time',
@@ -286,7 +286,6 @@ def __init__( self, app ):
             'creating_job',
             'rerunnable',
 
-            'tags',
             'uuid',
             'permissions',
             'file_name',
@@ -332,7 +331,6 @@ def add_serializers( self ):
             'misc_blurb'    : self._remap_from( 'blurb' ),
             'file_ext'      : self._remap_from( 'extension' ),
             'file_path'     : self._remap_from( 'file_name' ),
-            'nametags'      : self.serialize_nametags,
             'resubmitted'   : lambda i, k, **c: self.hda_manager.has_been_resubmitted( i ),
             'display_apps'  : self.serialize_display_apps,
             'display_types' : self.serialize_old_display_applications,
@@ -386,17 +384,6 @@ def serialize_display_apps( self, hda, key, trans=None, **context ):
 
         return display_apps
 
-    def serialize_nametags( self, hda, key, trans=None, **context ):
-        """
-        Return list of 'name' child tags attached to this dataset.
-        TODO: investigate faster ways to fetch 'name' tags and values
-        """
-        nametags = []
-        for tag in hda.tags:
-            if tag.tag.name == 'name':
-                nametags.append(tag.value)
-        return nametags
-
     def serialize_old_display_applications( self, hda, key, trans=None, **context ):
         """
         Return dictionary containing old-style display app urls.

lib/galaxy/managers/hdcas.py

@@ -235,6 +235,7 @@ def __init__( self, app ):
             'visible',
             'type', 'url',
             'create_time', 'update_time',
+            'tags',  # TODO: detail view only (maybe)
         ])
         self.add_view( 'detailed', [
             'elements'

lib/galaxy/managers/tags.py

@@ -306,6 +306,10 @@ def __init__( self, app ):
             ItemTagAssocInfo( model.HistoryDatasetAssociation,
                               model.HistoryDatasetAssociationTagAssociation,
                               model.HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id )
+        self.item_tag_assoc_info["HistoryDatasetCollectionAssociation"] = \
+            ItemTagAssocInfo( model.HistoryDatasetCollectionAssociation,
+                              model.HistoryDatasetCollectionTagAssociation,
+                              model.HistoryDatasetCollectionTagAssociation.table.c.history_dataset_collection_id )
         self.item_tag_assoc_info["Page"] = ItemTagAssocInfo( model.Page,
                                                              model.PageTagAssociation,
                                                              model.PageTagAssociation.table.c.page_id )

lib/galaxy/tools/actions/__init__.py

@@ -405,6 +405,7 @@ def handle_output( name, output, hidden=None ):
                     output_collections.create_collection(
                         output=output,
                         name=name,
+                        tags=preserved_tags,
                         **element_kwds
                     )
                 else:
@@ -678,7 +679,7 @@ def __init__(self, trans, history, tool, tool_action, input_collections, mapping
         self.out_collections = {}
         self.out_collection_instances = {}
 
-    def create_collection(self, output, name, **element_kwds):
+    def create_collection(self, output, name, tags=None, **element_kwds):
         input_collections = self.input_collections
         collections_manager = self.trans.app.dataset_collections_service
         collection_type = output.structure.collection_type
@@ -729,6 +730,7 @@ def create_collection(self, output, name, **element_kwds):
                 name=hdca_name,
                 collection_type=collection_type,
                 trusted_identifiers=True,
+                tags=tags,
                 **element_kwds
             )
             # name here is name of the output element - not name