Merge branch 'dev' into admin_grid_formbuilder

galaxyproject · Sep 13, 2017 · 809cabd · 809cabd
2 parents 87f2ad1 + 11d4380
commit 809cabd
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Showing 205 changed files with 4,365 additions and 2,918 deletions.
diff --git a/.ci/flake8_lint_include_list.txt b/.ci/flake8_lint_include_list.txt
@@ -101,7 +101,7 @@ lib/galaxy/webapps/galaxy/api/genomes.py
 lib/galaxy/webapps/galaxy/api/histories.py
 lib/galaxy/webapps/galaxy/api/__init__.py
 lib/galaxy/webapps/galaxy/api/jobs.py
-lib/galaxy/webapps/galaxy/api/lda_datasets.py
+lib/galaxy/webapps/galaxy/api/library_datasets.py
 lib/galaxy/webapps/galaxy/api/requests.py
 lib/galaxy/webapps/galaxy/api/roles.py
 lib/galaxy/webapps/galaxy/api/samples.py

diff --git a/.ci/jenkins/selenium/docker-compose.yml b/.ci/jenkins/selenium/docker-compose.yml
@@ -12,7 +12,7 @@ services:
     ports:
       - "${GALAXY_PORT}:8080"
   selenium:
-    image: selenium/standalone-chrome:3.0.1-aluminum
+    image: selenium/standalone-chrome:3.5.2
     ports:
       - "${SELENIUM_PORT}:4444"
     links:

diff --git a/client/galaxy/scripts/apps/admin.js b/client/galaxy/scripts/apps/admin.js
@@ -7,6 +7,7 @@ var jQuery = require( 'jquery' ),
     Ui = require( 'mvc/ui/ui-misc' ),
     QueryStringParsing = require( 'utils/query-string-parsing' ),
     Router = require( 'layout/router' ),
+    Utils = require( 'utils/utils' ),
     Page = require( 'layout/page' );
 
 window.app = function app( options, bootstrapped ){
@@ -127,9 +128,10 @@ window.app = function app( options, bootstrapped ){
 
     $(function() {
         _.extend( options.config, { active_view : 'admin' } );
+        Utils.setWindowTitle("Administration");
         Galaxy.page = new Page.View( _.extend( options, {
             Left    : AdminPanel,
             Router  : AdminRouter
         } ) );
     });
-};
+};
diff --git a/client/galaxy/scripts/layout/page.js b/client/galaxy/scripts/layout/page.js
@@ -1,4 +1,4 @@
-define( [ 'layout/masthead', 'layout/panel', 'mvc/ui/ui-modal' ], function( Masthead, Panel, Modal ) {
+define( [ 'layout/masthead', 'layout/panel', 'mvc/ui/ui-modal', 'utils/utils' ], function( Masthead, Panel, Modal, Utils) {
     var View = Backbone.View.extend({
         el : 'body',
         className : 'full-content',
@@ -16,7 +16,16 @@ define( [ 'layout/masthead', 'layout/panel', 'mvc/ui/ui-modal' ], function( Mast
 
             // attach global objects, build mastheads
             Galaxy.modal = this.modal = new Modal.View();
-            Galaxy.display = this.display = function( view ) { self.center.display( view ) };
+            Galaxy.display = this.display = function( view ) {
+                if ( view.title ){
+                    Utils.setWindowTitle( view.title );
+                    view.allow_title_display = false;
+                } else {
+                    Utils.setWindowTitle();
+                    view.allow_title_display = true;
+                }
+                self.center.display( view );
+            };
             Galaxy.router = this.router = options.Router && new options.Router( self, options );
             this.masthead = new Masthead.View( this.config );
             this.center = new Panel.CenterPanel();
@@ -155,7 +164,7 @@ define( [ 'layout/masthead', 'layout/panel', 'mvc/ui/ui-modal' ], function( Mast
                             }
                         }
                 })
-                .error( function( data ) { 
+                .error( function( data ) {
                     // hide the communication icon if the communication server is not available
                     $chat_icon_element.css( "visibility", "hidden" ); 
                 });
@@ -166,4 +175,4 @@ define( [ 'layout/masthead', 'layout/panel', 'mvc/ui/ui-modal' ], function( Mast
     });
 
     return { View: View }
-});
+});
diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
@@ -405,7 +405,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
 
     /** autopair by exact match */
     autopairSimple : autoPairFnBuilder({
-        scoreThreshold: function(){ return 1.0; },
+        scoreThreshold: function(){ return 0.6; },
         match : function _match( params ){
             params = params || {};
             if( params.matchTo === params.possible ){

diff --git a/client/galaxy/scripts/mvc/grid/grid-shared.js b/client/galaxy/scripts/mvc/grid/grid-shared.js
@@ -6,6 +6,7 @@ define( [ 'mvc/grid/grid-view' ], function( GridView ) {
             this.setElement( $( '<div/>' ) );
             this.model = new Backbone.Model( options );
             this.item = this.model.get( 'item' );
+            this.title = this.model.get('plural');
             $.ajax({
                 url     : Galaxy.root + this.item + '/' + this.model.get( 'action_id' ),
                 success : function( response ) {
@@ -55,4 +56,4 @@ define( [ 'mvc/grid/grid-view' ], function( GridView ) {
     return {
         View: View
     }
-});
+});
diff --git a/client/galaxy/scripts/mvc/grid/grid-view.js b/client/galaxy/scripts/mvc/grid/grid-view.js
@@ -20,6 +20,7 @@ return Backbone.View.extend({
     initialize: function(grid_config) {
         this.grid = new GridModel();
         this.dict_format = grid_config.dict_format;
+        this.title = grid_config.title;
         var self = this;
         window.add_tag_to_grid_filter = function( tag_name, tag_value ){
             // Put tag name and value together.
@@ -83,6 +84,9 @@ return Backbone.View.extend({
         // get options
         var options = this.grid.attributes;
 
+        if (this.allow_title_display && options.title){
+            Utils.setWindowTitle(options.title);
+        }
         // handle refresh requests
         this.handle_refresh(options.refresh_frames);
 

diff --git a/client/galaxy/scripts/mvc/history/history-list.js b/client/galaxy/scripts/mvc/history/history-list.js
@@ -2,6 +2,7 @@
 define( [ 'utils/utils', 'mvc/grid/grid-view', 'mvc/history/history-model', 'mvc/history/copy-dialog' ], function( Utils, GridView, HistoryModel, historyCopyDialog ) {
 
     var View = Backbone.View.extend({
+        title: "Histories",
         initialize: function( options ) {
             var self = this;
             this.setElement( $( '<div/>' ) );
@@ -46,4 +47,4 @@ define( [ 'utils/utils', 'mvc/grid/grid-view', 'mvc/history/history-model', 'mvc
     return {
         View: View
     }
-});
+});
diff --git a/client/galaxy/scripts/mvc/history/history-view-edit.js b/client/galaxy/scripts/mvc/history/history-view-edit.js
@@ -156,6 +156,7 @@ var HistoryViewEdit = _super.extend(
     renderItems : function( $whereTo ){
         var views = _super.prototype.renderItems.call( this, $whereTo );
         if( !this.searchFor ){ this._renderCounts( $whereTo ); }
+        else{ this._renderSearchFindings( $whereTo ); }
         return views;
     },
 
@@ -427,10 +428,10 @@ var HistoryViewEdit = _super.extend(
     },
 
     /** override to display number found in subtitle */
-    _renderSearchFindings : function(){
-        this.$( '> .controls .subtitle' ).html([
-            _l( 'Found' ), this.views.length
-        ].join(' '));
+    _renderSearchFindings : function( $whereTo ){
+        $whereTo = $whereTo instanceof jQuery? $whereTo : this.$el;
+        var html = this.templates.found( this.model.toJSON(), this );
+        $whereTo.find( '> .controls .subtitle' ).html( html );
         return this;
     },
 
@@ -598,8 +599,37 @@ HistoryViewEdit.prototype.templates = (function(){
         '<% } %>',
     ], 'history' );
 
+    var foundTemplate = BASE_MVC.wrapTemplate([
+        _l( 'Found' ), ' <%- view.views.length %>, ',
+
+        '<% if( history.contents_active.deleted ){ %>',
+            '<% if( view.model.contents.includeDeleted ){ %>',
+                '<a class="toggle-deleted-link" href="javascript:void(0);">',
+                    _l( 'hide deleted' ),
+                '</a>, ',
+            '<% } else { %>',
+                '<a class="toggle-deleted-link" href="javascript:void(0);">',
+                    _l( 'show deleted' ),
+                '</a>, ',
+            '<% } %>',
+        '<% } %>',
+
+        '<% if( history.contents_active.hidden ){ %>',
+            '<% if( view.model.contents.includeHidden ){ %>',
+                '<a class="toggle-hidden-link" href="javascript:void(0);">',
+                    _l( 'hide hidden' ),
+                '</a>',
+            '<% } else { %>',
+                '<a class="toggle-hidden-link" href="javascript:void(0);">',
+                    _l( 'show hidden' ),
+                '</a>',
+            '<% } %>',
+        '<% } %>',
+    ], 'history' );
+
     return _.extend( _.clone( _super.prototype.templates ), {
-        counts : countsTemplate
+        counts : countsTemplate,
+        found : foundTemplate 
     });
 }());
 

diff --git a/client/galaxy/scripts/mvc/history/options-menu.js b/client/galaxy/scripts/mvc/history/options-menu.js
@@ -65,7 +65,7 @@ var menu = [
         anon    : true,
         func    : function() {
             if( Galaxy && Galaxy.currHistoryPanel && confirm( _l( 'Really delete the current history?' ) ) ){
-                galaxy_main.window.location.href = 'history/delete?id=' + Galaxy.currHistoryPanel.model.id;
+                Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory();});
             }
         },
     },
@@ -76,7 +76,7 @@ var menu = [
         func    : function() {
             if( Galaxy && Galaxy.currHistoryPanel
             &&  confirm( _l( 'Really delete the current history permanently? This cannot be undone.' ) ) ){
-                galaxy_main.window.location.href = 'history/delete?purge=True&id=' + Galaxy.currHistoryPanel.model.id;
+                Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory();});
             }
         },
     },