Merge pull request #2 from jmchilton/Reports_homepage

Merge Reports_homepage against latest dev.

.ci/flake8_wrapper.sh

@@ -2,11 +2,7 @@
 
 set -e
 
-# Run broad range of checks over specific white-listed files, this uses
-# the default checks defined in setup.cfg.
-while read p; do
-    flake8 $(eval echo "$p")
-done <.ci/pep8_sources.txt
+flake8 --exclude database/,.venv/,`paste -sd, .ci/pep8_sources.txt` .
 
 # Look for obviously broken stuff lots more places.
 flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/galaxy/util/pastescript/serve.py,lib/pkg_resources.py lib/ test/{api,unit}

.ci/pep8_sources.txt

@@ -1,47 +1,24 @@
-cron/parse_builds.py
-lib/galaxy/auth
-lib/galaxy/config.py
-lib/galaxy/datatypes/{data,proteomics}.py
-lib/galaxy/exceptions/error_codes.py
-lib/galaxy/jobs/{__init__,error_level,manager,stock_rules}.py
-lib/galaxy/main.py
-lib/galaxy/managers/{api_keys,citations,collections,collections_util,datasets,folders,pages,tags,workflows}.py
-lib/galaxy/model/orm/{engine_factory,now}.py
-lib/galaxy/model/{base,custom_types,search,util}.py
-lib/galaxy/model/tool_shed_install/__init__.py
-lib/galaxy/objectstore/{__init__,pulsar,rods,s3}.py
-lib/galaxy/openid/__init__.py
-lib/galaxy/queues.py
-lib/galaxy/queue_worker.py
-lib/galaxy/tags
-lib/galaxy/tools
-lib/galaxy/util/{__init__,json,permutations,plugin_config,properties,simplegraph,sockets,sleeper,streamball,submodules,xml_macros}.py
-lib/galaxy/web/{proxy,security}
-lib/galaxy/web/base/{__init__,interactive_environments}.py
-lib/galaxy/web/formatting.py
-lib/galaxy/webapps/__init__.py
-lib/galaxy/webapps/galaxy/__init__.py
-lib/galaxy/webapps/galaxy/api/{__init__,authenticate,dataset_collections,datatypes,folder_contents,folders,lda_datasets,job_files,libraries,library_contents,provenance,remote_files,search,users}.py
-lib/galaxy/webapps/galaxy/controllers/{__init__,admin,cloudlaunch,workflow}.py
-lib/galaxy/webapps/reports/app.py
-lib/galaxy/webapps/reports/controllers/{__init__,jobs,query,workflows,home}.py
-lib/galaxy/webapps/tool_shed/app.py
-lib/galaxy/webapps/tool_shed/controllers/__init__.py
-lib/galaxy/webapps/tool_shed/framework/__init__.py
-lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py
-lib/galaxy/webapps/tool_shed/util/{__init__,shed_statistics}.py
-lib/galaxy/work
-lib/galaxy/workflow
-lib/galaxy/version.py
-lib/pulsar
-lib/tool_shed/__init__.py
-lib/tool_shed/galaxy_install/{install_manager,repair_repository_manager}.py
-lib/tool_shed/galaxy_install/repository_dependencies
-lib/tool_shed/galaxy_install/tools/{__init__,tool_panel_manager}.py
-lib/tool_shed/repository_types/{__init__,registry,unrestricted}.py
-lib/tool_shed/util/{__init__,repository_content_util,tool_util,web_util,workflow_util}.py
-test/functional/tools
-test/unit/jobs/test_job_configuration.py
-test/unit/tools
-tools/data_source/upload.py
-tools/evolution/codingSnps_filter.py
+contrib/
+doc/patch.py
+doc/source/conf.py
+lib/galaxy/model/migrate/versions/
+lib/galaxy/model/tool_shed_install/migrate/versions/
+lib/galaxy/util/pastescript/serve.py
+lib/galaxy/webapps/tool_shed/model/migrate/versions/
+lib/galaxy_utils/
+lib/pkg_resources.py
+lib/tool_shed/
+scripts/api/
+scripts/data_libraries/
+scripts/loc_files/
+scripts/microbes/
+scripts/others/
+scripts/scramble/
+scripts/tool_shed/
+scripts/tools/
+scripts/transfer.py
+test/base/
+test/casperjs/
+test/install_and_test_tool_shed_repositories/
+test/tool_shed/
+tools/

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

@@ -61,15 +61,18 @@ var DatasetCollectionElementMixin = {
 
     /** merge the attributes of the sub-object 'object' into this model */
     _mergeObject : function( attributes ){
-        _.extend( attributes, attributes.object );
+        // if we don't preserve and correct ids here, the element id becomes the object id
+        // and collision in backbone's _byId will occur and only
+        _.extend( attributes, attributes.object, { element_id: attributes.id });
         delete attributes.object;
         return attributes;
     },
 
     /** override to merge this.object into this */
     constructor : function( attributes, options ){
-        this.debug( '\t DatasetCollectionElement.constructor:', attributes, options );
+        // console.debug( '\t DatasetCollectionElement.constructor:', attributes, options );
         attributes = this._mergeObject( attributes );
+        this.idAttribute = 'element_id';
         Backbone.Model.apply( this, arguments );
     },
 

client/galaxy/scripts/mvc/library/library-folderlist-view.js

@@ -28,6 +28,7 @@ var FolderListView = Backbone.View.extend({
     events: {
         'click #select-all-checkboxes'  : 'selectAll',
         'click .dataset_row'            : 'selectClickedRow',
+        'click .folder_row'             : 'selectClickedRow',
         'click .sort-folder-link'       : 'sortColumnClicked'
     },
 
@@ -175,7 +176,7 @@ var FolderListView = Backbone.View.extend({
      */
     postRender: function(){
         var fetched_metadata = this.folderContainer.attributes.metadata;
-        fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined';
+        fetched_metadata.contains_file_or_folder = typeof this.collection.findWhere({type: 'file'}) !== 'undefined' || typeof this.collection.findWhere({type: 'folder'}) !== 'undefined';
         Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata);
         $('.library-row').hover(function() {
           $(this).find('.show_on_hover').show();
@@ -201,10 +202,10 @@ var FolderListView = Backbone.View.extend({
      * @param {Item or FolderAsModel} model of the view that will be rendered
      */
     renderOne: function(model){
-        if (model.get('type') !== 'folder'){
-            this.options.contains_file = true;
+        this.options.contains_file_or_folder = true;
+        //if (model.get('type') !== 'folder'){
             // model.set('readable_size', this.size_to_string(model.get('file_size')));
-          }
+        //}
         model.set('folder_id', this.id);
         var rowView = new mod_library_folderrow_view.FolderRowView(model);
 
@@ -329,12 +330,14 @@ var FolderListView = Backbone.View.extend({
         $row.removeClass('light').addClass('dark');
         $row.find('a').removeClass('light').addClass('dark');
         $row.find('.fa-file-o').removeClass('fa-file-o').addClass('fa-file');
+        $row.find('.fa-folder-o').removeClass('fa-folder-o').addClass('fa-folder');
     },
 
     makeWhiteRow: function($row){
         $row.removeClass('dark').addClass('light');
         $row.find('a').removeClass('dark').addClass('light');
         $row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o');
+        $row.find('.fa-folder').removeClass('fa-folder').addClass('fa-folder-o');
     },
 
     renderSortIcon: function(){

client/galaxy/scripts/mvc/library/library-folderrow-view.js

@@ -85,7 +85,7 @@ var FolderRowView = Backbone.View.extend({
     tmpl_array.push('  <td>');
     tmpl_array.push('    <span title="Folder" class="fa fa-folder-o"></span>');
     tmpl_array.push('  </td>');
-    tmpl_array.push('  <td></td>');
+    tmpl_array.push('  <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');
     tmpl_array.push('  <td>');
     tmpl_array.push('    <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');
     tmpl_array.push('  </td>');

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -26,9 +26,9 @@ var FolderToolbarView = Backbone.View.extend({
   },
 
   defaults: {
-    'can_add_library_item'  : false,
-    'contains_file'         : false,
-    'chain_call_control'    : {
+    'can_add_library_item'    : false,
+    'contains_file_or_folder' : false,
+    'chain_call_control'      : {
                                 'total_number'  : 0,
                                 'failed_number' : 0
                               },
@@ -116,7 +116,7 @@ var FolderToolbarView = Backbone.View.extend({
     } else{
       $('.add-library-items').hide();
     }
-    if (this.options.contains_file === true){
+    if (this.options.contains_file_or_folder === true){
       if (Galaxy.currUser){
         if (!Galaxy.currUser.isAnonymous()){
           $('.logged-dataset-manipulation').show();
@@ -250,9 +250,12 @@ var FolderToolbarView = Backbone.View.extend({
     // we can save last used history to pre-select it next time
     this.options.last_used_history_id = history_id;
     var dataset_ids = [];
+    var folder_ids = [];
     $('#folder_table').find(':checked').each(function(){
-        if (this.parentElement.parentElement.id !== '') {
+        if (this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('dataset_row') ) {
             dataset_ids.push(this.parentElement.parentElement.id);
+        } else if (this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('folder_row') ) {
+            folder_ids.push(this.parentElement.parentElement.id);
         }
     });
     // prepare the dataset objects to be imported
@@ -265,6 +268,18 @@ var FolderToolbarView = Backbone.View.extend({
         historyItem.source = 'library';
         datasets_to_import.push(historyItem);
     }
+
+    // prepare the folder objects to be imported
+    var folders_to_import = [];
+    for (var i = folder_ids.length - 1; i >= 0; i--) {
+        var library_folder_id = folder_ids[i];
+        var historyItem = new mod_library_model.HistoryItem();
+        historyItem.url = historyItem.urlRoot + history_id + '/contents';
+        historyItem.content = library_folder_id;
+        historyItem.source = 'library_folder';
+        datasets_to_import.push(historyItem);
+    }
+
     this.initChainCallControl( { length: datasets_to_import.length, action: 'to_history', history_name: history_name } );
     // set the used history as current so user will see the last one 
     // that he imported into in the history panel on the 'analysis' page
@@ -289,13 +304,16 @@ var FolderToolbarView = Backbone.View.extend({
    */
   download : function( folder_id, format ){
     var dataset_ids = [];
+    var folder_ids = [];
         $( '#folder_table' ).find( ':checked' ).each( function(){
-            if ( this.parentElement.parentElement.id !== '' ) {
+            if ( this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('dataset_row') ) {
                 dataset_ids.push( this.parentElement.parentElement.id );
+            } else if ( this.parentElement.parentElement.id !== '' && this.parentElement.parentElement.classList.contains('folder_row') ) {
+                folder_ids.push( this.parentElement.parentElement.id );
             }
         } );
     var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/' + format;
-    var data = { 'ld_ids' : dataset_ids };
+    var data = { 'ld_ids' : dataset_ids, 'folder_ids' : folder_ids };
     this.processDownload( url, data, 'get' );
   },