whitespace

lib/galaxy/datatypes/registry.py

@@ -350,7 +350,7 @@ class Registry( object ):
                             except Exception, e:
                                 self.log.exception( 'Error calling method %s from class %s: %s', str( datatype_class_name ), str( module ), str( e ) )
                                 ok = False
-                            if ok: 
+                            if ok:
                                 if deactivate:
                                     # We are deactivating or uninstalling an installed Tool Shed repository, so eliminate the appropriate sniffers.
                                     sniffer_class = elem.get( 'type', None )

lib/galaxy/model/__init__.py

@@ -1850,7 +1850,7 @@ class HistoryDatasetAssociation( DatasetInstance, Dictifiable, UsesAnnotations,
 
         if hda.copied_from_library_dataset_dataset_association is not None:
             rval['copied_from_ldda_id'] = hda.copied_from_library_dataset_dataset_association.id
-            
+
         if hda.history is not None:
             rval['history_id'] = hda.history.id
 

lib/galaxy/tools/parameters/basic.py

@@ -1621,7 +1621,7 @@ class DataToolParameter( ToolParameter ):
             if type( value ) != list:
                 value = [ value ]
         field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values )
-        
+
         # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field()
         def dataset_collector( hdas, parent_hid ):
             current_user_roles = trans.get_current_user_roles()

lib/galaxy/tools/parameters/grouping.py

@@ -501,7 +501,7 @@ class Conditional( Group ):
             else:
                 input.visit_inputs( prefix, value[input.name], callback )
     def get_initial_value( self, trans, context, history=None ):
-        # State for a conditional is a plain dictionary. 
+        # State for a conditional is a plain dictionary.
         rval = {}
         # Get the default value for the 'test element' and use it
         # to determine the current case

lib/galaxy/webapps/galaxy/buildapp.py

@@ -138,9 +138,9 @@ def app_factory( global_conf, **kwargs ):
     webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
     webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
     webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' )
-    webapp.mapper.resource( 'datatype', 
-                            'datatypes', 
-                            path_prefix='/api', 
+    webapp.mapper.resource( 'datatype',
+                            'datatypes',
+                            path_prefix='/api',
                             collection={ 'sniffers': 'GET' },
                             parent_resources=dict( member_name='datatype', collection_name='datatypes' ) )
     #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) )
@@ -180,41 +180,41 @@ def app_factory( global_conf, **kwargs ):
     # ============================
 
     webapp.mapper.connect( 'api_key_retrieval',
-                           '/api/authenticate/baseauth/', 
-                           controller='authenticate', 
-                           action='get_api_key', 
+                           '/api/authenticate/baseauth/',
+                           controller='authenticate',
+                           action='get_api_key',
                            conditions=dict( method=[ "GET" ] ) )
 
     # =======================
     # ===== LIBRARY API =====
     # =======================
-    
+
     webapp.mapper.connect( 'show_lda_item',
-                           '/api/libraries/datasets/:id', 
-                           controller='lda_datasets', 
-                           action='show', 
+                           '/api/libraries/datasets/:id',
+                           controller='lda_datasets',
+                           action='show',
                            conditions=dict( method=[ "GET" ] ) )
 
-    webapp.mapper.connect( 'download_lda_items', 
-                           '/api/libraries/datasets/download/:format', 
-                           controller='lda_datasets', 
-                           action='download', 
+    webapp.mapper.connect( 'download_lda_items',
+                           '/api/libraries/datasets/download/:format',
+                           controller='lda_datasets',
+                           action='download',
                            conditions=dict( method=[ "POST", "GET" ] ) )
 
-    webapp.mapper.connect( 'create_folder', 
-                           '/api/folders/:encoded_parent_folder_id', 
-                           controller='folders', 
-                           action='create', 
+    webapp.mapper.connect( 'create_folder',
+                           '/api/folders/:encoded_parent_folder_id',
+                           controller='folders',
+                           action='create',
                            conditions=dict( method=[ "POST" ] ) )
 
     webapp.mapper.resource_with_deleted( 'library',
-                                         'libraries', 
+                                         'libraries',
                                          path_prefix='/api' )
-    webapp.mapper.resource( 'folder', 
-                            'folders', 
+    webapp.mapper.resource( 'folder',
+                            'folders',
                             path_prefix='/api' )
 
-    webapp.mapper.resource( 'content', 
+    webapp.mapper.resource( 'content',
                             'contents',
                             controller='folder_contents',
                             name_prefix='folder_',
@@ -233,9 +233,9 @@ def app_factory( global_conf, **kwargs ):
                             'permissions',
                             path_prefix='/api/libraries/:library_id',
                             parent_resources=dict( member_name='library', collection_name='libraries' ) )
-    
-    webapp.mapper.resource( 'job', 
-                            'jobs', 
+
+    webapp.mapper.resource( 'job',
+                            'jobs',
                             path_prefix='/api' )
     webapp.mapper.connect( 'job_search', '/api/jobs/search', controller='jobs', action='search', conditions=dict( method=['POST'] ) )
 
@@ -243,7 +243,7 @@ def app_factory( global_conf, **kwargs ):
     _add_item_extended_metadata_controller( webapp,
                                name_prefix="library_dataset_",
                                path_prefix='/api/libraries/:library_id/contents/:library_content_id' )
-    
+
     _add_item_extended_metadata_controller( webapp,
                                name_prefix="history_dataset_",
                                path_prefix='/api/histories/:history_id/contents/:history_content_id' )
@@ -251,14 +251,14 @@ def app_factory( global_conf, **kwargs ):
     # ====================
     # ===== TOOLSHED =====
     # ====================
-    
+
     # Handle displaying tool help images and README file images contained in repositories installed from the tool shed.
     webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file',
                       controller='admin_toolshed',
                       action='display_image_in_repository',
                       repository_id=None,
                       image_file=None )
-    
+
     # Galaxy API for tool shed features.
     webapp.mapper.resource( 'tool_shed_repository',
                             'tool_shed_repositories',

lib/galaxy/webapps/galaxy/controllers/tool_runner.py

@@ -239,7 +239,7 @@ class ToolRunner( BaseUIController ):
         Redirects a user accessing a Data Source tool to its target action link.
         This method will subvert mix-mode content blocking in several browsers when
         accessing non-https data_source tools from an https galaxy server.
-        
+
         Tested as working on Safari 7.0 and FireFox 26
         Subverting did not work on Chrome 31
         """
@@ -255,13 +255,13 @@ class ToolRunner( BaseUIController ):
             trans.log_event( "Tool id '%s' does not exist" % tool_id )
             trans.response.status = 404
             return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd )
-        
+
         if isinstance( tool, DataSourceTool ):
             link = url_for( tool.action, **tool.get_static_param_values( trans ) )
         else:
             link = url_for( controller='tool_runner', tool_id=tool.id )
         return trans.response.send_redirect( link )
-    
+
     @web.expose
     def redirect( self, trans, redirect_url=None, **kwd ):
         if not redirect_url:

tools/data_source/upload.py

@@ -126,7 +126,7 @@ def add_file( dataset, registry, json_file, output_path ):
         elif is_gzipped and is_valid:
             if link_data_only == 'copy_files':
                 # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
-                CHUNK_SIZE = 2**20 # 1Mb   
+                CHUNK_SIZE = 2**20 # 1Mb
                 fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_gunzip_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
                 gzipped_file = gzip.GzipFile( dataset.path, 'rb' )
                 while 1:
@@ -159,7 +159,7 @@ def add_file( dataset, registry, json_file, output_path ):
             elif is_bzipped and is_valid:
                 if link_data_only == 'copy_files':
                     # We need to uncompress the temp_name file
-                    CHUNK_SIZE = 2**20 # 1Mb   
+                    CHUNK_SIZE = 2**20 # 1Mb
                     fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_bunzip2_' % dataset.dataset_id, dir=os.path.dirname( output_path ), text=False )
                     bzipped_file = bz2.BZ2File( dataset.path, 'rb' )
                     while 1: