Address W503 and E721 errors now enforced by pep8 1.7.

lib/galaxy/jobs/__init__.py

@@ -1195,8 +1195,8 @@ class JobWrapper( object ):
                     # either use the metadata from originating output dataset, or call set_meta on the copies
                     # it would be quicker to just copy the metadata from the originating output dataset,
                     # but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta()
-                    if ( self.app.config.retry_metadata_internally
-                            and not self.external_output_metadata.external_metadata_set_successfully(dataset, self.sa_session ) ):
+                    if ( self.app.config.retry_metadata_internally and
+                            not self.external_output_metadata.external_metadata_set_successfully(dataset, self.sa_session ) ):
                         # If Galaxy was expected to sniff type and didn't - do so.
                         if dataset.ext == "_sniff_":
                             extension = sniff.handle_uploaded_dataset_file( dataset.dataset.file_name, self.app.datatypes_registry )
@@ -1204,8 +1204,8 @@ class JobWrapper( object ):
 
                         # call datatype.set_meta directly for the initial set_meta call during dataset creation
                         dataset.datatype.set_meta( dataset, overwrite=False )
-                    elif ( job.states.ERROR != final_job_state
-                            and not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) ):
+                    elif ( job.states.ERROR != final_job_state and
+                            not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) ):
                         dataset._state = model.Dataset.states.FAILED_METADATA
                     else:
                         # load metadata from file

lib/galaxy/managers/rbac_secured.py

@@ -259,6 +259,6 @@ class AccessDatasetRBACPermission( DatasetRBACPermission ):
 
     def _role_is_permitted( self, dataset, role ):
         current_roles = self._roles( dataset )
-        return ( self._is_public_from_roles( current_roles )
-            # if there's only one role and this is it, let em in
-            or ( ( len( current_roles ) == 1 ) and ( role == current_roles[0] ) ) )
+        return ( self._is_public_from_roles( current_roles ) or
+                 # if there's only one role and this is it, let em in
+                 ( ( len( current_roles ) == 1 ) and ( role == current_roles[0] ) ) )

lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py

@@ -61,7 +61,7 @@ def upgrade(migrate_engine):
         if r[1]:
             dataset_files = loads(r[1])
             for df in dataset_files:
-                if type(df) == type(dict()):
+                if isinstance(df, dict):
                     cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')"
                     cmd = cmd % ( nextval(migrate_engine, 'sample_dataset'),
                                   localtimestamp(migrate_engine),

lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py

@@ -77,7 +77,7 @@ def upgrade(migrate_engine):
         if not str( row[2] ).strip():
             continue
         fields_list = loads( str( row[2] ).strip() )
-        if fields_list and type(values_list) == type(list()):
+        if fields_list and isinstance(values_list, list):
             values_dict = {}
             for field_index, field in enumerate( fields_list ):
                 field_name = field[ 'name' ]

lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py

@@ -136,7 +136,7 @@ def get_sequencer_id( migrate_engine, sequencer_info ):
             continue
         values = loads( values )
         # proceed only if sequencer_info is a valid list
-        if values and type( values ) == type( dict() ):
+        if values and isinstance(values, dict):
             if sequencer_info.get( 'host', '' ) == values.get( 'field_0', '' ) \
                and sequencer_info.get( 'username', '' ) == values.get( 'field_1', '' ) \
                and sequencer_info.get( 'password', '' ) == values.get( 'field_2', '' ) \
@@ -236,7 +236,7 @@ def upgrade(migrate_engine):
                 continue
             sequencer_info = loads( sequencer_info.strip() )
             # proceed only if sequencer_info is a valid dict
-            if sequencer_info and type( sequencer_info ) == type( dict() ):
+            if sequencer_info and isinstance(sequencer_info, dict):
                 # check if this sequencer has already been added to the sequencer table
                 sequencer_id = get_sequencer_id( migrate_engine, sequencer_info )
                 if not sequencer_id:

lib/galaxy/util/pastescript/loadwsgi.py

@@ -63,9 +63,9 @@ def fix_type_error(exc_info, callable, varargs, kwargs):
     """
     if exc_info is None:
         exc_info = sys.exc_info()
-    if (exc_info[0] != TypeError
-            or str(exc_info[1]).find('arguments') == -1
-            or getattr(exc_info[1], '_type_error_fixed', False)):
+    if (exc_info[0] != TypeError or
+            str(exc_info[1]).find('arguments') == -1 or
+            getattr(exc_info[1], '_type_error_fixed', False)):
         return exc_info
     exc_info[1]._type_error_fixed = True
     argspec = inspect.formatargspec(*inspect.getargspec(callable))

lib/pulsar/client/amqp_exchange.py

@@ -186,8 +186,8 @@ class PulsarExchange(object):
         key = self.__queue_name(name)
         publish_log_prefix = self.__publish_log_prefex(transaction_uuid)
         log.debug("%sBegin publishing to key %s", publish_log_prefix, key)
-        if (self.acks_enabled and not name.endswith(ACK_QUEUE_SUFFIX)
-                and ACK_FORCE_NOACK_KEY not in payload):
+        if (self.acks_enabled and not name.endswith(ACK_QUEUE_SUFFIX) and
+                ACK_FORCE_NOACK_KEY not in payload):
             # Publishing a message on a normal queue and it's not a republish
             # (or explicitly forced do-not-ack), so add ack keys
             ack_uuid = str(transaction_uuid)

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -97,7 +97,7 @@ def main():
                       help="From address to use to send email. "
                       "Default: [read from galaxy ini file]")
     (options, args) = parser.parse_args()
-    if len(args) != 1 :
+    if len(args) != 1:
         parser.print_help()
         sys.exit()
     ini_file = args[0]
@@ -177,8 +177,7 @@ def administrative_delete_datasets(app, cutoff_time, cutoff_days,
          app.model.HistoryDatasetAssociation.table.c.deleted),
         whereclause=and_(
             app.model.Dataset.table.c.deleted == false(),
-            app.model.HistoryDatasetAssociation.table.c.update_time
-            < cutoff_time,
+            app.model.HistoryDatasetAssociation.table.c.update_time < cutoff_time,
             app.model.HistoryDatasetAssociation.table.c.deleted == false()),
         from_obj=[sa.outerjoin(
                   app.model.Dataset.table,

test/casperjs/casperjs_runner.py

@@ -112,8 +112,10 @@ class CasperJSTestCase( unittest.TestCase ):
         process_command_list = self.build_command_line( rel_script_path, *args, **kwargs )
         log.debug( 'process_command_list: %s', str( process_command_list ) )
         try:
-            process = subprocess.Popen( process_command_list, shell=False,
-                stdout=subprocess.PIPE, stderr=subprocess.PIPE )
+            process = subprocess.Popen( process_command_list,
+                                        shell=False,
+                                        stdout=subprocess.PIPE,
+                                        stderr=subprocess.PIPE )
 
             # output from the browser (stderr only) immediately
             while process.poll() is None:
@@ -145,9 +147,9 @@ class CasperJSTestCase( unittest.TestCase ):
         #   provide information (as it won't be included by default with galaxy)
         except OSError, os_err:
             if os_err.errno == errno.ENOENT:
-                log.error( 'No path to headless browser executable: %s\n'
-                    + 'These tests were designed to use the following headless browser:\n%s',
-                    self.exec_path, self.casper_info )
+                log.error( 'No path to headless browser executable: %s\n' +
+                           'These tests were designed to use the following headless browser:\n%s',
+                           self.exec_path, self.casper_info )
             raise
 
         return self.handle_js_results( stdout_output )
@@ -206,7 +208,7 @@ class CasperJSTestCase( unittest.TestCase ):
             js_test_results = json.loads( stdout_output )
             last_error = get_error( js_test_results )
             err_string = ( "%s\n%s" % ( get_msg( last_error ),
-                self.browser_backtrace_to_string( get_trace( last_error ) ) ) )
+                           self.browser_backtrace_to_string( get_trace( last_error ) ) ) )
 
         # if we couldn't parse json from what's returned on the error, dump stdout
         except ValueError, val_err:
@@ -250,8 +252,8 @@ class CasperJSTestCase( unittest.TestCase ):
             js_test_results = json.loads( results )
             failures = js_test_results[ 'failures' ]
             assert len( failures ) == 0, (
-                "%d assertions failed in the headless browser tests" % ( len( failures ) )
-                + " (see the log for details)" )
+                "%d assertions failed in the headless browser tests" % ( len( failures ) ) +
+                " (see the log for details)" )
 
     # ---------------------------------------------------------------- TestCase overrides
     def setUp( self ):