Remove unreachable statements

lib/galaxy/datatypes/dataproviders/base.py

@@ -256,7 +256,6 @@ class LimitedOffsetDataProvider(FilteredDataProvider):
         """
         if self.limit is not None and self.limit <= 0:
             return
-            yield
 
         parent_gen = super(LimitedOffsetDataProvider, self).__iter__()
         for datum in parent_gen:

lib/galaxy/datatypes/dataproviders/dataset.py

@@ -168,9 +168,9 @@ class ConvertedDatasetDataProvider(DatasetDataProvider):
 
     def __init__(self, dataset, **kwargs):
         raise NotImplementedError('Abstract class')
-        self.original_dataset = dataset
-        self.converted_dataset = self.convert_dataset(dataset, **kwargs)
-        super(ConvertedDatasetDataProvider, self).__init__(self.converted_dataset, **kwargs)
+        # self.original_dataset = dataset
+        # self.converted_dataset = self.convert_dataset(dataset, **kwargs)
+        # super(ConvertedDatasetDataProvider, self).__init__(self.converted_dataset, **kwargs)
         # NOTE: now self.converted_dataset == self.dataset
 
     def convert_dataset(self, dataset, **kwargs):
@@ -553,12 +553,12 @@ class BigWigDataProvider(base.LimitedOffsetDataProvider):
         raise NotImplementedError('Work in progress')
         # TODO: validate is a wig
         # still good to maintain a ref to the raw source bc Reader won't
-        self.raw_source = source
-        self.parser = bx_bbi.bigwig_file.BigWigFile(source)
-        super(BigWigDataProvider, self).__init__(self.parser, **kwargs)
+        # self.raw_source = source
+        # self.parser = bx_bbi.bigwig_file.BigWigFile(source)
+        # super(BigWigDataProvider, self).__init__(self.parser, **kwargs)
 
-        self.named_columns = named_columns
-        self.column_names = column_names or self.COLUMN_NAMES
+        # self.named_columns = named_columns
+        # self.column_names = column_names or self.COLUMN_NAMES
 
     def __iter__(self):
         parent_gen = super(BigWigDataProvider, self).__iter__()
@@ -586,8 +586,8 @@ class DatasetSubprocessDataProvider(external.SubprocessDataProvider):
         :type args: variadic function args
         """
         raise NotImplementedError('Abstract class')
-        super(DatasetSubprocessDataProvider, self).__init__(*args, **kwargs)
-        self.dataset = dataset
+        # super(DatasetSubprocessDataProvider, self).__init__(*args, **kwargs)
+        # self.dataset = dataset
 
 
 class SamtoolsDataProvider(line.RegexLineDataProvider):
@@ -699,7 +699,7 @@ class BcftoolsDataProvider(line.RegexLineDataProvider):
     def __init__(self, dataset, **kwargs):
         # TODO: as samtools
         raise NotImplementedError()
-        super(BcftoolsDataProvider, self).__init__(dataset, **kwargs)
+        # super(BcftoolsDataProvider, self).__init__(dataset, **kwargs)
 
 
 class BGzipTabixDataProvider(base.DataProvider):
@@ -712,7 +712,7 @@ class BGzipTabixDataProvider(base.DataProvider):
     def __init__(self, dataset, **kwargs):
         # TODO: as samtools - need more info on output format
         raise NotImplementedError()
-        super(BGzipTabixDataProvider, self).__init__(dataset, **kwargs)
+        # super(BGzipTabixDataProvider, self).__init__(dataset, **kwargs)
 
 
 class SQliteDataProvider(base.DataProvider):

lib/galaxy/datatypes/dataproviders/external.py

@@ -156,8 +156,8 @@ class TempfileDataProvider(base.DataProvider):
         # TODO:
         raise NotImplementedError()
         # write the file here
-        self.create_file
-        super(TempfileDataProvider, self).__init__(self.tmp_file, **kwargs)
+        # self.create_file
+        # super(TempfileDataProvider, self).__init__(self.tmp_file, **kwargs)
 
     def create_file(self):
         self.tmp_file = tempfile.NamedTemporaryFile()

lib/galaxy/jobs/runners/state_handlers/_safe_eval.py

@@ -23,9 +23,6 @@ VALID_FUNCTIONS = BUILTIN_AND_MATH_FUNCTIONS + STRING_AND_LIST_METHODS
 def _check_name(ast_node, allowed_variables=[]):
     name = ast_node.id
     return name in (VALID_FUNCTIONS + allowed_variables)
-    if re.match(r'^c\d+$', name):
-        return True
-    return name in VALID_FUNCTIONS
 
 
 def _check_attribute(ast_node):

lib/galaxy/jobs/runners/tasks.py

@@ -206,15 +206,6 @@ class TaskedJobRunner(BaseJobRunner):
     def _check_pid(self, pid):
         # DBTODO Need to check all subtask pids and return some sort of cumulative result.
         return True
-        try:
-            os.kill(pid, 0)
-            return True
-        except OSError as e:
-            if e.errno == errno.ESRCH:
-                log.debug("_check_pid(): PID %d is dead" % pid)
-            else:
-                log.warning("_check_pid(): Got errno %s when attempting to check PID %d: %s" % (errno.errorcode[e.errno], pid, e.strerror))
-            return False
 
     def _stop_pid(self, pid, job_id):
         """

lib/galaxy/model/metadata.py

@@ -781,7 +781,6 @@ class JobExternalOutputMetadataWrapper(object):
             config_root = os.path.abspath(os.getcwd())
         if datatypes_config is None:
             raise Exception('In setup_external_metadata, the received datatypes_config is None.')
-            datatypes_config = 'datatypes_conf.xml'
         metadata_files_list = []
         for dataset in datasets:
             key = self.get_dataset_metadata_key(dataset)

lib/galaxy/objectstore/azure_blob.py

@@ -427,8 +427,6 @@ class AzureBlobObjectStore(ObjectStore):
         #     return cache_path
         raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-        return cache_path  # Until the upload tool does not explicitly create the dataset, return expected path
-
     def update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create is True:
             self.create(obj, **kwargs)

lib/galaxy/objectstore/pulsar.py

@@ -63,7 +63,6 @@ class PulsarObjectStore(ObjectStore):
     def __build_kwds(self, obj, **kwds):
         kwds['object_id'] = obj.id
         return kwds
-        pass
 
     def __build_pulsar_client(self, config_xml):
         if ObjectStoreClientManager is None:

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -1255,7 +1255,6 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                     'status' : 'info',
                     'inputs' : [build_select_input('in_roles', 'Roles', all_roles, in_roles),
                                 build_select_input('in_users', 'Users', all_users, in_users)]}
-            return {'message' : 'Not showing associated datasets, there are too many.', 'info' : 'info'}
         else:
             in_users = [trans.sa_session.query(trans.app.model.User).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_users'))]
             in_roles = [trans.sa_session.query(trans.app.model.Role).get(trans.security.decode_id(x)) for x in util.listify(payload.get('in_roles'))]

lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py

@@ -264,7 +264,6 @@ class Repository(RecipeTag, SyncDatabase):
             message = "Unable to retrieve required tool_dependencies.xml file from the Tool Shed for revision "
             message += "%s of installed repository %s owned by %s." % (str(changeset_revision), str(name), str(owner))
             raise Exception(message)
-            return None
 
     def create_tool_dependency_with_initialized_env_sh_file(self, dependent_install_dir, tool_shed_repository,
                                                             required_repository, package_name, package_version,

lib/tool_shed/grids/repository_grids.py

@@ -116,7 +116,6 @@ class RepositoryGrid(grids.Grid):
                 rev_label, rev_date = option_items.split(' ')
                 rev_date = '<i><font color="#666666">%s</font></i>' % rev_date
                 return '%s %s' % (rev_label, rev_date)
-                return select_field.options[0][0]
             return ''
 
     class LatestInstallableRevisionColumn(grids.GridColumn):