From 60dd7306d04c47aa4a9b2efed149cb3c4d259a10 Mon Sep 17 00:00:00 2001 From: E Rasche Date: Wed, 13 Sep 2017 05:59:03 +0000 Subject: [PATCH] Remove unreachable statements --- lib/galaxy/datatypes/dataproviders/base.py | 1 - lib/galaxy/datatypes/dataproviders/dataset.py | 24 +++++++++---------- .../datatypes/dataproviders/external.py | 4 ++-- .../jobs/runners/state_handlers/_safe_eval.py | 3 --- lib/galaxy/jobs/runners/tasks.py | 9 ------- lib/galaxy/model/metadata.py | 1 - lib/galaxy/objectstore/azure_blob.py | 2 -- lib/galaxy/objectstore/pulsar.py | 1 - .../webapps/galaxy/controllers/admin.py | 1 - .../tool_dependencies/recipe/tag_handler.py | 1 - lib/tool_shed/grids/repository_grids.py | 1 - 11 files changed, 14 insertions(+), 34 deletions(-) diff --git a/lib/galaxy/datatypes/dataproviders/base.py b/lib/galaxy/datatypes/dataproviders/base.py index 6fb3fb5850b..7c3347478be 100644 --- a/lib/galaxy/datatypes/dataproviders/base.py +++ b/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: diff --git a/lib/galaxy/datatypes/dataproviders/dataset.py b/lib/galaxy/datatypes/dataproviders/dataset.py index 2d77ccc2de5..83e0372fa07 100644 --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/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): diff --git a/lib/galaxy/datatypes/dataproviders/external.py b/lib/galaxy/datatypes/dataproviders/external.py index 888fe2a3905..f932656ff4e 100644 --- a/lib/galaxy/datatypes/dataproviders/external.py +++ b/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() diff --git a/lib/galaxy/jobs/runners/state_handlers/_safe_eval.py b/lib/galaxy/jobs/runners/state_handlers/_safe_eval.py index de68e599d35..59d93e78221 100644 --- a/lib/galaxy/jobs/runners/state_handlers/_safe_eval.py +++ b/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): diff --git a/lib/galaxy/jobs/runners/tasks.py b/lib/galaxy/jobs/runners/tasks.py index 5362e7254f0..b3685abeeab 100644 --- a/lib/galaxy/jobs/runners/tasks.py +++ b/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): """ diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py index b9730131b33..a1dd075ffd8 100644 --- a/lib/galaxy/model/metadata.py +++ b/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) diff --git a/lib/galaxy/objectstore/azure_blob.py b/lib/galaxy/objectstore/azure_blob.py index 4afd8751eb7..c3e12a7bd89 100644 --- a/lib/galaxy/objectstore/azure_blob.py +++ b/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) diff --git a/lib/galaxy/objectstore/pulsar.py b/lib/galaxy/objectstore/pulsar.py index 61ca8209fb8..d7d1e8b7cff 100644 --- a/lib/galaxy/objectstore/pulsar.py +++ b/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: diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index 4c82a359d28..10d91cc8e0b 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/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'))] diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py index 069960f87c9..f4734b7240e 100644 --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/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, diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py index d62f9cbde37..e305bfb8e59 100644 --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -116,7 +116,6 @@ class RepositoryGrid(grids.Grid): rev_label, rev_date = option_items.split(' ') rev_date = '%s' % rev_date return '%s %s' % (rev_label, rev_date) - return select_field.options[0][0] return '' class LatestInstallableRevisionColumn(grids.GridColumn):