diff --git a/galaxy/objectstore/__init__.py b/galaxy/objectstore/__init__.py
index 528193e8f819658243386b5ac5d64481705fc285..5cd54c18707b498eb2508966a5897b6d62bc3566 100644
--- a/galaxy/objectstore/__init__.py
+++ b/galaxy/objectstore/__init__.py
@@ -174,15 +174,6 @@ class ObjectStore(object):
"""
raise NotImplementedError()
- ## def get_staging_command( id ):
- ## """
- ## Return a shell command that can be prepended to the job script to stage the
- ## dataset -- runs on worker nodes.
- ##
- ## Note: not sure about the interface here. Should this return a filename, command
- ## tuple? Is this even a good idea, seems very useful for S3, other object stores?
- ## """
-
class DiskObjectStore(ObjectStore):
"""
@@ -206,7 +197,7 @@ class DiskObjectStore(ObjectStore):
self.check_old_style = config.object_store_check_old_style
self.extra_dirs['job_work'] = config.job_working_directory
self.extra_dirs['temp'] = config.new_file_path
- #The new config_xml overrides universe settings.
+ # The new config_xml overrides universe settings.
if config_xml is not None:
for e in config_xml:
if e.tag == 'files_dir':
@@ -343,8 +334,8 @@ class DiskObjectStore(ObjectStore):
def update_from_file(self, obj, file_name=None, create=False, **kwargs):
""" `create` parameter is not used in this implementation """
preserve_symlinks = kwargs.pop( 'preserve_symlinks', False )
- #FIXME: symlinks and the object store model may not play well together
- #these should be handled better, e.g. registering the symlink'd file as an object
+ # FIXME: symlinks and the object store model may not play well together
+ # these should be handled better, e.g. registering the symlink'd file as an object
if create:
self.create(obj, **kwargs)
if file_name and self.exists(obj, **kwargs):
@@ -354,8 +345,7 @@ class DiskObjectStore(ObjectStore):
else:
shutil.copy( file_name, self.get_filename( obj, **kwargs ) )
except IOError, ex:
- log.critical('Error copying %s to %s: %s' % (file_name,
- self._get_filename(obj, **kwargs), ex))
+ log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex))
raise ex
def get_object_url(self, obj, **kwargs):
@@ -392,39 +382,39 @@ class NestedObjectStore(ObjectStore):
super(NestedObjectStore, self).shutdown()
def exists(self, obj, **kwargs):
- return self.__call_method('exists', obj, False, False, **kwargs)
+ return self._call_method('exists', obj, False, False, **kwargs)
def file_ready(self, obj, **kwargs):
- return self.__call_method('file_ready', obj, False, False, **kwargs)
+ return self._call_method('file_ready', obj, False, False, **kwargs)
def create(self, obj, **kwargs):
random.choice(self.backends.values()).create(obj, **kwargs)
def empty(self, obj, **kwargs):
- return self.__call_method('empty', obj, True, False, **kwargs)
+ return self._call_method('empty', obj, True, False, **kwargs)
def size(self, obj, **kwargs):
- return self.__call_method('size', obj, 0, False, **kwargs)
+ return self._call_method('size', obj, 0, False, **kwargs)
def delete(self, obj, **kwargs):
- return self.__call_method('delete', obj, False, False, **kwargs)
+ return self._call_method('delete', obj, False, False, **kwargs)
def get_data(self, obj, **kwargs):
- return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs)
+ return self._call_method('get_data', obj, ObjectNotFound, True, **kwargs)
def get_filename(self, obj, **kwargs):
- return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
+ return self._call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
def update_from_file(self, obj, **kwargs):
if kwargs.get('create', False):
self.create(obj, **kwargs)
kwargs['create'] = False
- return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
+ return self._call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
def get_object_url(self, obj, **kwargs):
- return self.__call_method('get_object_url', obj, None, False, **kwargs)
+ return self._call_method('get_object_url', obj, None, False, **kwargs)
- def __call_method(self, method, obj, default, default_is_exception, **kwargs):
+ def _call_method(self, method, obj, default, default_is_exception, **kwargs):
"""
Check all children object stores for the first one with the dataset
"""
@@ -432,8 +422,7 @@ class NestedObjectStore(ObjectStore):
if store.exists(obj, **kwargs):
return store.__getattribute__(method)(obj, **kwargs)
if default_is_exception:
- raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s'
- % ( method, str( obj ), str( kwargs ) ) )
+ raise default( 'objectstore, _call_method failed: %s on %s, kwargs: %s' % ( method, str( obj ), str( kwargs ) ) )
else:
return default
@@ -527,21 +516,19 @@ class DistributedObjectStore(NestedObjectStore):
try:
obj.object_store_id = random.choice(self.weighted_backend_ids)
except IndexError:
- raise ObjectInvalid( 'objectstore.create, could not generate obj.object_store_id: %s, kwargs: %s'
- % ( str( obj ), str( kwargs ) ) )
+ raise ObjectInvalid( 'objectstore.create, could not generate obj.object_store_id: %s, kwargs: %s' % ( str( obj ), str( kwargs ) ) )
create_object_in_session( obj )
log.debug("Selected backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id))
else:
log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id))
self.backends[obj.object_store_id].create(obj, **kwargs)
- def __call_method(self, method, obj, default, default_is_exception, **kwargs):
+ def _call_method(self, method, obj, default, default_is_exception, **kwargs):
object_store_id = self.__get_store_id_for(obj, **kwargs)
if object_store_id is not None:
return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs)
if default_is_exception:
- raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s'
- % ( method, str( obj ), str( kwargs ) ) )
+ raise default( 'objectstore, _call_method failed: %s on %s, kwargs: %s' % ( method, str( obj ), str( kwargs ) ) )
else:
return default
diff --git a/galaxy/objectstore/rods.py b/galaxy/objectstore/rods.py
index 4b814d55d0e023cf5bf16d62befaf8936d57e2da..4754156ad5b5635e189c4e6ef81e47090002112c 100644
--- a/galaxy/objectstore/rods.py
+++ b/galaxy/objectstore/rods.py
@@ -89,9 +89,6 @@ class IRODSObjectStore( DiskObjectStore, ObjectStore ):
path = path_join( path, alt_name if alt_name else default_name )
path = path_join( self.root_collection_path, path )
-
- #log.debug( 'iRODS path for %s %s is %s', obj.__class__.__name__, obj.id, path )
-
return path
def __get_cache_path( self, obj, **kwargs ):
@@ -225,10 +222,6 @@ class IRODSObjectStore( DiskObjectStore, ObjectStore ):
@local_extra_dirs
def get_filename( self, obj, **kwargs ):
log.debug( "get_filename(): called on %s %s. For better performance, avoid this method and use get_data() instead.", obj.__class__.__name__, obj.id )
-
- # For finding all places where get_filename is called...
- #log.debug( ''.join( traceback.format_stack() ) )
-
cached_path = self.__get_cache_path( obj, **kwargs )
if not self.exists( obj, **kwargs ):
@@ -270,7 +263,7 @@ class IRODSObjectStore( DiskObjectStore, ObjectStore ):
# otherwise deal with this potential deadlock and interrupted
# transfers
time.sleep( 5 )
- log.debug( "get_filename(): waiting on incoming '%s' for %s %s", incoming_path, obj.__class__.__name__, obj.id )
+ log.debug( "get_filename(): waiting on incoming '%s' for %s %s", incoming_path, obj.__class__.__name__, obj.id )
return os.path.abspath( cached_path )