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Merge branch 'dev' of github.com:dannon/galaxy into dev

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This commit is contained in:
Dannon Baker
2015-03-16 08:52:54 -04:00
parent a84740a4d4 8f195588c9
commit 05ece6f592
2 changed files with 8 additions and 28 deletions
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lib/galaxy/objectstore/__init__.py
+7 -20
View File
@@ -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):
@@ -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
@@ -527,8 +516,7 @@ 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:
@@ -540,8 +528,7 @@ class DistributedObjectStore(NestedObjectStore):
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
lib/galaxy/objectstore/rods.py
+1 -8
View File
@@ -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 )