From 8f195588c900beb165d09462dc3cf00a459daf0d Mon Sep 17 00:00:00 2001 From: dannon Date: Sat, 14 Mar 2015 15:31:06 -0400 Subject: [PATCH] Cleanup while looking for objectstore bug. --- lib/galaxy/objectstore/__init__.py | 27 +++++++-------------------- lib/galaxy/objectstore/rods.py | 9 +-------- 2 files changed, 8 insertions(+), 28 deletions(-) diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py index 528193e8f81..486bf174a17 100644 --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/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): @@ -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 diff --git a/lib/galaxy/objectstore/rods.py b/lib/galaxy/objectstore/rods.py index 4b814d55d0e..4754156ad5b 100644 --- a/lib/galaxy/objectstore/rods.py +++ b/lib/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 )