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Properly handle subdirectory collection in a job output's extra_files_path.

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This commit is contained in:
Nate Coraor
2013-02-19 10:07:14 -05:00
parent dde00ed000
commit fa73c2108e
1 changed files with 15 additions and 8 deletions
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lib/galaxy/tools/__init__.py
+15 -8
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@@ -2635,19 +2635,26 @@ class Tool( object ):
"""
for name, hda in output.items():
temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) )
extra_dir = None
try:
a_files = os.listdir( temp_file_path )
if len( a_files ) > 0:
for f in a_files:
# This skips creation of directories - object store
# automatically creates them. However, empty directories will
# not be created in the object store at all, which might be a
# problem.
for root, dirs, files in os.walk( temp_file_path ):
extra_dir = root.replace(job_working_directory, '', 1).lstrip(os.path.sep)
for f in files:
self.app.object_store.update_from_file(hda.dataset,
extra_dir="dataset_%d_files" % hda.dataset.id,
extra_dir=extra_dir,
alt_name = f,
file_name = os.path.join(temp_file_path, f),
file_name = os.path.join(root, f),
create = True,
preserve_symlinks = True )
# Clean up after being handled by object store.
# FIXME: If the object (e.g., S3) becomes async, this will
# cause issues so add it to the object store functionality?
# Clean up after being handled by object store.
# FIXME: If the object (e.g., S3) becomes async, this will
# cause issues so add it to the object store functionality?
if extra_dir is not None:
# there was an extra_files_path dir, attempt to remove it
shutil.rmtree(temp_file_path)
except Exception, e:
log.debug( "Error in collect_associated_files: %s" % ( e ) )