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When uploading compressed files to a data library, remove the compressed file extension only if copying files into Galaxy's file store.

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This commit is contained in:
Greg Von Kuster
2012-01-20 10:26:54 -05:00
parent a29eb66d87
commit 7e7cf3edbe
1 changed files with 8 additions and 6 deletions
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lib/galaxy/web/controllers/library_common.py
+8 -6
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@@ -1052,14 +1052,17 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
trans.sa_session.flush()
return output
def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ):
link_data_only = params.get( 'link_data_only', 'copy_files' )
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
# Remove compressed file extensions, if any
new_name = name
if new_name.endswith( '.gz' ):
new_name = new_name.rstrip( '.gz' )
elif new_name.endswith( '.zip' ):
new_name = new_name.rstrip( '.zip' )
# Remove compressed file extensions, if any, but only if
# we're copying files into Galaxy's file space.
if link_data_only == 'copy_files':
if new_name.endswith( '.gz' ):
new_name = new_name.rstrip( '.gz' )
elif new_name.endswith( '.zip' ):
new_name = new_name.rstrip( '.zip' )
uploaded_dataset.name = new_name
uploaded_dataset.path = path
uploaded_dataset.type = type
@@ -1070,7 +1073,6 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
if in_folder:
uploaded_dataset.in_folder = in_folder
uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch )
link_data_only = params.get( 'link_data_only', 'copy_files' )
uploaded_dataset.link_data_only = link_data_only
if link_data_only == 'link_to_files':
uploaded_dataset.data.file_name = os.path.abspath( path )