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Fix uploading sorted BAMs to libraries when using the link method rather than copying.

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This commit is contained in:
Nate Coraor
2011-08-26 15:59:29 -04:00
parent 19ed039b6c
commit 7d8b701df6
1 changed files with 2 additions and 2 deletions
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tools/data_source/upload.py
+2 -2
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@@ -297,7 +297,7 @@ def add_file( dataset, registry, json_file, output_path ):
datatype = registry.get_datatype_by_extension( ext )
if dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only == 'link_to_files':
# Never alter a file that will not be copied to Galaxy's local file store.
if datatype.dataset_content_needs_grooming( output_path ):
if datatype.dataset_content_needs_grooming( dataset.path ):
err_msg = 'The uploaded files need grooming, so change your <b>Copy data into Galaxy?</b> selection to be ' + \
'<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.'
file_err( err_msg, dataset, json_file )
@@ -324,7 +324,7 @@ def add_file( dataset, registry, json_file, output_path ):
name = dataset.name,
line_count = line_count )
json_file.write( to_json_string( info ) + "\n" )
if datatype.dataset_content_needs_grooming( output_path ):
if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ):
# Groom the dataset content if necessary
datatype.groom_dataset_content( output_path )
def add_composite_file( dataset, registry, json_file, output_path, files_path ):