1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4b3fefa396cf/ changeset: 4b3fefa396cf user: natefoo date: 2011-08-26 21:59:29 summary: Fix uploading sorted BAMs to libraries when using the link method rather than copying. affected #: 1 file (36 bytes)
--- a/tools/data_source/upload.py Fri Aug 26 15:53:16 2011 -0400 +++ b/tools/data_source/upload.py Fri Aug 26 15:59:29 2011 -0400 @@ -297,7 +297,7 @@ 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 @@ 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 ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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