Hello Leandro, I believe this behavior is due to the make_library_uploaded_dataset() method in the ~/lib/galaxy/web/controllers/library_common controller. The current method looks like this: def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ): 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' ) uploaded_dataset.name = new_name uploaded_dataset.path = path uploaded_dataset.type = type uploaded_dataset.ext = None uploaded_dataset.file_type = params.file_type uploaded_dataset.dbkey = params.dbkey uploaded_dataset.space_to_tab = params.space_to_tab 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 ) # Since we are not copying the file into Galaxy's managed # default file location, the dataset should never be purgable. uploaded_dataset.data.dataset.purgable = False trans.sa_session.add_all( ( uploaded_dataset.data, uploaded_dataset.data.dataset ) ) trans.sa_session.flush() return uploaded_dataset Here are the code changes that I believe will resolve the issue. However, I have not tested this, so if you wouldn't mind letting me know if this works for you, I'll commit the changes to the central repo. 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() new_name = name # 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 uploaded_dataset.ext = None uploaded_dataset.file_type = params.file_type uploaded_dataset.dbkey = params.dbkey uploaded_dataset.space_to_tab = params.space_to_tab if in_folder: uploaded_dataset.in_folder = in_folder uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch ) uploaded_dataset.link_data_only = link_data_only if link_data_only == 'link_to_files': uploaded_dataset.data.file_name = os.path.abspath( path ) # Since we are not copying the file into Galaxy's managed # default file location, the dataset should never be purgable. uploaded_dataset.data.dataset.purgable = False trans.sa_session.add_all( ( uploaded_dataset.data, uploaded_dataset.data.dataset ) ) trans.sa_session.flush() return uploaded_dataset Thanks! Greg On Jan 20, 2012, at 7:42 AM, Leandro Hermida wrote:
Hello,
We've created a new binary datatype for .fastq.gz files following the same methodology as the BAM files since we don't want our fasta.gz files to be gunzipped. I added the appropriate code in upload.py to make sure of this. This new datatype and extension successfully does not gunzip our files. But when we upload it into a data library via the data library "Upload via filesystem paths" it for some reason automatically strips the .gz part out. When we take the same .fastq.gz file and upload it via Get Data -> Upload File it works fine, nothing is stripped from file name. Where is it doing this and how can prevent from stripping the .gz via the data library menus?
thanks, Leandro ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu