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
> ___________________________________________________________
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



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