It is not easy...
I think it is in this :
if dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only ==
> # Never alter a file that will not be copied to Galaxy's local file
> 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 )
In fact, I have to say that the file does not diseappear. The file is still
existing, but it is* empty* and it is occur only when the owner of the file
is the same that the galaxy user (the galaxy service is running under galaxy
Where can i find the dataset class ?
Perhaps, the operation does not work and there is a link with this stuff :
2011/9/2 Nate Coraor <n...@bx.psu.edu>
> remy d1 wrote:
> > Hi,
> > We found a little problem in the new galaxy release. When we upload a
> > dataset library from filesystem :
> > Admin > Manage data libraries > create new data library > Add dataset >
> > Upload files from filesystem path > Link to files without copying
> > If galaxy user is the owner of this file or if he has write permission on
> > (on the filesystem), the file is deleted !!
> > I do not think it is the normal behaviour...
> Hi Remy,
> I'm unable to duplicate this behavior. Would it be possible for you to
> do some debugging on your end to determine when this is happening? If
> it's Galaxy's code it would probably be somewhere in
> > Regards.
> > ___________________________________________________________
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