Hello Nate,

It is not easy...

I think it is in this :

    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( 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 )
>
>             return
>
>
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
user too).

Where can i find the dataset class ?

Perhaps, the operation does not work and there is a link with this stuff :

http://bytes.com/topic/python/answers/26169-shutil-move-error-errno-17-file-exists-win32

 - Regards

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
> it
> > (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
> tools/data_source/upload.py
>
> --nate
>
> >
> >
> > Regards.
>
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