link file bug in the new version
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... Regards.
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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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-... - Regards 2011/9/2 Nate Coraor <nate@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.
___________________________________________________________ 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:
remy d1 wrote:
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).
Hi Remy, I still can't duplicate this. Is it with a specific file type (and are you setting the file type explicitly, or using auto-detection)?
Where can i find the dataset class ?
The datatypes are defined in galaxy-dist/lib/galaxy/datatypes/ --nate
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-...
- Regards
2011/9/2 Nate Coraor <nate@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.
___________________________________________________________ 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:
participants (2)
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Nate Coraor -
remy d1