George, David wrote:
> Hi,
> 
>  
> 
> I'm a Galaxy and Python newbie and I'm working on project that desires
> to upload files from a directory to the Galaxy server.  We'd like to
> physically copy the files rather than maintain references to them.
> 
>  
> 
> I'm starting by following the examples in scripts/api/README.  All the
> display and library_create_library examples work.  However, the
> library_upload_from_import_dir fails.  In my universe...ini,
> library_import_dir is defined to be /home/dgeorge/galaxy/import and
> there is a bed directory under that with a short file, bed1.bed in the
> correct format.  I'm not sure what to provide for the last parameter,
> the dbkey - maybe that's my problem?

Hi David,

Sorry for the delay in response, we're just getting back into gear
post-conference.

Your dbkey (hg19) should be fine, so I doubt that's the issue.

>   I ran:
> 
>  
> 
> ./library_upload_from_import_dir.py 59d2fd4e020e178f8c48e61150e513c2
> http://localhost:8080/api/libraries/f597429621d6eb2b/contents
> c6ca0ddb55be603a10e891fff2e902c3 bed bed hg19
> 
>  
> 
> And I get the error:
> 
>  
> 
> Exception happened during processing of request from ('127.0.0.1',
> 38857)
> 
> Traceback (most recent call last):
> 
>   File
> "/home/dgeorge/galaxy/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/http
> server.py", line 1053, in process_request_in_thread
> 
>     self.finish_request(request, client_address)
> 
>   File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request
> 
>     self.RequestHandlerClass(request, client_address, self)
> 
>   File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__
> 
>     self.finish()
> 
>   File "/usr/lib/python2.6/SocketServer.py", line 661, in finish
> 
>     self.wfile.flush()
> 
>   File "/usr/lib/python2.6/socket.py", line 297, in flush
> 
>     self._sock.sendall(buffer(data, write_offset, buffer_size))
> 
> error: [Errno 32] Broken pipe

This will happen fairly often with an interrupted connection and can
usually be ignored.  Does this happen every time you try the upload
script?  Have you checked to see if the file has been uploaded anyway?

Is there any output from the script on the command line?  It should
print the response of the POST.

Thanks,
--nate

> 
>  
> 
> Any ideas or suggestions?
> 
>  
> 
> Thanks!
> 
>  
> 
> David George
> 
> Staff Software Engineer
> 
> Illumina, Inc.
> 
> 25861 Industrial Blvd.
> 
> Hayward, CA 94545
> 
> Tel:  510-670-9326
> 
> Fax:  510-670-9302
> 
> Email:  dgeo...@illumina.com <mailto:dgeo...@illumina.com> 
> 
>  
> 

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