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: dgeorge@illumina.com <mailto:dgeorge@illumina.com>

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