Hello John,

Yes it helps a little but I still have the following error:
_______________________________________________________________________
Traceback (most recent call last):
  File "script_testBioblend_distant.py", line 16, in <module>
giLocal.tools.run_tool(history_id='0a248a1f62a0cc04',tool_id='export',tool_inputs=tool_inputs_loc)
File "/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxy/tools/__init__.py", line 26, in run_tool
    return Client._post(self, payload)
File "/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxy/client.py", line 181, in _post r = self.gi.make_post_request(url, payload=payload, files_attached=files_attached) File "/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galaxyclient.py", line 94, in make_post_request
    r.status_code, body=r.text)     # @see self.body for HTTP response body
bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 500: <html>
  <head><title>Internal Server Error</title></head>
  <body>
    <h1>Internal Server Error</h1>
    <p>The server has either erred or is incapable of performing
the requested operation.

<br/>
<!--  --></p>
    <hr noshade>
    <div align="right">WSGI Server</div>
  </body>
</html>
___________________________________________________________________________________________

I'm currently trying to understand this error. Please tell me if you know anything about this error.

Have a nice day,

--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur




Le 21/02/14 15:49, John Chilton a écrit :
I copied the HTML into a new document, opened it, and copied the
stacktrace produced by Galaxy - it looks like this:

Internal Server Error

Galaxy was unable to successfully complete your request

URL: http://galaxy.web.pasteur.fr/api/tools?key=c23d8cb98671911813305051710d4ae1
Module galaxy.web.framework.middleware.error:149 in __call__
  app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:96 in __call__
  return self.app( environ, start_response )
Module paste.httpexceptions:633 in __call__
  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
  body = method( trans, **kwargs )
Module galaxy.web.framework:201 in decorator
  log.exception( 'Uncaught exception in exposed API method:'+ 
str(err),exc_info=True)
TypeError: exception() got an unexpected keyword argument 'exc_info'


So what is happening here is and error is occurring when Galaxy is
trying to log another error - causing the API to break down. I don't
think the newest release of Galaxy has this line:

log.exception( 'Uncaught exception in exposed API method:'+
str(err),exc_info=True)

I am not sure what exc_info is - but it looks like it shouldn't be
there. You may want to remove that and see if you get a cleaner error
message that is easier to interpret.

Hope this helps.

-John


On Fri, Feb 21, 2014 at 3:50 AM, Olivia Doppelt
<olivia.dopp...@pasteur.fr> wrote:
Dear Developers,

I would like to use bioblend to export the result of a galaxy workflow.

To do that, we want to use an implemented tool called export_data; which
enables the copy of a result file from galaxy arborescence to a local
directory which belong to the user making the analysis and the export.

We tried to launch this tool using the run_tool function but it doesn't
work.


giOlivia.tools.run_tool(history_id='xxxxxxxxxxx',tool_id='yyyyyyyy/export_data/export/2.2',tool_inputs={'input':'id_data','name':"data"})

I get an error message which is very long and attached to this email.

Please help me on that it is the final step of several ones using bioblend.

Have a nice day,

--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur


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