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.doppelt@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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