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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