From olivia.doppelt@pasteur.fr Mon Feb 24 05:36:03 2014 From: Olivia Doppelt-Azeroual To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] bioblend problem trying to use run_tool function Date: Mon, 24 Feb 2014 11:36:02 +0100 Message-ID: <530B2092.3060502@pasteur.fr> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============8552322640838998316==" --===============8552322640838998316== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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 giLocal.tools.run_tool(history_id=3D'0a248a1f62a0cc04',tool_id=3D'export',too= l_inputs=3Dtool_inputs_loc) File=20 "/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galax= y/tools/__init__.py",=20 line 26, in run_tool return Client._post(self, payload) File=20 "/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galax= y/client.py",=20 line 181, in _post r =3D self.gi.make_post_request(url, payload=3Dpayload,=20 files_attached=3Dfiles_attached) File=20 "/home/odoppelt/localStuff_VM/galaxy_work/SBW_project/bioblend/bioblend/galax= yclient.py",=20 line 94, in make_post_request r.status_code, body=3Dr.text) # @see self.body for HTTP response body bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy:=20 500: Internal Server Error

Internal Server Error

The server has either erred or is incapable of performing the requested operation.

WSGI Server
_____________________________________________________________________________= ______________ I'm currently trying to understand this error. Please tell me if you=20 know anything about this error. Have a nice day, --=20 Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur Le 21/02/14 15:49, John Chilton a =C3=A9crit : > 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=3Dc23d8cb986719118133050517= 10d4ae1 > Module galaxy.web.framework.middleware.error:149 in __call__ >>> app_iter =3D 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 =3D method( trans, **kwargs ) > Module galaxy.web.framework:201 in decorator >>> log.exception( 'Uncaught exception in exposed API method:'+ str(err),ex= c_info=3DTrue) > 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=3DTrue) > > 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 > 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=3D'xxxxxxxxxxx',tool_id=3D'yyyyyyyy/exp= ort_data/export/2.2',tool_inputs=3D{'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 >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ --===============8552322640838998316==--