Yes, indeed,

the log from galaxy are the following:

The first error was due to the fact that bioblend function run_tools; gave galaxy a dump of the input_dicts which type is string where galaxy was waiting for an item structure.
I removed the dump:

        payload["inputs"] = tool_inputs
instead of
        payload["inputs"] = dumps(tool_inputs)


However, there is another error afterwards which is:


___________________________________________________________________

/home/odoppelt/localStuff_VM/tools/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.

galaxy.web.framework ERROR 2014-02-24 15:15:15,374 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 203, in decorator
    rval = func( self, trans, *args, **kwargs)
File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py", line 123, in create template, vars = tool.handle_input( trans, params.__dict__, history=target_history ) File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/__init__.py", line 1921, in handle_input
    state = self.new_state( trans, history=history )
File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/__init__.py", line 1846, in new_state
    self.fill_in_new_state( trans, inputs, state.inputs, history=history )
File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/__init__.py", line 1855, in fill_in_new_state state[ input.name ] = input.get_initial_value( trans, context, history=history ) File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/parameters/grouping.py", line 116, in get_initial_value
    rval_dict[ input.name ] = input.get_initial_value( trans, context )
File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1657, in get_initial_value return self.get_initial_value_from_history_prevent_repeats(trans, context, None, history=history); File "/home/odoppelt/localStuff_VM/tools/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1670, in get_initial_value_from_history_prevent_repeats
    assert history is not None, "DataToolParameter requires a history"
AssertionError: DataToolParameter requires a history
127.0.0.1 - - [24/Feb/2014:15:15:15 +0200] "POST /api/tools?key=cd065330048989af4ae266cf94685e6b HTTP/1.1" 500 - "-" "python-requests/2.0.1 CPython/2.7.5+ Linux/3.11.0-15-generic"

___________________________________________________________________

Thanks for your help,

Olivia Doppelt-Azeroual

Le 24/02/14 15:21, John Chilton a écrit :
Hard to infer much from this, usually when I get this error there is a
full stack trace for this error in the Galaxy logs giving some
indication what went wrong.

-John

On Mon, Feb 24, 2014 at 4:36 AM, Olivia Doppelt-Azeroual
<olivia.dopp...@pasteur.fr> wrote:
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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--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur

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