Yes, the get_intial_value bug was a bug that has been fixed in a
recent Galaxy release (I think the most recent one, but maybe the
previous one). Unfortunately though, I fixed other bugs related to
running more sophisticated tools through the API at the same time - so
I would again strongly recommend upgrading before proceeding or you
going to find all the same bugs I did. The tool running API has
significantly improved over the last couple releases.

As for removing the dumps statement in bioblend - I think (though am
not certain) that is the wrong thing to do. I think you are likely
somehow doing this at a level above the client call and shouldn't be -
i.e. my guess is you are passing in a string instead of a dictionary
and the result is that dumps it dumping an escaped string - instead of
jsonifing a dictionary.

For instance, the API driven test framework runs by calling this API
and does almost this exact dumps.

https://bitbucket.org/galaxy/galaxy-central/src/f573461f3667e8f120dc05bbd11a019d5fae1960/test/base/interactor.py?at=default#cl-251

Hope this helps.

-John


On Mon, Feb 24, 2014 at 8:51 AM, Olivia Doppelt-Azeroual
<olivia.dopp...@pasteur.fr> wrote:
> I detected another problem which enables me to go further, however doesn't
> resolve the whole problem yet.
>
> the function get_initial value didn't use the history in the recursive call,
> which led to an empty history. I changed it juste adding history to the
> input.get_initial_value
>
>  def get_initial_value( self, trans, context, history=None ):
>         rval = []
>         for i in range( self.default ):
>             rval_dict = { '__index__': i}
>             for input in self.inputs.itervalues():
>                 rval_dict[ input.name ] = input.get_initial_value( trans,
> context, history )
>             rval.append( rval_dict )
>         return rval
>
> There is another problem though.
>
> On the bioblend side:
> _____________________________________________
> 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={'input':'8ad39366bdad8699','name':"data"})
>
>   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:
> 400: {
>     "message": {
>         "data": {
>             "inputs": [
>                 {
>                     "input": "History does not include a dataset of the
> required format / build"
>                 }
>             ]
>         },
>         "type": "error"
>     }
> }
>
> On the galaxy side, there is no error message.
>
> Sorry for the many mails but I prefer to keep you updated so you don"t waste
> time.
>
> --
> Olivia
>
>
> Le 24/02/14 15:29, Olivia Doppelt-Azeroual a écrit :
>
> 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
>
>
> ___________________________________________________________
> 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/
>
>
>
>
>
>
>
> --
> Olivia Doppelt-Azeroual, PhD
> Tel: 92 15
> CIB - Institut Pasteur

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