hello galaxy-community,

we stored a lot of peak-information in a database. to import these files into galaxy, i read the DataConnectionProtocol (https://bitbucket.org/galaxy/galaxy-central/wiki/DataSources) and i also took a look at the biomart.xml example

(https://bitbucket.org/galaxy/galaxy-dist/src/8729d2e29b02/tools/data_source/biomart.xml).

biomart does exactly what i want. 

here is my full tool configuration xml-file:

content of http://localhost:8888/index.html:

i also tried a different action="http://galaxy/tool_runner?tool_id=regionDb&type=text&name=new%20history%20entry&URL=http://localhost:8888/getfile.php" with the same error message (shown below).

what actually works is, if i try to receive biomart data with this request.

my question is: was there some extra hack to get the biomart tool to run? i found some lines in the lib/galaxy/web/controllers/tool_runner.py  which confirm that assumption:

    #Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back

    @web.expose

    def biomart(self, trans, tool_id='biomart', **kwd):

        """Catches the tool id and redirects as needed"""

        return self.index(trans, tool_id=tool_id, **kwd)

Server Error

URL: http://galaxy/tool_runner/regionDb?type=text&name=new%20history%20entry&URL=http://localhost:8888/getfile.php
Module paste.exceptions.errormiddleware:143 in __call__
>>  app_iter = self.application(environ, start_response)
Module paste.debug.prints:98 in __call__
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:109 in __call__
>>  return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:145 in __call__
>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.tool_runner:27 in regionDb
>>  return self.index(trans, tool_id=tool_id, **kwd)
Module galaxy.web.controllers.tool_runner:75 in index
>>  template, vars = tool.handle_input( trans, params.__dict__ )
Module galaxy.tools:933 in handle_input
>>  _, out_data = self.execute( trans, incoming=params )
Module galaxy.tools:1225 in execute
>>  return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history )
Module galaxy.tools.actions:291 in execute
>>  wrap_values( tool.inputs, params )
Module galaxy.tools.actions:154 in wrap_values
>>  input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming )
KeyError: 'GALAXY_URL'
extra data