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__
<<          try:
                __traceback_supplement__ = Supplement, self, environ
                app_iter = self.application(environ, start_response)
                return self.make_catching_iter(app_iter, environ)
            except:>>  app_iter = self.application(environ, start_response)
Module paste.debug.prints:98 in __call__
<<          try:
                status, headers, body = wsgilib.intercept_output(
                    environ, self.app)
                if status is None:
                    # Some error occurred
    >>  environ, self.app)
Module paste.wsgilib:539 in intercept_output
<<          data.append(headers)
            return output.write
        app_iter = application(environ, replacement_start_response)
        if data[0] is None:
            return (None, None, app_iter)>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
<<          environ['paste.recursive.script_name'] = my_script_name
            try:
                return self.application(environ, start_response)
            except ForwardRequestException, e:
                middleware = CheckForRecursionMiddleware(>>  return self.application(environ, start_response)
Module galaxy.web.framework.middleware.remoteuser:109 in __call__
<<                  """
                    return self.error( start_response, title, message )
                return self.app( environ, start_response )
            elif path_info.startswith( '/api/' ):
                # The API handles its own authentication via keys>>  return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__
<<                             []).append(HTTPException)
            try:
                return self.application(environ, start_response)
            except HTTPException, exc:
                return exc(environ, start_response)>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:145 in __call__
<<          kwargs.pop( '_', None )
            try:
                body = method( trans, **kwargs )
            except Exception, e:
                body = self.handle_controller_exception( e, trans, **kwargs )>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.tool_runner:27 in regionDb
<<      def regionDb(self, trans, tool_id='regionDb', **kwd):
            """Catches the tool id and redirects as needed"""
            return self.index(trans, tool_id=tool_id, **kwd)
   
        #Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back
    >>  return self.index(trans, tool_id=tool_id, **kwd)
Module galaxy.web.controllers.tool_runner:75 in index
<<          # so make sure to create a new history if we've never had one before.
            history = trans.get_history( create=True )
            template, vars = tool.handle_input( trans, params.__dict__ )
            if len(params) > 0:
                trans.log_event( "Tool params: %s" % (str(params)), tool_id=tool_id )>>  template, vars = tool.handle_input( trans, params.__dict__ )
Module galaxy.tools:933 in handle_input
<<              # If we've completed the last page we can execute the tool
                elif state.page == self.last_page:
                    _, out_data = self.execute( trans, incoming=params )
                    try:
                        assert isinstance( out_data, odict )>>  _, out_data = self.execute( trans, incoming=params )
Module galaxy.tools:1225 in execute
<<          when run will build the tool's outputs, e.g. `DefaultToolAction`.
            """
            return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history )
           
        def params_to_strings( self, params, app ):>>  return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history )
Module galaxy.tools.actions:291 in execute
<<                          #     <data format="input" name="output" label="Blat on ${<input_param>.name}" />
                            # </outputs>
                            wrap_values( tool.inputs, params )
                        #tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined
                        params['tool'] = tool>>  wrap_values( tool.inputs, params )
Module galaxy.tools.actions:154 in wrap_values
<<                      input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming )
                    else:
                        input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming )
           
            # Set history.>>  input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming )
KeyError: 'GALAXY_URL'
extra data