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:
<tool id="regionDb" name="RegionDb-Import">
  <description>Import from regionDb</description>
  <command interpreter="python">../data_source/data_source.py $output 
$__app__.config.output_size_limit</command>
  <inputs action="http://localhost:8888/index.html"; check_values="false" 
method="get">
          <display>Display-Text</display>
      <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
      <param name="tool_id" type="hidden" value="regionDb" />
  </inputs>
  <request_param_translation>
          <request_param galaxy_name="URL" remote_name="URL" missing=""/>
          <request_param galaxy_name="URL_method" remote_name="URL_method" 
missing="get" />
          <request_param galaxy_name="name" remote_name="name" missing="Biomart 
test query" />
  </request_param_translation>
  <outputs>
    <data name="regionDb File" format="bed" label="regionDb import" />
  </outputs>
  
  <help>        
**What it does**

        import ...
  </help>
</tool>


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

<form method="POST" type="text" 
action="http://galaxy/tool_runner/regionDb?type=text&name=new%20history%20entry&URL=http://localhost:8888/getfile.php";
 >
 <input type="submit" value="Send to Galaxy"/>
</form>

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.
                <form method="POST" type="text" 
action="http://gen43/galaxy/tool_runner/biomart?type=text&name=ne%20history%20entry&URL=http://www.biomart.org/biomart/martview/4905f90905e8f4b362a96b887cc7c452?do_export=1&resultsButton=1";
 >
                 <input type="submit" value="Send to Galaxy"/>
                </form>


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

CGI Variables
CONTENT_LENGTH  '-1'
CONTENT_TYPE    'application/x-www-form-urlencoded'
HTTP_ACCEPT     
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_CHARSET     'ISO-8859-1,utf-8;q=0.7,*;q=0.7'
HTTP_ACCEPT_ENCODING    'gzip,deflate'
HTTP_ACCEPT_LANGUAGE    'en-us,en;q=0.5'
HTTP_CONNECTION         'Keep-Alive'
HTTP_COOKIE     
'galaxysession=c6ca0ddb55be603af8ffade046cb8ca7fe7a18f326db29b947c846a3b24831e1362e15c491e90b43'
HTTP_HOST       'gen43'
HTTP_REFERER    
'http://localhost:8888/index2.php?GALAXY_URL=http%3A//gen43/galaxy/tool_runner&tool_id=regionDb'
HTTP_REMOTE_USER        'perdac...@genau.at'
HTTP_USER_AGENT         'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; 
rv:1.9.2.3) Gecko/20100401 Firefox/3.6.3'
HTTP_VIA        '1.1 gen43.imp.univie.ac.at'
PATH_INFO       '/tool_runner/regionDb'
QUERY_STRING    
'type=text&name=new%20history%20entry&URL=http://localhost:8888/getfile.php'
REMOTE_ADDR     '10.42.111.27'
REQUEST_METHOD  'POST'
SCRIPT_NAME     '/galaxy'
SERVER_NAME     'gen43.imp.univie.ac.at'
SERVER_PORT     '9191'
SERVER_PROTOCOL         'HTTP/1.1'

Configuration
__file__        
'/projects/solexadst/serverData/galaxy-devel/universe_wsgi.webapp.ini'
admin_users     'ta...@genau.at'
apache_xsendfile        'False'
brand   'GenAu-Epx Development!!!'
cookie_path     '/galaxy'
debug   'TRUE'
enable_api      'True'
enable_job_running      'False'
enable_pages    'True'
here    '/projects/solexadst/serverData/galaxy-devel'
log_level       'DEBUG'
new_user_dataset_access_role_default_private    'True'
remote_user_logout_href         '/logout'
remote_user_maildomain  'genau.at'
require_login   'True'
set_metadata_externally         'True'
static_cache_time       '360'
static_dir      '/projects/solexadst/serverData/galaxy-devel/static/'
static_enabled  'True'
static_favicon_dir      
'/projects/solexadst/serverData/galaxy-devel/static/favicon.ico'
static_images_dir       
'/projects/solexadst/serverData/galaxy-devel/static/images'
static_scripts_dir      
'/projects/solexadst/serverData/galaxy-devel/static/scripts/'
static_style_dir        
'/projects/solexadst/serverData/galaxy-devel/static/june_2007_style/blue'
upstream_gzip   'False'
use_interactive         'False'
use_remote_user         'True'

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to