Question: Toolbox filters problem
0
gravatar for fiebig
19 months ago by
fiebig30
fiebig30 wrote:

Hello,

I intentended to use the toolbox filters in my local galaxy instance v. 16.04. To get a first impression, I did the following:

  1. Read the documention
  2. uncommented the "user_tool_filters*" lines in the galaxy.ini
  3. moved lib/galaxy/tools/toolbox/filters/examples.py.sample to examples.py

When I tried to apply the filters in Users->Preferencees->Manage Toolbox Filters it got the following error:

"Error - <type 'exceptions.importerror'="">: No module named examples

URL: http://vm-113.de:8080/user/toolbox_filters?cntrller=user sys.path: [ '/opt/galaxy/scripts', enter code here '/opt/galaxy/lib', enter code here '/opt/galaxy/.venv/lib64/python27.zip', '/opt/galaxy/.venv/lib64/python2.7', '/opt/galaxy/.venv/lib64/python2.7/plat-linux2', '/opt/galaxy/.venv/lib64/python2.7/lib-tk', '/opt/galaxy/.venv/lib64/python2.7/lib-old', '/opt/galaxy/.venv/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7', '/usr/lib/python2.7', '/opt/galaxy/.venv/lib/python2.7/site-packages'] File '/opt/galaxy/lib/galaxy/web/framework/middleware/error.py', line 151 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/opt/galaxy/lib/galaxy/web/framework/base.py', line 131 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, *kwargs ) File '/opt/galaxy/lib/galaxy/web/framework/decorators.py', line 65 in decorator return func( self, trans, *args, *kwargs ) File '/opt/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', line 1331 in toolbox_filters tool_filters = get_filter_mapping( saved_user_tool_filters, trans.app.config.user_tool_filters ) File '/opt/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', line 1284 in get_filter_mapping module = __import__( module_name, globals(), fromlist=['temp_module'] )

ImportError: No module named examples"

What did I miss? How can I fix the problem? Any help is welcome.

Regards, Anne

galaxy • 496 views
ADD COMMENTlink modified 19 months ago by Dannon Baker3.7k • written 19 months ago by fiebig30

What happens if the server is restarted?

ADD REPLYlink written 19 months ago by Jennifer Hillman Jackson23k

unfortunately, the message stays the same.

ADD REPLYlink written 19 months ago by fiebig30

Hi Anne

Try moving "examples.py" to lib/galaxy/tools/filters/ (and restart again)

see also: https://wiki.galaxyproject.org/UserDefinedToolboxFilters#For_Administrators

Regards, Hans-Rudolf

ADD REPLYlink written 19 months ago by Hotz, Hans-Rudolf1.7k

Hello Hans,

bingo, that does the the trick. Thank you! Just a little remark for a more user-friendly "documentation". In the galaxy.ini script there is a line: "user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode", but my examples.py(.samples) does not contain a definition for "restrict_encode" and therefore complains about the missing module. Ok, this is a quite obvious issue to solve, but I think it would be helpful to bring bring back the example from the wiki or adjust the galaxy.ini file accordingly.

The thread can be closed :)

ADD REPLYlink written 19 months ago by fiebig30
2
gravatar for Dannon Baker
19 months ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

I see you worked around this issue with the help of Hans-Rudolf given above, but a more permanent fix can be found in the second commit here:

https://github.com/galaxyproject/galaxy/pull/2499

Thanks for reporting the error!

ADD COMMENTlink written 19 months ago by Dannon Baker3.7k

Thanks for your affords, Dannon.

ADD REPLYlink written 19 months ago by fiebig30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 130 users visited in the last hour