Test all installed tools


I’m migrating from galaxy 19.05 to 20.05.
It seems to be in a good way :grinning: .

I wanted to launch tests: tests that are defined in the XML.

I’ve tried (based on the results of ./run_tests.sh -list):
./run_tests.sh -id my_tool_id --external_url my_url --external_master_key my_master_key
But it ends (both with -id or -sid) with error:

    functional.test_toolbox_pytest.test_tool ... ERROR

    ERROR: functional.test_toolbox_pytest.test_tool
    Traceback (most recent call last):
      File "/softs/bioinfo/galaxy-dev/.venv/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
    TypeError: test_tool() missing 2 required positional arguments: 'testcases' and 'driver'

    Ran 1 test in 0.007s

    FAILED (errors=1)

The tool I tried pass its test with planemo and works on the interface…

So I tried without the --external_url option, but I think there is a problem in my job_conf.xml (even if it works, or seems to work on the interface):

galaxy.tools.actions.upload: DEBUG: Checked uploads (748.951 ms)
galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 14
galaxy.web_stack.handlers: DEBUG: (Job[id=14,tool_id=upload1]) No handler pool (uWSGI farm) for '_default_' found
galaxy.web_stack.handlers: DEBUG: (Job[id=14,tool_id=upload1]) Handler assignment method 'uwsgi-mule-message' did not assign a handler, trying next method
galaxy.web_stack.handlers: ERROR: (Job[id=14,tool_id=upload1]) Failed to select handler
galaxy.tools: ERROR: Tool execution failed for job: 14
galaxy.tools: ERROR: Exception caught while attempting to execute tool with id 'upload1':
Traceback (most recent call last):
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/jobs/manager.py", line 79, in enqueue
    job, configured=configured_handler, queue_callback=queue_callback, message_callback=message_callback)
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/web_stack/handlers.py", line 460, in assign_handler
    raise HandlerAssignmentError("Job handler assignment failed.", obj=obj)
galaxy.exceptions.HandlerAssignmentError: Job handler assignment failed.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/tools/__init__.py", line 1601, in handle_single_execution
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/tools/__init__.py", line 1685, in execute
    return self.tool_action.execute(self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs)
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/tools/actions/upload.py", line 29, in execute
    rval = self._setup_job(tool, trans, incoming, dataset_upload_inputs, history)
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/tools/actions/upload.py", line 56, in _setup_job
    trans, incoming, tool, json_file_path, data_list, history=history
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/tools/actions/upload.py", line 38, in _create_job
    rval = upload_common.create_job(*args, **kwds)
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/tools/actions/upload_common.py", line 468, in create_job
    trans.app.job_manager.enqueue(job, tool=tool)
  File "/softs/bioinfo/galaxy-dev/lib/galaxy/jobs/manager.py", line 81, in enqueue
    raise ToolExecutionError(exc.args[0], job=exc.obj)
galaxy.exceptions.ToolExecutionError: Job handler assignment failed.
galaxy.tools.execute: WARNING: There was a failure executing a job for tool [upload1] - Error executing tool with id 'upload1': Job handler assignment failed.

Could you please help me?

Thank you


Galaxy Gitter Channel may be more appropriate for this question -> https://gitter.im/galaxyproject/Lobby

ok, I was not sure, thank you Anton.