Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Topic/empty data table #6957

merged 2 commits into from Nov 4, 2018


Copy link

bernt-matthias commented Nov 1, 2018

For empty loc files the following happens:

Traceback (most recent call last):
  File "lib/galaxy/jobs/runners/", line 152, in queue_job
    self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code)
  File "lib/galaxy/jobs/runners/", line 455, in _finish_or_resubmit_job
    job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state)
  File "lib/galaxy/jobs/", line 1493, in finish
    self.tool.exec_after_process(, inp_data, out_data, param_dict, job=job)
  File "lib/galaxy/tools/", line 2310, in exec_after_process
  File "lib/galaxy/tools/data_manager/", line 319, in process_result
    data_table.add_entry(data_table_value, persist=True, entry_source=self)
  File "lib/galaxy/tools/data/", line 264, in add_entry
    self._add_entry(entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd)
  File "lib/galaxy/tools/data/", line 636, in _add_entry
AttributeError: 'list' object has no attribute 'encode'

because the fields list needs to turned into a string also for nonempty files.

mvdbeek approved these changes Nov 1, 2018
Copy link

mvdbeek left a comment

Good one, thanks @bernt-matthias !

@galaxybot galaxybot added the triage label Nov 1, 2018
@galaxybot galaxybot added this to the 19.01 milestone Nov 1, 2018
@mvdbeek mvdbeek merged commit 0ede377 into galaxyproject:dev Nov 4, 2018
6 checks passed
6 checks passed
api test Build finished. 438 tests run, 1 skipped, 0 failed.
continuous-integration/travis-ci/pr The Travis CI build passed
framework test Build finished. 190 tests run, 0 skipped, 0 failed.
integration test Build finished. 267 tests run, 10 skipped, 0 failed.
selenium test Build finished. 147 tests run, 2 skipped, 0 failed.
toolshed test Build finished. 577 tests run, 0 skipped, 0 failed.
@bernt-matthias bernt-matthias deleted the bernt-matthias:topic/empty-data-table branch Nov 14, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
None yet
3 participants
You can’t perform that action at this time.