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Topic/empty data table #6957

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merged 2 commits into from Nov 4, 2018
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@bernt-matthias
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bernt-matthias commented Nov 1, 2018

For empty loc files the following happens:

Traceback (most recent call last):
  File "lib/galaxy/jobs/runners/local.py", line 152, in queue_job
    self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code)
  File "lib/galaxy/jobs/runners/__init__.py", 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/__init__.py", line 1493, in finish
    self.tool.exec_after_process(self.queue.app, inp_data, out_data, param_dict, job=job)
  File "lib/galaxy/tools/__init__.py", line 2310, in exec_after_process
    data_manager.process_result(out_data)
  File "lib/galaxy/tools/data_manager/manager.py", line 319, in process_result
    data_table.add_entry(data_table_value, persist=True, entry_source=self)
  File "lib/galaxy/tools/data/__init__.py", 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/__init__.py", line 636, in _add_entry
    data_table_fh.write(fields.encode('utf-8'))
AttributeError: 'list' object has no attribute 'encode'

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

@mvdbeek
mvdbeek approved these changes Nov 1, 2018
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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
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@bernt-matthias bernt-matthias deleted the bernt-matthias:topic/empty-data-table branch Nov 14, 2018
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