Column argument validation breaks on empty tabular files

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Column argument validation breaks on empty tabular files

Peter Cock
Hello all,

I'm testing a workflow which uses my filter tool where one of the parameters
is a tabular file, and a related parameter is a multi-column selector:


Snippet from tool XML,

<param name="input_tabular" type="data" format="tabular"
label="Tabular file containing sequence identifiers"/>
<param name="columns" type="data_column" data_ref="input_tabular"
multiple="True" numerical="False" label="Column(s) containing sequence
identifiers" help="Multi-select list - hold the appropriate key while
clicking to select multiple columns">
<validator type="no_options" message="Pick at least one column"/>

In most cases, the preceding tool will generate a tabular file with
two columns - and the workflow has column 1 as the saved value.

However, it is quite valid for the tabular file to actually be empty - in
which case the number of columns is unknown and so the arguments
can't be checked. Despite this, Galaxy attempts to check the column
argument from the workflow and fails:

Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/",
line 119, in prepare_job
  File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/", line
656, in prepare
    self.tool.handle_unvalidated_param_values( incoming, )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/", line
2330, in handle_unvalidated_param_values
    self.handle_unvalidated_param_values_helper( self.inputs,
input_values, app )
  File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/", line
2369, in handle_unvalidated_param_values_helper
    raise LateValidationError( message )

Tool execution generated the following error message:

Failed runtime validation of Column(s) containing sequence identifiers
(An invalid option was selected, please verify)

It seems to me this is a bug, and the late validation is being too
strict where as in this case the number of columns is undefined.

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