[23.0] Fix implicit converters with optional parameters

[mvdbeek]

In this case

galaxy/lib/galaxy/datatypes/converters/bigwig_to_wig_converter.xml

Line 25 in 1c8462d

<param argument="-chrom" type="text" value="" optional="true" label="Restrict output to given chromosome">

Fixes:

KeyError: 'chrom'
  File "galaxy/tools/__init__.py", line 1909, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2005, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 392, in execute
    ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
  File "galaxy/tools/actions/__init__.py", line 327, in _collect_inputs
    inp_data, all_permissions = self._collect_input_datasets(
  File "galaxy/tools/actions/__init__.py", line 268, in _collect_input_datasets
    tool.visit_inputs(param_values, visitor)
  File "galaxy/tools/__init__.py", line 1748, in visit_inputs
    visit_input_values(self.inputs, values, callback)
  File "galaxy/tools/parameters/__init__.py", line 224, in visit_input_values
    callback_helper(
  File "galaxy/tools/parameters/__init__.py", line 159, in callback_helper
    new_value = callback(**args)
  File "galaxy/tools/actions/__init__.py", line 191, in visitor
    input_datasets[prefix + input.name] = process_dataset(value)
  File "galaxy/tools/actions/__init__.py", line 126, in process_dataset
    data = data.get_converted_dataset(trans, target_ext, target_context=parent, history=history)
  File "galaxy/model/__init__.py", line 4211, in get_converted_dataset
    self.datatype.convert_dataset(
  File "galaxy/datatypes/data.py", line 795, in convert_dataset
    job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)
  File "galaxy/tools/__init__.py", line 2005, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 453, in execute
    params=wrapped_params.params,
  File "galaxy/tools/parameters/wrapped.py", line 43, in params
    self.wrap_values(self.tool.inputs, params, skip_missing_values=not self.tool.check_values)
  File "galaxy/tools/parameters/wrapped.py", line 58, in wrap_values
    value = input_values[input.name]

in https://sentry.galaxyproject.org/share/issue/4f2171798f214f7ba8b947eaaebe2776/

(Please replace this header with a description of your pull request. Please include BOTH what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
(If fixing a bug, please add any relevant error or traceback)
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How to test the changes?

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• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
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  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

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[bernt-matthias]

Looks good to me. Was just wondering if the order of the if-elif branches matters. And maybe you can explain how the test works.

[mvdbeek]

The test is round-tripping from bigwig to wig to bigwig, exercising the code that didn't work.
input_name is the primary input, that's not one of the dependencies, and the rest is potentially optional parameters, so i think it needs to be that way.

[bernt-matthias]

Are tools contained in the galaxy code base tested (#15229)?

[mvdbeek]

No, I don't think it's worth the CI time to test all of them. I can add this one to the framework tests.

[bernt-matthias]

test/functional/test_toolbox_pytest.py::TestFrameworkTools::test_tool[wig_to_bigWig/1.1.1-0] SKIPPED (tool in skiplist) [ 57%]
test/functional/test_toolbox_pytest.py::TestFrameworkTools::test_tool[wig_to_bigWig/1.1.1-1] SKIPPED (tool in skiplist) [ 57%]
test/functional/test_toolbox_pytest.py::TestFrameworkTools::test_tool[wig_to_bigWig/1.1.1-2] SKIPPED (tool in skiplist) [ 58%]
test/functional/test_toolbox_pytest.py::TestFrameworkTools::test_tool[wig_to_bigWig/1.1.1-3] SKIPPED (tool in skiplist) [ 58%]

[bernt-matthias]

maybe remove

galaxy/tools/filters/wig_to_bigwig.xml

Line 20 in 1dea295

2>&1 || echo "Error running wigToBigWig." >&2

[mvdbeek]

Don't really want to touch this, I'm just gonna do a separate framework test tool.

[bernt-matthias]

Excellent :)