Draft: Fix xcms_group and xcms_fillpeaks

[lecorguille]

This PR aims to fix this issue on xcms_group:

galaxy.web.framework.decorators ERROR 2023-11-21 09:48:39,643 [pN:main.5,p:1423968,tN:WSGI_1] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/shared/ifbstor1/galaxy/server/lib/galaxy/web/framework/decorators.py", line 337, in decorator
    rval = func(self, trans, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/ifbstor1/galaxy/server/lib/galaxy/webapps/galaxy/api/workflows.py", line 589, in build_module
    "tool_state": module.get_state(),
                  ^^^^^^^^^^^^^^^^^^
  File "/shared/ifbstor1/galaxy/server/lib/galaxy/workflow/modules.py", line 311, in get_state
    return self.state.encode(Bunch(inputs=inputs), self.trans.app, nested=nested)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/ifbstor1/galaxy/server/lib/galaxy/tools/__init__.py", line 533, in encode
    value = params_to_strings(tool.inputs, self.inputs, app, nested=nested)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/ifbstor1/galaxy/server/lib/galaxy/tools/parameters/__init__.py", line 266, in params_to_strings
    value = params[key].value_to_basic(value, app, use_security=use_security)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/ifbstor1/galaxy/server/lib/galaxy/tools/parameters/grouping.py", line 749, in value_to_basic
    current_case = rval["__current_case__"] = self.get_current_case(value[self.test_param.name])
                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/ifbstor1/galaxy/server/lib/galaxy/tools/parameters/grouping.py", line 742, in get_current_case
    raise ValueError("No case matched value:", self.name, str_value)
ValueError: ('No case matched value:', 'peaklist', 'True')

This error is raised from the workflow edition.

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[lecorguille]

It seems to come from: <filter>peaklist['peaklistBool'] == 'true'</filter> 🤔

https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/xcms/macros_xcms.xml#L106-L124

<xml name="input_peaklist_conditional">
        <conditional name="peaklist">
            <param name="peaklistBool" type="select" label="Get the Peak List">
                <option value="true">Yes</option>
                <option value="false">No</option>
            </param>
            <when value="true">
              <expand macro="input_peaklist"/>
            </when>
            <when value="false" />
        </conditional>
    </xml>

    <xml name="output_peaklist"  token_function="">
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@[email protected]" from_work_dir="variableMetadata.tsv" >
            <filter>peaklist['peaklistBool'] == 'true'</filter>
        </data>
        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@[email protected]" from_work_dir="dataMatrix.tsv" >
            <filter>peaklist['peaklistBool'] == 'true'</filter>
        </data>
    </xml>

[lecorguille]

Another issue with fillpeasks

3.12.0+galaxy0

3.12.0+galaxy1

The filter seems broken

<xml name="input_peaklist_section">
        <section name="peaklist" title="Peak List" expanded="True">
            <param name="peaklistBool" type="hidden" label="Get the Peak List" value="true" />
            <expand macro="input_peaklist"/>
        </section>
    </xml>

    <xml name="output_peaklist"  token_function="">
        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@[email protected]" from_work_dir="variableMetadata.tsv" >
            <filter>peaklist['peaklistBool'] == 'true'</filter>
        </data>
        <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@[email protected]" from_work_dir="dataMatrix.tsv" >
            <filter>peaklist['peaklistBool'] == 'true'</filter>
        </data>
    </xml>

[lecorguille]

The main changes between the two version : f1f3799

[lecorguille]

@bernt-matthias , do you have an idea?

[bernt-matthias]

It seems to come from: peaklist['peaklistBool'] == 'true'

If I remember correctly then all exceptions raised by filter code are "swallowed" and the filter is evaluated to true.

The traceback indicates that an conditional (probably the select) is the culprit. Is there a way that I can reproduce the error?

The filter seems broken

The best to elucidate this would be to extend the test, e.g. by adding expect_num_outputs to the test tags .. and likely (re)add test cases.

Also odd tat the 3.12.0+galaxy1 are not available on the usegalaxy.* instances.

[lecorguille]

I wasn't able to reproduce this with planemo serve and a refresh install of the tool :/