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.

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

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

[hechth]

@yguitton and @lecorguille seems like the actual changes had already been merged, hence no changes to be seen here.

The update of the tools on the toolshed still didn't work out, so if the CI passes here we can merge this to get the latest version of the XCMS tool onto the toolshed.

[bernt-matthias]

We should setup this step here:

tools-metabolomics/.github/workflows/pr.yaml

Line 390 in 132c30f

deploy-report:

for the repo. Then there will be a comment in the PR when deployment failed.

Therefore a personal access token of an owner needs to be added as secret named PAT.

Check for "PAT" here https://github.com/peter-evans/create-or-update-comment