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Allow param_value filter to refer to parameters with multiple values #13039

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merged 6 commits into from
Jan 14, 2022
Merged

Allow param_value filter to refer to parameters with multiple values #13039

merged 6 commits into from
Jan 14, 2022

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bernt-matthias
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@bernt-matthias bernt-matthias commented Dec 8, 2021 •
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Consider this:

<param name="A"/>
<param name="B" type="select">
    <options ...>
        <filter type="param_value" column="0" ref="A" keep="false"/>
    </options>
</param>

then this already works if A is a simple parameter (text, int, ...) but it failed if A is a select is a select parameter with multiple="true".

The filter also did not work if ref_attribute is used for data parameters with multiple="true" and collection inputs.

Also there were no test so far for the param_value filter.

I would like to call this a bug and backport it .. ?

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

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@github-actions github-actions bot added this to the 22.01 milestone Dec 8, 2021
@bernt-matthias bernt-matthias force-pushed the topic/filter-param-value-multiple branch 3 times, most recently from 6e9b6d1 to d30d49a Compare December 10, 2021 09:39
@bernt-matthias bernt-matthias force-pushed the topic/filter-param-value-multiple branch from d30d49a to 385dbaa Compare December 16, 2021 08:55
mvdbeek
mvdbeek approved these changes Jan 6, 2022
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Looks great, can you also run the IUC tests against this branch ?

@bernt-matthias
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Looks great, can you also run the IUC tests against this branch ?

Good idea. I tried galaxyproject/tools-iuc#4318 but it seems that I have insufficient permissions: Command 'run-all-tool-tests' is not configured for the user's permission level 'none'.

@bernt-matthias
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Seems that tests of two tools reproducibly (also local) time out. For macs2 it seems that no param_value filter is used. I will investigate.

@bernt-matthias bernt-matthias force-pushed the topic/filter-param-value-multiple branch from 25e9dfb to 147bea5 Compare January 8, 2022 13:03
@bernt-matthias bernt-matthias mentioned this pull request Jan 8, 2022
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@bernt-matthias
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Seems that the two tools timing out also timeout on dev because of #13136

So at the moment I can not answer if IUC tool tests are affected.

@bernt-matthias bernt-matthias force-pushed the topic/filter-param-value-multiple branch from 147bea5 to 2e33be7 Compare January 11, 2022 14:53
@bernt-matthias
allow param_value filter to refer parameters with multiple values
f5f3f47 
For instance if we want to have a parameter B to select values
that have not been selected in a parameter A .. and A has
`multiple="true"`

```
<param name="A" type="select" multiple="true"/>
<param name="B" type="select">
    <options ...>
        <filter type="param_value" column="0" ref="A" keep="false"/>
    </options>
</param>
```
@bernt-matthias
add test for param_value filter
c809003
@bernt-matthias
remove debug messages
dddf201
@bernt-matthias
do not add hg38 to test data table
07d66b8 
interferes with another test
@bernt-matthias
comment forward reference
b53f294 
seems that it is not possible to refer other input parameters
that are defined below in the xml
@bernt-matthias
make param_value filter work with multi data inputs
2e33be7 
ie data with multiple=true and collections
@bernt-matthias
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The IUC tests are finished now: 11 failure 3678 success (compared to 12 in the recent test for the dont_template_version_command branch). the 11 are a subset of the 12.

@mvdbeek mvdbeek merged commit 6fdf4da into galaxyproject:dev Jan 14, 2022
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This PR was merged without a "kind/" label, please correct.

@bernt-matthias bernt-matthias mentioned this pull request Jan 19, 2022
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@bernt-matthias bernt-matthias deleted the topic/filter-param-value-multiple branch March 14, 2022 15:08
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