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[24.1] xsd: allow change_format and actions also in statically defined collection elements, and break recursion #18605

Merged
merged 11 commits into from
Jul 31, 2024
Merged

[24.1] xsd: allow change_format and actions also in statically defined collection elements, and break recursion #18605

merged 11 commits into from
Jul 31, 2024

Commits on Jul 30, 2024

  1. allow change_format and actions in all data elements 

    also those contained in collections. Used for instance here:

https://github.com/galaxyproject/tools-iuc/blob/695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82/tools/hybpiper/hybpiper.xml#L198
https://github.com/galaxyproject/tools-iuc/blob/695ea582a8d3bf7845dd4cddbc8b591e4b6c4e82/tools/krakentools/extract_kraken_reads.xml#L145
    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  2. extend tool test for change_format in statically defined collection e… 

    …lements
    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  3. xsd: add OutputDiscoverDatasetsCommon 

    to describe attributes common to OutputDiscoverDatasets and OutputCollectionDiscoverDatasets
    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  4. XSD: break recursion in collection data

    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  5. also check schema doc template

    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  6. add test for output actions for collection elements

    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  7. add test for filters in statically defined collection elements

    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  8. Revert "add test for filters in statically defined collection elements" 

    This reverts commit c0ce2a7.
    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  9. test actions in statically defined collection elements

    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  10. xsd: do not allow filter and discover_datasets in statically defined … 

    …collection elements

and remove actions and change_format from the collection definition
(again)
    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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  11. remove test for actions from collection_creates_pair_format 

    now in metadata_column_names
    @bernt-matthias
    bernt-matthias committed Jul 30, 2024
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