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[WIP] Implement Sample Sheets #19305

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Implements #19085.

Currently workflows that work with data that have more structure than just a list of a list of pairs require exposing users to very advanced workflow features (rule builder for nested collections and/or group tags) or hacks that aren't very user friend, traceable, or robust. Allowing workflow developers to describe a spreadsheet with structure (columns for pairing, treatment type, control status, repeat/replicate number, condition) and then letting them just use that readily within the workflow from the Apply Rules tool will provide a much easier interface to the workflow runner and will make a whole slew of common workflow types much more accessible. Workflow developers can build better more robust workflows more rapidly and not need to focus on communication and education as intensely. Users will be able to leverage these workflows without needing to understand collections - let alone advanced collection features like nesting, the rule builder, etc..

The column specification and validation of the data against it is already included in this PR. Hooking the data up into the Apply Rules tool seems to just work with some small changes also included. From this point I think the whole endeavor is mostly just UI, but there is a lot to be done in this realm I think. Starting with #19303 so we can describe the sample sheet columns. After that, I think it might just be a new collection builder interface for the sample sheet that renders the spreadsheet and allows the user to fill it in after selecting initial datasets from file sources or a list of URIs or an actual spreadsheet file.

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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  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@jmchilton jmchilton force-pushed the sample_sheets branch 2 times, most recently from d0fd0df to 53324a9 Compare December 22, 2024 20:28
This uses the wizard introduced by David for workflow exports instead of adapting the upload paradigm. The old component was very compact but also very unintuitive and just hacked together as quickly as possible and never really revisited. The wizard provides more space to explain things and is probably the way we want to go but still needs some serious love from someone better at UI than me.

I need a component like this... but different for sample sheet seeding so I wanted to do a refresh and get something we're all more comfortable with ahead of that.
Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
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