Feature/Integrated Dataset Pages

[NickAkhmetov]

Summary

This branch contains the integrated dataset pages functionality.

Context:
We've received recurring asks for dedicated detail pages for EPICs, rather than having them redirect to the parent dataset. I am taking care of early prototyping then handing off any remaining TODOs to polish the functionality and accelerate development.

Lisa also highlighted that we have received previous feedback that the representation of SNARE-Seq2 data in the portal is not ideal. EPICs and SNARE-Seq2 are both instances where users' interest is in processed outputs that integrate data from multiple component datasets, rather than individual datasets' raw data. Therefore, an Integrated Dataset detail page handles both use-cases, while also allowing us to avoid presenting the internal "EPIC" name which users are not familiar with.

When users navigate directly to an integrated dataset's detail page (from dataset search, from being included in a publication's list of datasets, from copying/pasting the URL, etc), rather than displaying the unified view that focuses on the raw data, an alternative view is presented which prioritizes displaying the visualization of the processed data and provides tools to read the metadata/download the bulk data for the integrated analysis and its component datasets.

Integrated datasets will also remain visible in their comprising datasets' processed data section.

TODOs

• Sample-related information needs to combine the parent datasets' origin samples, since the processed datasets do not have a direct connection to the source samples.
• The multi assay relationships section needs to be able to handle being requested by the processed descendant. The displayed relationships need to be combined from all parent datasets that feed into the processed one. The prototype is currently working around this by providing the first ancestor dataset.
• Multiomic view confs take a long time to generate since they provide a separate genomic profiles config for each clustering column. As a result, the Visualization section takes a while to become visible for these datasets. The implementation will need to be adjusted to display a loading skeleton while the conf is generated.
  • A future improvement outside of the scope of this work is to find a way to pass an additional parameter to the builder so that only the currently-visible Vitessce conf is generated but all the different options are still provided - i.e. making building the other variants of the conf lazy rather than eager.
• The contributors table needs to be populated from the parent datasets for SnareSeq2 datasets. EPIC contributors will be directly associated.
• Bulk data transfer should include tabs for the integrated datasets.

Potential TODOs/Open Questions

• The ingested object x analyte EPICs were removed, so I've only been working with the SnareSeq2 side of this so far. Additional component-level disambiguation logic may be necessary to handle differences in the data model.
• We will need to adjust wording/language on the raw SnareSeq2 page as well.
• The provenance table may need to be hidden since the long list of datasets on snareseq2 pages is rather confusing
• Parent datasets don't contribute much value to the Metadata table - they all contain the same information about the processing pipeline. Maybe possible to consolidate into one tab?
• The Integrated Datasets table can be enhanced with selection (for workspaces/metadata export) and additional columns as desired.
• The multi assay relationship diagram/section can be relocated if desired - maybe into the Integrated Datasets section, especially once it's showing all the ancestors appropriately.

Design Documentation/Original Tickets

Link to any design documents, diagrams, or JIRA tickets relevant to this feature.

Testing

Describe how the feature has been tested, including both automated and manual testing strategies.

Screenshots/Video

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Checklist

• Code follows the project's coding standards
  • Lint checks pass locally
  • New CHANGELOG-your-feature-name-here.md is present in the root directory, describing the change(s) in full sentences.
• Unit tests covering the new feature have been added
• All existing tests pass
• Any relevant documentation in JIRA/Confluence has been updated to reflect the new feature
• Any new functionalities have appropriate analytics functionalities added

Additional Notes

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