Multiple Tomograms

[junxini]

The following should be built behind a feature flag

Link to CTF/Alignment/Multiple Tomogram updates to API and client: https://docs.google.com/document/d/1InjJKrx78Sv44QguMXR0p1o9Y34oPnMOY9J3aj375ks/edit#heading=h.eoh3rqmh58k2

The content below can get started while design is WIP:

• Update single run overview section to include multiple tomogram information #993
• Add Tomogram tab to the single run page #994
• Multiple tomogram table (structure not column content) #995

After design handoff is completed:

• Download single tomogram updates + BE integration #1005
• Download all annotation dialog updates + BE integration #1045
• No items edge cases UX #1065
• Updates to info panel #1063
• multiple tomogram filter updates (across all pages) #1064
• Finalize multiple tomograms scope based on latest designs #1047
• Launch MT in prod #1048
• Download single annotation dialog updates + BE integration #1046
• Changes to View Tomogram buttons #1095
• Tomograms table + BE integration (post UX handoff) #1097
• Various tooltips #1098
• Tomogram info sidebar + BE integration #1099
• Annotation sidebar updates #1100

API migration:

• Migrate run query #1101
• Migrate dataset query #1102

TODO(bchu): Make other download flow tickets

Punted (low priority, high effort):

• Trigger inline list collapse on container height in Annotated Objects field #1022

[bchu1]

BE things needed from the final UX mocks:

1. run.frames
2. run.alignments
3. alignment.defocus_value
4. alignment.is_canonical
5. alignment.alignment_type
6. alignment.volume_{x|y|z}_dimension
7. alignment.volume_{x|y|z}_offset
8. alignment.rotation
9. alignment.tilt_offset
10. alignment.affine_transformation_matrix
11. tomogram.alignment
12. tomogram.is_portal_standard
13. tomogram.is_author_submitted
14. tomogram.is_viz_default
15. tomogram.related_database_entries
16. tomogram.publications
17. annotation_file.alignment
18. Download transformed annotation Portal CLI code snippet
19. Download transformed annotation Python API code snippet
20. New S3 directory structure for downloading all annotations of a run (or where the new s3_prefix will live if that's possible)
21. New download all annotations Python API code snippet

[manasaV3]

@junxini Do we have a decision on the defocus_value being a P1 feature for the backend?

[manasaV3]

@bchu1 This document spec should address most of the fields specified in your comment. I will add the ones it doesn't address below:

1. run.frames

This is currently sourced from tiltseries.frame_count this can continue to be sourced from there

The python code snippets will be shared out once that has been finalized.

[junxini]

@junxini Do we have a decision on the defocus_value being a P1 feature for the backend?

@uermel could you confirm if this is dependent on frames being imported? If so, frames likely won't get in until early Q4

[bchu1]

@codemonkey800

The remaining work is all related to the API migration #1101

• The run header image and View Tomogram button should point to the isAuthorSubmitted tomogram. This is blocked by isAuthorSubmitted.
• The images and View Tomogram buttons in the tomogram table should point to the isAuthorSubmitted tomogram. This is blocked on isAuthorSubmitted. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=998-14910&node-type=instance&m=dev
• The tomogram table row should display Author Submitted badge with a tooltip on hover when tomogram isAuthorSubmitted. There's already a badge component that is used for isStandardized. This is blocked by isAuthorSubmitted. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=998-17700&node-type=instance&m=dev
• The Alignment column in the tomogram table should show Canonical subtext with a tooltip when alignment isStandardized. This is blocked on isStandardized. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=998-17723&node-type=instance&m=dev
• The tomogram table should be ordered by first showing isStandardized tomograms, then isAuthorSubmitted tomograms, then by ID highest to lowest. This is blocked by isAuthorSubmitted. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=581-9326&node-type=frame&m=dev
• Alignment ID and Alignment Type in the tomogram sidebar need tooltips. This is not blocked. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=1015-20352&node-type=frame&m=dev
• Tomogram sidebar needs to integrate with deposition.title. This is blocked by the name change from depositionTitle to title not having made it to APIv2 prod yet. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=1015-20369&node-type=instance&m=dev
• Tomogram sidebar needs to integrate with dataset.datasetPublications. This is blocked by the name change from publications to datasetPublications not having made it to APIv2 prod yet. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=1015-20365&node-type=instance&m=dev
• Download tomogram selector needs to also get Author Submitted badge. This is blocked by isAuthorSubmitted. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=876-26590&node-type=instance&m=dev
• Download annotation metadata needs to show Alignment ID. This requires migrating the entire annotations query to V2 first. This is blocked by methodLinks being null in APIv2. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=1358-15181&node-type=text&m=dev
• Disabled states and tooltips for unavailable download options. This is not blocked. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=417-119499&node-type=rounded_rectangle&m=dev
• The misaligned alignment callout in the single annotation download modal needs to display the annotation ID and the tomograms whose alignments are different from the annotation's. This requires migrating the entire annotations query to V2 first. This is blocked by methodLinks being null in APIv2. https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=1358-15181&node-type=text&m=dev

Here's the final copy spreadsheet: https://docs.google.com/spreadsheets/d/1QEPiDcjGJYWSZXsbRjwHd9aeZjbk_tvv2UQ4DKyMwxk/edit?gid=1179230519#gid=1179230519

Here's a PR I started for migrating the annotations field to V2: #1190

Here's the updated mocks for the download flow now that we're not supporting annotation transformation: https://www.figma.com/design/RsjklVi95DFKatU4Uzi2OG/Janeece---Multiple-Tomograms?node-id=1358-15181&node-type=text&m=dev

[bchu1]

Note: tomogram.is_canonical in V1 for the intents and purposes of the launch is tomogram.isAuthorSubmitted in V2.

[Janeece]

@codemonkey800 Here are the prioritized design review comments doc: https://docs.google.com/document/d/1NpMvWUqCvGowvl9MxZP0XlL2qBJBvyB_OJVHl3jqEjE/edit?usp=sharing

Overall this is looking so good (yay @bchu1!), very few P0 comments. If I called out anything that is blocked by the items Bryan listed above, isnt technically feasible, or was previously deprioritized just leave a comment in the doc so I can note it in the designs.