Y24-099 Tube Rack Banking Sequencescape API

[yoldas]

User story
As PSD, we would like to update Sequencescape v2 API to provide Limber support for TubeRack model similar to Plates using the versioned tube rack model proposed in Reuse of TubeRacks document.

Who are the primary contacts for this story
Abdullah, Katy, Andrew

Who is the nominated tester for UAT
TBD

Acceptance criteria

• Check existing labware creator (in DPL-811) for Sequencescape API calls and replace them for tube racks.
• Check TubeRacks and associated objects are retrieved by using JSONAPI includes, i.e. Tubes and RackedTube.
• Add resource methods to TubeRacks and RackedTubes so that they are similar to Plate and Wells.
• Add TubeRack barcode into new TubeRack poly_metadata in order to enable history tracking of physical tube rack

Dependencies
This story is blocked by the following dependencies:

• DPL-1011 Re-use of tube racks #1482

References
This story has a non-blocking relationship with:

• DPL-811 Transfer PBMC isolations into FluidX tube racks #1314
• Y24-088 Implement (Banking) DPL-811 Transfer PBMC Isolations into FluidX tube racks using the versioned TubeRack model #1713

Additional context
The versioned tube rack model is researched in DPL-1011 Re-use of tube racks and the model is summarised in the Google Document DPL-1011 Re-use of tube racks

This story is part of re-implementation of DPL-811 Transfer PBMC isolations into FluidX tube racks (Banking) using the versioned tube rack model.

Story relationships are shown in the Lucidchart diagram TubeRack Stories .

It is not possible to release the implementation of this story in isolation.

[TWJW-SANGER]

A couple of queries:

• Do the features that require these APIs already exist or need to created? I suspect "API Support to allow History tracking of physical tube rack.." is a feature that does not yet exist? Would it make sense to split that feature out into its own user story so that we understand what the business need before designing this API call?
• I can see "API Support to find a tube on a tube rack" would be useful / needed. Curious as to how it works at the moment and/or where this is being called from. In the sense of - could this be split out into another smaller story?

[KatyTaylor]

"API Support to allow History tracking of physical tube rack using poly_metadata" - a bit more detail would be good. I think what we mean here is that the tube rack barcode will be saved into poly_metadata when the tube rack is created - is that correct?

[yoldas]

I have updated the criteria to address the comments.

• History tracking is part of the versioned TubeRack model described in the Google Doc DPL-1011 Re-use of tube racks . A code example is shown on Sequencescape side for this. It is a simple operation to future-proof the links between tubes and tube racks.
• Saving barcode in poly_metadata is covered in criteria better now and described in the document in the previous item.
• There is already a resource to find out the tube rack of a tube (RackedTube) because a tube is linked to a specific version of a tube rack but there is no support for finding historical locations of a tube through multiple tube racks. It is not a requirement for re-implementing banking. There is no need for that now.

[KatyTaylor]

Updated: rearranged list to make it easier to see which points have been dealt with (e.g. made into stories or added to existing ones), and which haven't yet.

Dealt with - relating to the 'banking' set of stories:

1. spec/models/labware_creators/plate_split_to_tube_racks_spec.rb fix breaking tests - part of this story
2. understand / fix lots of other broken tests on PR into epic branch - part of this story
3. tube rack state - currently have a method on TubeRackPresenter for state, move to model? causes bug in relatives tab code if not present - put this into the presenter story.
4. driver file for Bank plate to tubes is not working 'Hamilton LRC PBMC Bank plate to LRC Bank Seq and Spare tubes CSV' - story to fix this
5. bed verification is not working 'Hamilton LRC PBMC Bank => LRC Bank Seq and LRC Bank Spare' - have existing story
6. manual transfer not working - integration suite cannot progress without bed verification OR 'Manual Transfer' - make story to fix this
7. tube custom metadata for rack and coordinate - needed? - this is OK, we want this to be removed - racked_tubes should replace this
8. Check on work completion code - is it triggered, test it after manual transfer is done. Relates to tube rack state (point 4) - new story
9. Fix integration suite - make sure written down in acceptance criteria. Create new epic branch and merge Andrew's branch in.

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Not yet dealt with - relating to the 'defrosting' set of stories, or enhancements:

3. see if we can refactor the labware creator code into common tube rack includes modules - leave until Cryostor work, when new labware creator will be needed
4. submission of tube racks - is this needed? currently using tube submission 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p' on the tubes, and then scan them in for cryostor creation - part of the cryostor block of stories - write it down somewhere on those. If submission is on tube rack, need a way to create a tube rack before making the submission.
5. Think about the 'redoing the step' scenario & re-jig the existing backlog stories for the new data model.
6. Before doing Cryostor set of stories - Check if Cryostor is a normal FluidX tube rack. Why aren’t we accepting a tube rack scan here? Do they want the arraying page still?