"Black box" acquisition

[saskiad]

Need to accomodate use case where sample is mailed to someone else who collects data and sends data back.

• acquisition probably needs some modifications - e.g. not require data stream, or modify data stream?
• instrument not required
• validators hinge on modalities to determine which fields are required for valid metadata.

[dougollerenshaw]

Use barseq and slap2 examples that Dan wrote to help here.

Solve this when solving: https://github.com/AllenNeuralDynamics/aind-scientific-computing/issues/569

[dougollerenshaw]

Don't worry about coordinate system or calibrations. Data stream has modality and nothing else. In notes, add "acquired externally".

One schema change necessary is that we need specimen_id to accept a union of strings or list of strings.

[dougollerenshaw]

@dbirman, could you share a link to the new barseq procedures that you created for reference?

[dbirman]

@dbirman, could you share a link to the new barseq procedures that you created for reference?

#1763

[dbirman]

Probably best to branch off of that procedures branch so that you have the code available. We can merge all the barseq examples (and any changes to schema) into a single PR that way. If you need the instrument PR we can roll that into these as well.

[dougollerenshaw]

One necessary change in acquisition was to allow specimen_id to be a list to accomodate multiple slices. That is complete in #1770

[saskiad]

I think we want something more prominent than the notes in the data stream to convey that this was acquired externally (and that's not even the right phrase - but externally to the team that owns it). There should be top level field for this, and that should drive validation on other fields (e.g. instrument ID needs to become optional so that in this situation it's not provided but we do validate against it for most data)

[dougollerenshaw]

Following up on the Teams discussion with @dbirman and @saskiad. The agreed approach is:

1. Add an ExternalDataStream class — a simplified stream type with only stream_start_time, stream_end_time, modalities, and notes
2. Make instrument_id validation conditional: required when a standard DataStream is present, optional when only ExternalDataStream is used