Replace `Sample.collection_time_point*` properties with `TimePoint` object

[bussec]

The TimePoint object is currently only used once in the schema (as part of RepertoireGroup). As this is semantically identical to the separate collection_time_point* properties of the Sample object, it should be replaced with the following mapping:

• Sample.collection_time_point_relative -> TimePoint.value
• Sample.collection_time_point_relative_unit -> TimePoint.unit
• Sample.collection_time_point_reference -> TimePoint.label

[jday1]

Quick question on this one. Are you suggesting deprecating TimePoint or Sample.collection_time_point...?

If one is deprecating Sample.collection_time_point..., this is problematic because a single Repertoire object can contain multiple samples. A typical use case for this is to store samples from a repertoire at multiple points in time.

If Sample.collection_time_point... is deprecated in favour of TimePoint, then this functionality is lost. In this case, the change would be a breaking one. If this is implemented, then this implicitly creates an AIRR standard that samples from the same subject at different time points should be stored as separate Repertoire objects. Is this intended?

Would it then be worth enforcing 'one sample per repertorie' which is the iReceptor standard and modify Sample from an array to a single object?

[scharch]

If Sample.collection_time_point... is deprecated in favour of TimePoint, then this functionality is lost. In this case, the change would be a breaking one. If this is implemented, then this implicitly creates an AIRR standard that samples from the same subject at different time points should be stored as separate Repertoire objects. Is this intended?

This is currently the expectation, I believe, although the docs don't reflect it. RepertoireGroup is intended for the use case you describe.

[bcorrie]

In re-visiting this in #735 I think we are more talking about deprecating:

• Sample.collection_time_point_relative = 43
• Sample.collection_time_point_relative_unit = id: UO:0000033, label: day
• Sample.collection_time_point_reference = "post vaccination"

But adding:

• Sample.collection_time_point, a field of type TimePoint

So we would have:

• Sample.collection_time_point_relative -> sample.collection_time_point.value = 43
• Sample.collection_time_point_relative_unit -> sample.collection_time_point.unit = id: UO:0000033, label: day
• Sample.collection_time_point_reference -> sample.collection_time_point.label = "post vaccination"

So no loss of functionality - we are just formalizing that collection_time_point is a TimePoint.

In #735 we are going a bit further than this and talking about creating a generic Event object and in this case we would likely use an Event of type SampleCollection or something along those lines.

[bcorrie]

This is done...