Gp 4415.detailed case format

[grapigeau]

Jira ticket: https://jira.oicr.on.ca/browse/GP-4415

• Includes a change file
• Updates developer documentation

[djcooke]

You're now not adding non-sequencing samples to the sequencing for library qualification, but you're still creating a sequencing object that will never have any limsIds because there is no sequencing of that type for that test/case.

There is also a sequencing object for tests that don't yet have any sequencing (no limsIds). Is that wanted? There's no good way to tell whether a test has low-depth sequencing from the Cardea data if there are no samples, but if we avoid creating a sequencing object when there is no sequencing (whether that means yet or ever), that takes care of the problem.

[grapigeau]

You're now not adding non-sequencing samples to the sequencing for library qualification, but you're still creating a sequencing object that will never have any limsIds because there is no sequencing of that type for that test/case.

There is also a sequencing object for tests that don't yet have any sequencing (no limsIds). Is that wanted? There's no good way to tell whether a test has low-depth sequencing from the Cardea data if there are no samples, but if we avoid creating a sequencing object when there is no sequencing (whether that means yet or ever), that takes care of the problem.

I think it does make sense to exclude objects aka tests where there are no samples.
To confirm we're on the same page, I'm thinking a case without any sequencing have the field: "sequencing": [] ?

[djcooke]

I think it does make sense to exclude objects aka tests where there are no samples.
To confirm we're on the same page, I'm thinking a case without any sequencing have the field "sequencing": [] ?

The sequencing field could be omitted, null, or an empty array - whatever works. What I meant is that we shouldn't have something like this:

"sequencing": [
  {
    "type": "LIBRARY_QUALIFICATION",
    "limsIds": [] <- nothing here, and possibly never will be
    ...
  }
]