airr-community / airr-standards

AIRR Community Data Standards
https://docs.airr-community.org
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Formalize relations between x-airr fields #297

Closed bussec closed 4 years ago

bussec commented 4 years ago

Given the recent discussion in #213, #272, #282 and other issues/PRs, would it be helpful if we would formalize the relations between the following x-airr fields?

Where "formalizing" means

  1. having a comprehensive set of if-then rules regarding the state of the fields
  2. mapping frequently encountered requirement groups to combination of states
  3. defining the default values and whether fields withs default values MUST, MAY or MUST NOT be included in the schema

There is already some information in the docs and there is also a table from the ADC API perspective, but IMO they don't address all those point. If I missing something, please let me know.

javh commented 4 years ago

I'm not sure. I'd have to look at it, but I think we can just update all existing tags, at least as a first pass.

I'm sure we'll need to have some conversations about what gets labeled as required, x-airr: adc-query-support and x-airr: nullable, which will slow the process down.

Maybe we could just do an update pass quickly in #342 so master isn't broken, merge that in, and then tackle the slower task of making sure all the tags are reasonable in a second pass?

bussec commented 4 years ago

Sounds good, will do that now.

javh commented 4 years ago

Great. Thanks, @bussec. I'm a bit short on bandwidth right now, so that's super helpful. :)

bussec commented 4 years ago

@javh The tests are passing. However, there was some hickup with Travis, who was hung up for hours... but apparently this was unrelated to the changes. Should we merge?

javh commented 4 years ago

Not quite... Looks like we'll also have to:

bussec commented 4 years ago

Sorry, missed those. They are in #342 now, still passing.

javh commented 4 years ago

Awesome, thanks. I pushed a couple tweaks:

I think we are good to merge.

schristley commented 4 years ago

I think we are good to merge.

Looks good to me. I will handle setting all of the x-airr: adc-query-support flags in a separate PR.

bcorrie commented 4 years ago

So can we close this issue given #342 is closed?

bussec commented 4 years ago

@bcorrie Once you reviewed #319, as it contains part of the documentation ;-)

bcorrie commented 4 years ago

Agghhhh my head is going to explode keeping these issues/pull request sorted out. I have approved... But given that my head just exploded (and in case I missed something else), I will let someone else close the issue... 8-)

bussec commented 4 years ago

319 is merged. Closing...