What are the validation implications of the requirement values: -, C, E, M, and X?

turbomam commented 2 years ago

This is regarding the MIxS 6 Term Updates "core" sheet

For example, if no value is provided for a field with a term with cardinality M (mandatory?), then the validation will not pass?

What about the others?

[ ] -: Not applicable. If a value is provided for this slot/term, the validation will fail
[ ] C: Conditionally mandatory. What are the conditions? Implementing as Recommended for now, expressed with schemasheets' "R" code
[ ] E: Environment-dependent. I don't see how this column in the core sheet adds any value. In fact, it could contradict the "packages" sheet. I intend to leave these as optional in the core sheet, and upgrades to "mandatory" will come from the "packages" sheet.
[ ] M: Mandatory: if data are submitted and this value is omitted, validation will fail
[ ] X: Optional. My have to change to schemasheets' optional code, "O". Validation will not be affected by whether a value is provided for this slot/term.

turbomam commented 2 years ago

See also

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ramonawalls commented 2 years ago

Mandatory is a flag for INSDC. It will pass, but a notice will be sent back to user.

We have a missing value vocabulary we developed with INSDC. https://ena-docs.readthedocs.io/en/latest/submit/samples/missing-values.html

The Mandatory (and other) flag is from the community members who build a package. Therefore, we allow that there will be missing values for some of them.

only1chunts commented 4 months ago

@turbomam from this ticket am I correct to assert that the LinkML implentation now has 3 basic levels of requirement for any given term in any given checklist/extension combination, ie a term can be: 1 - Mandatory (those terms that are required for strict compliance) or 2 - Recommended (what previously GSC would have called "Conditionally mandatory") or 3 - Optional If so, I like it! That would be much cleaners and clearer than the previous M, E, C, X way we did it previously! (Terms that are not applicable simply aren't included in a particular extension, so this status seem redundant.)

only1chunts commented 3 months ago

discussed at CIG call 25Jun - proposal of the use of the simplified 3 states mentioned above. However, the LinkML backend actually has a slightly different set up, every term in a checklist or extension has 2 flags (Required, or Recomended) that can be either True or False which gives a totla of 4 possible states for a term:

--	Recomended =T	Recomended = F
Required = T	-1-	-2-
Required = F	-3-	-4-

We need to define how those state relate to the mandatory/recomended/option trio ?

my proposal is this:	--	Recomended =T	Recomended = F
Required = T	Mandatory	Mandatory
Required = F	Recomended	Optional

There is an additional level of complexity, when a term is listed in BOTH a checklist and an Extension it may have different Required and Recomended states!

I believe the Checklist level states over-ride the extension level states, but I may be wrong! @turbomam please confirm?

I would like to propose that we move towards a place where terms are exclusive to either checklist OR extensions and not present in both to save confusion.

turbomam commented 3 months ago

GenomicsStandardsConsortium / mixs

What are the validation implications of the requirement values: -, C, E, M, and X? #468

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