Align `rna_volume` validation constraints with comments

turbomam commented 1 year ago

slot_usage for JgiMtInterface

rna_volume:
  name: rna_volume
  title: RNA volume in ul
  comments:
    - Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only.
  examples:
    - value: '25'
  from_schema: https://raw.githubusercontent.com/microbiomedata/nmdc-schema/main/src/schema/nmdc
  rank: 6
  string_serialization: '{float}'
  owner: Biosample
  domain_of:
    - Biosample
  slot_group: jgi_metatranscriptomics_section
  range: float
  required: true
  recommended: true

Needs minimum_value and maximum_value specifications.

Should the minimum be 0 or 25?

A good way to check this sort of thing by generating local/usage_template.tsv with the project.Makefile. I see that there are no slots with a minimum_value set to anything higher than 0. @mslarae13 what behavior do you want here? We should make sure that the comment and the validation rules are harmonious. Maybe we need to say more about what "special permission" is and who to get it from.

Typo? Value must 0-1000

cc @brynnz22 @mslarae13

turbomam commented 1 year ago

Should apply the changes upstream, to the nmdc-schema. Then regenerate to take advantage of the slot inheritance.

bmeluch commented 8 months ago

https://microbiomedata.github.io/submission-schema/rna_volume/ rna_volume shows minimum = 0 and maximum = 1000 in the submission schema documentation, and won't validate when I test numbers outside 0-1000 in the data sandbox. Can this issue be closed?

turbomam commented 8 months ago

Whether we are going to leave this slot in nmdc-schema or move it so that it only appears in submission-schema, minimum and maximum value constrains should be added in the YAML definitions, if those constraints are not modifid for different situations.

The constraints are being added by sheets_and_freinds now, but they should be pushed as far upstream as possible.

mslarae13 commented 5 months ago

@bmeluch does @turbomam 's most recent comment make sense? Can you check the constraints on nmdc-schema? Looks like this is a schema issue, not submission-schema?

bmeluch commented 5 months ago

It looks like the constraints are being applied in the nmdc-schema YAML slot definition.

The only modification that the submission schema is making to rna_volume is to make it required for JgiMtInterface.

but they should be pushed as far upstream as possible.

So I think they have been pushed upstream, and this is done? @turbomam

mslarae13 commented 4 months ago

@bmeluch so are you saying the only modification is rna_volume, or that it's the only one that still needs done?

bmeluch commented 4 months ago

Afaik nothing more needs to be done - the modifications discussed in this issue have been moved upstream already, the way Mark wanted them. There is only one modification being applied to rna_volume in the submission schema, and it's for something else.

ssarrafan commented 3 months ago

Afaik nothing more needs to be done - the modifications discussed in this issue have been moved upstream already, the way Mark wanted them. There is only one modification being applied to rna_volume in the submission schema, and it's for something else.

@bmeluch does this mean that we can close this issue?

ssarrafan commented 3 months ago

@turbomam can you please confirm that this issue is resolved? @bmeluch So I can close the old sprint I'll move this to the new sprint for Mark to review.

mslarae13 commented 3 months ago

@turbomam we need your confirmation to close this out or move to the next sprint.

ssarrafan commented 3 months ago

I'm going to close this issue based on the comment from Bea and since we can't get a response from Mark. @turbomam if this is not ok to close please re-open.
@mslarae13 @bmeluch

microbiomedata / submission-schema

Align `rna_volume` validation constraints with comments #116