examples in slot `slope gradient` don't validate

[mslarae13]

See here

slot slope_gradient has 10% as a valid example but it won't validate with out a .. so 10 %

[turbomam]

good catch. we are inheriting this from an old version of MIxS. I will check v6.2 to see if the examples that violate our expectations are still there.

if they aren't, then I need to get my act together and update the import process to use v6.2, which will require lots of review form tohers

alternatively we could do either or both of these:

• ask GSC to use our recommended examples
• change the examples in the submission-schema to our preferred style

[mslarae13]

Pending your inspection of 'if examples that violate our expectations are still there' ...

If MIxS still has invalid examples I recommend we update the validator to not REQUIRE a 'space' between the # and % .. so 10% WILL validate We put in an issue to MIxS asking for an update to their validator

If MIxS has removed the invalid examples We should pull that in, still make the suggestion to MIxS to allow for 'no space' between # and % but not change it on our end. Wait for MIxS to update.

@turbomam thoughts?

[turbomam]

I forgot to look last week. I'll do it now.

[turbomam]

I wonder where those examples came from? I don't see them in MIxS 6.0-6.2

Transposed rows from MIxS 6.1 "mixs_v6.xlsx"

Environmental package	soil	agriculture
Structured comment name	slope_gradient	slope_gradient
Package item	slope gradient	slope gradient
Definition	Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer	Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer
Expected value	measurement value	measurement value
Value syntax	{float} {unit}	{float} {unit}
Example
Requirement	X	C
Preferred unit	percentage	percentage
Occurrence	1	1
MIXS ID	MIXS:0000646	MIXS:0000646

MIxS v6.2.0 documentation page

• https://genomicsstandardsconsortium.github.io/mixs/0000646/

linkml source for the slot, v6.2.0:

name: slope_gradient
annotations:
  Preferred_unit:
    tag: Preferred_unit
    value: percentage
description: Commonly called 'slope'. The angle between ground surface and a horizontal
  line (in percent). This is the direction that overland water would flow. This measure
  is usually taken with a hand level meter or clinometer
title: slope gradient
from_schema: https://w3id.org/mixs
keywords:
- slope
slot_uri: MIXS:0000646
alias: slope_gradient
domain_of:
- Agriculture
- Soil
range: string
pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
  *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
structured_pattern:
  syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
  interpolated: true
  partial_match: true

[turbomam]

Regexr sandbox for the current submission-schema examples vs the MIxS 6.2.0 validation pattern

• https://regexr.com/7nn8d

[turbomam]

If you look at the modifications_long.tsv section in the submission-schema search results for slope_gradient you'll see how we have asserted our own examples and a todo:

Slope is a percent. How does the validation work? Check to correct examples

[turbomam]

submission-schema has a validation pattern of ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ for slope_gradient, but it isn't coming from MIxS 6.2.0 or from NMDC's frozen MIxS v6.0 either. See https://microbiomedata.github.io/mixs/slope_gradient/

As far as I am concerned we can assert whatever examples we want in the Biosample slot usage in nmdc.yaml and whatever validation pattern we want in https://github.com/microbiomedata/submission-schema/blob/main/sheets_and_friends/tsv_in/modifications_long.tsv

@pkalita-lbl and @mslarae13 this is the kind of thing we will have to keep an eye on when we switch to importing MIxS terms directly from https://github.com/GenomicsStandardsConsortium/mixs/blob/v6.2.0/src/mixs/schema/mixs.yaml. See

• https://github.com/microbiomedata/nmdc-schema/pull/1386

[turbomam]

@mslarae13 I have emphasize a minimal number of abstracted structured_patterns in MIxS v6.2.0. If you want to suggest changing GSC's pattern for slope_gradient, let's to look for the other slots that are using the same pattern and be consistent.

[mslarae13]

Thanks @turbomam forgot we added those! Regardless, I think it's the same solution. It's weird to allow "10 %" and not "10%".