analysis_type is both required and recommended for class WaterInterface

[aclum]

See https://microbiomedata.github.io/submission-schema/WaterInterface/ If I look at the linkml source for slot analysis_type for this class has both required and recommended are both set to true. analysis_type: name: analysis_type description: Select all the data types associated or available for this biosample title: analysis/data type examples:

• value: metagenomics; metabolomics; proteomics from_schema: https://w3id.org/nmdc/nmdc see_also:
• MIxS:investigation_type rank: 3 multivalued: true alias: analysis_type owner: WaterInterface domain_of:
• Biosample
• DhMultiviewCommonColumnsMixin slot_group: sample_id_section range: analysis_type_enum required: true recommended: true

[bmeluch]

analysis_type is "recommended" in the NMDC schema definition

Then, in the submission schema, modifications_long.tsv updates it to "required" for all interface classes that use DhMultiviewCommonColumnsMixin (which is all the interfaces)

Except instead of replacing "recommended" with "required", both stick around.

As another example, the same thing is happening with dna_concentration in JgiMgInterface. dna_concentration is "recommended" in the NMDC schema definition, and then updated to be "required" in modifications_long.tsv. The result in the submission schema LinkML source is this:

  dna_concentration:
    name: dna_concentration
    title: DNA concentration in ng/ul
    comments:
    - Units must be in ng/uL. Enter the numerical part only. Must be calculated using
      a fluorometric method. Acceptable values are 0-2000.
    examples:
    - value: '100'
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - nmdc:nucleic_acid_concentration
    rank: 5
    owner: Biosample
    domain_of:
    - Biosample
    - ProcessedSample
    - JgiMgInterface
    slot_group: jgi_metagenomics_section
    range: float
    required: true
    recommended: true
    minimum_value: 0
    maximum_value: 2000

tl;dr I don't know how to fix this but it's happening in a bunch of places in addition to WaterInterface

[turbomam]

Thanks for looking. Should we Zoom and look at it together?

[mslarae13]

@sierra-moxon @turbomam @bmeluch Will you have time to work on this this sprint? Do you think it'll take a couple sprints to identify the issue & resolve it?

[bmeluch]

I looked some more at modifications_long.tsv.

As far as I can tell, the modification action "replace_attribute" should really be named "replace_value". It's updating the value of an attribute but the modifications_and_validation function in sheets-and-friends doesn't actually change the attribute that's there.

People who know about sheets-and-friends, does that sound right? Could we add another possible value for "action" that makes modifications_and_validation work with two attribute names, rather than an attribute name and a value?

[bmeluch]

From the metadata meeting today, 24 Apr 2024, we decided that the most straightforward fix for this is to update modifications_long.tsv so that wherever it adds "required = true" to a slot with "recommended = true" in nmdc-schema, it also updates "recommended = false". Both attributes will still show up in the submission-schema documentation page for slots with this modification, but they will no longer be redundantly both true.

[mslarae13]

I don't think this is fixed... recommended:true is still appearing

@bmeluch @turbomam @sujaypatil96

https://microbiomedata.github.io/nmdc-schema/analysis_type/ https://microbiomedata.github.io/submission-schema/analysis_type/

[bmeluch]

oh no! It looks like the Github Pages documentation site hasn't been updated in a year, if I'm reading this right? Maybe it just hasn't captured recent fixes?

[aclum]

This looks right on the water interface which is I think all we can hope for. This was changed in modifications_long.tsv not in nmdc-schema itself. analysis_type: name: analysis_type description: Select all the data types associated or available for this biosample title: analysis/data type examples:

• value: metagenomics; metabolomics; proteomics from_schema: https://w3id.org/nmdc/nmdc see_also:
• MIxS:investigation_type rank: 3 multivalued: true alias: analysis_type owner: WaterInterface domain_of:
• Biosample
• DhMultiviewCommonColumnsMixin slot_group: sample_id_section range: AnalysisTypeEnum required: true recommended: false

[bmeluch]

Nvm, @aclum is right. This is a correction at the interface level, not the slot level, and the interface pages now read correctly. @mslarae13 we're good!

[mslarae13]

Reviewed with Bea. I was looking at https://microbiomedata.github.io/submission-schema/analysis_type/ & needed to look at the individual (type)Interface pages like https://microbiomedata.github.io/submission-schema/BiofilmInterface/

Separately, we could start a discussion around why analysis_type is only recommended in nmdc-schema. Not required for this issue