JgiMg and JgiMt: Add rule that requires a dna_cont_well when the dna_cont_type is "plate"

[turbomam]

But not vice versa

[turbomam]

https://github.com/microbiomedata/nmdc-schema/blob/6455ce2350c134ecce12c993d429d26883f39b6f/src/schema/nmdc.yaml#L227-L250

  Biosample:
    rules:
      - description: Samples in tubes can't have a plate position.
          But plate_position currently does have to be asserted as an empty string.
          Can't be null, None, un-asserted,etc.
          Had wanted to use value_present, but that may not be implemented in the linkml-runtime yet.
        preconditions:
          slot_conditions:
            dna_cont_type:
              equals_string: tube
        postconditions:
          slot_conditions:
            dna_cont_well:
              none_of:
                pattern: ".+"
      - description: Samples in plates must have a plate position that matches the regex. Note the requirement for an empty string in the tube case. Waiting for value_present validation to be added to runtime
        preconditions:
          slot_conditions:
            dna_cont_type:
              equals_string: plate
        postconditions:
          slot_conditions:
            dna_cont_well:
              pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$

[turbomam]

try a simpler rule first?

• when the dna_cont_type= plate, then the dna_volume must be less than 1 (mL?)
• when the dna_cont_type = tube, then the dna_volume must be greater than 1

[turbomam]

JgiMgInterface:
  rules:
    - preconditions:
        slot_conditions:
          dna_cont_type:
            equals_string: plate
      postconditions:
        slot_conditions:
          dna_volume:
            maximum_value: 1
    - preconditions:
        slot_conditions:
          dna_cont_type:
            equals_string: tube
      postconditions:
        slot_conditions:
          dna_volume:
            minimum_value: 1

[turbomam]

[{"preconditions":{"slot_conditions":{"dna_cont_type":{"equals_string":"plate"}}},"postconditions":{"slot_conditions":{"dna_volume":{"maximum_value":1}}}},{"preconditions":{"slot_conditions":{"dna_cont_type":{"equals_string":"tube"}}},"postconditions":{"slot_conditions":{"dna_volume":{"minimum_value":1}}}}]

[turbomam]

yq -i '(.classes.[] | select(.name == "JgiMgInterface") | .rules) = [{"preconditions":{"slot_conditions":{"dna_cont_type":{"equals_string":"plate"}}},"postconditions":{"slot_conditions":{"dna_volume":{"maximum_value":1}}}},{"preconditions":{"slot_conditions":{"dna_cont_type":{"equals_string":"tube"}}},"postconditions":{"slot_conditions":{"dna_volume":{"minimum_value":1}}}}]' local/with_modifications.yaml

[turbomam]

@pkalita-lbl will be working on the emission of rules by gen-jsonschema

[mslarae13]

Duplicate microbiomedata/nmdc-schema#1433

Closing in favor of the issue that includes DNA/RNA plate and other slot dependancies.