Several DataHarmonizer columns don't accept input, as if they're an empty multi-select enumeration

turbomam commented 2 years ago

reported by @mslarae13

Applies to slots whose range is string and whose multivalued attribute is True.

A tabular representation of the class-slot-usages in the NMDC submission schema was generated following this code snippet.

At least in the short term, this problem will be solved by adding modifications to sheets-for-nmdc-submission-schema with the modifications_and_validation step in this repo's Makefile

Not all of these slots are used in every template.

agrochem_addition
air_particulate_matter_concentration
air_temp_regm
antibiotic_regm
atmospheric_data
biomass
chem_administration
chem_mutagen
climate_environment
diether_lipids
emulsions
fertilizer_regm
fungicide_regm
gaseous_environment
gaseous_substances
gravity
growth_hormone_regm
heavy_metals
herbicide_regm
host_diet
host_family_relation
host_last_meal
host_subspecf_genlin
host_symbiont
humidity_regm
inorg_particles
mechanical_damage
mineral_nutr_regm
misc_param
n_alkanes
non_min_nutr_regm
org_particles
particle_class
perturbation
pesticide_regm
ph_regm
phaeopigments
phosplipid_fatt_acid
pollutants
radiation_regm
rainfall_regm
salt_regm
samp_sort_meth
season_environment
soluble_inorg_mat
soluble_org_mat
standing_water_regm
suspend_solids
volatile_org_comp
water_temp_regm
watering_regm

sample LinkML snippets from `plant-associated`'s slot usage:

      air_temp_regm:
        name: air_temp_regm
        annotations:
          expected_value:
            tag: expected_value
            value: temperature value;treatment interval and duration
          preferred_unit:
            tag: preferred_unit
            value: meter
          occurrence:
            tag: occurrence
            value: m
        description: Information about treatment involving an exposure to varying
          temperatures; should include the temperature, treatment regimen including
          how many times the treatment was repeated, how long each treatment lasted,
          and the start and end time of the entire treatment; can include different
          temperature regimens
        title: air temperature regimen
        examples:
        - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
        from_schema: http://w3id.org/mixs/terms
        aliases:
        - air temperature regimen
        rank: 16
        is_a: core field
        string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
        slot_uri: MIXS:0000551
        multivalued: true
        owner: MIMS
        slot_group: MIxS (modified)
        range: string
        recommended: true

      gaseous_environment:
        name: gaseous_environment
        annotations:
          expected_value:
            tag: expected_value
            value: gaseous compound name;gaseous compound amount;treatment interval
              and duration
          preferred_unit:
            tag: preferred_unit
            value: micromole per liter
          occurrence:
            tag: occurrence
            value: m
        description: Use of conditions with differing gaseous environments; should
          include the name of gaseous compound, amount administered, treatment duration,
          interval and total experimental duration; can include multiple gaseous environment
          regimens
        title: gaseous environment
        examples:
        - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
        from_schema: http://w3id.org/mixs/terms
        aliases:
        - gaseous environment
        rank: 20
        is_a: core field
        string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
        slot_uri: MIXS:0000558
        multivalued: true
        owner: MIMS
        slot_group: MIxS (modified)
        range: string
        recommended: true

      humidity_regm:
        name: humidity_regm
        annotations:
          expected_value:
            tag: expected_value
            value: humidity value;treatment interval and duration
          preferred_unit:
            tag: preferred_unit
            value: gram per cubic meter
          occurrence:
            tag: occurrence
            value: m
        description: Information about treatment involving an exposure to varying
          degree of humidity; information about treatment involving use of growth
          hormones; should include amount of humidity administered, treatment regimen
          including how many times the treatment was repeated, how long each treatment
          lasted, and the start and end time of the entire treatment; can include
          multiple regimens
        title: humidity regimen
        examples:
        - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M
        from_schema: http://w3id.org/mixs/terms
        aliases:
        - humidity regimen
        rank: 21
        is_a: core field
        string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
        slot_uri: MIXS:0000568
        multivalued: true
        owner: MIMS
        slot_group: MIxS (modified)
        range: string
        recommended: true

ddooley commented 2 years ago

I believe this is now fixed with a commit to the master branch script/dataharmonizer/index.js file.

mslarae13 commented 2 years ago

I agree. I have stopped having this issue. @turbomam can we close?

microbiomedata / sheets_and_friends