uganda-vri-v1.toml

#:schema ../../schemas/dev/parser.schema.json

[adtl]
  name = "uganda-vri.toml"
  description = "uganda.toml"
  defaultDateFormat = "%d/%m/%Y"

  [adtl.tables.subject]
    kind = "groupBy"
    groupBy = "subject_id"
    aggregation = "lastNotNull"
    schema = "../../schemas/dev/subject.schema.json"
    optional-fields = ["ethnicity"]

  [adtl.tables.visit]
    kind = "groupBy"
    groupBy = "visit_id"
    aggregation = "lastNotNull"
    schema = "../../schemas/dev/visit.schema.json"

  [adtl.tables.observation]
    kind = "oneToMany"
    schema = "../../schemas/dev/observation.schema.json"
    common = { visit_id = { field = "record_id", sensitive = true } }

  [adtl.defs."Y/N"]
    values = { 0 = false, 1 = true }

[subject]
  pathogen = "COVID-19"

  [subject.subject_id]
    field = "record_id"
    sensitive = true

  [subject.enrolment_date]
    field = "investigate_date"

  [subject.earliest_admission_date]
    combinedType = "min"
    fields = [{ field = "hospitalization_date" }]

  [subject.age]
    field = "age"
    source_unit = { field = "age_unit", values = { 1 = "years", 2 = "months", 3 = "days" } }
    unit = "years"

  [subject.dob_year]
    combinedType = "firstNonNull"
    fields = [
      { field = "age", if = { age_unit = 1 }, apply = { function = "startYear", params = [
        "$hospitalization_date",
        2022,
        "%d/%m/%Y",
      ] } },
      { field = "age", if = { age_unit = 2 }, apply = { function = "startYear", params = [
        "$hospitalization_date",
        2022,
        "%d/%m/%Y",
        "months",
      ] } },
      { field = "age", if = { age_unit = 3 }, apply = { function = "startYear", params = [
        "$hospitalization_date",
        2022,
        "%d/%m/%Y",
        "days",
      ] } },
    ]

  [subject.dob_month]
    combinedType = "firstNonNull"
    fields = [
      { field = "age", if = { age_unit = 2 }, apply = { function = "startMonth", params = [
        "$hospitalization_date",
        2022,
        "%d/%m/%Y",
      ] } },
      { field = "age", if = { age_unit = 3 }, apply = { function = "startMonth", params = [
        "$hospitalization_date",
        2022,
        "%d/%m/%Y",
        "days",
      ] } },
    ]

  [subject.sex]
    field = "sex"
    values = { 1 = "male", 0 = "female" }

  [subject.works_lab]
    field = "occupation"
    values = { 1 = false, 2 = false, 3 = false, 4 = false, 5 = false, 6 = true, 7 = false, 8 = false, 9 = false, 10 = false, 11 = false, 12 = false }

  [subject.works_healthcare]
    field = "occupation"
    values = { 1 = false, 2 = false, 3 = false, 4 = false, 5 = true, 6 = false, 7 = false, 8 = false, 9 = false, 10 = false, 11 = false, 12 = false }

  [subject.has_hiv]
    field = "hiv_aids"
    ref = "Y/N"

  [subject.has_hypertension]
    field = "hypertens"
    ref = "Y/N"

  [subject.has_smoking]
    field = "smok"

    [subject.has_smoking.values]
      1 = "current"
      2 = "former"
      0 = "never"

[subject.has_asthma]
  field = "asthma"
  ref = "Y/N"

[subject.has_chronic_kidney_disease]
  field = "kidney_dse"
  ref = "Y/N"

[subject.has_diabetes]
  field = "diab"
  ref = "Y/N"

[subject.has_liver_disease]
  field = "liver_dse"
  ref = "Y/N"

[subject.has_hiv_art]
  field = "art"
  ref = "Y/N"

[subject.has_chronic_cardiac_disease]
  field = "heart_dse"
  ref = "Y/N"

[subject.has_tuberculosis]
  field = "activ_tb"
  ref = "Y/N"

[subject.has_tuberculosis_past]
  field = "priortb"
  ref = "Y/N"

[subject.has_malignant_neoplasm]
  field = "hem_dse"
  ref = "Y/N"

[subject.has_died] # type - boolean
  field = "outcome"
  values = { 2 = true }

[subject.date_death]
  field = "outcome_date"
  if = { outcome = 2 }


  # VISIT
  # required fields - "visit_id", "subject_id", "country_iso3", "start_date", "outcome", "date_outcome"

[visit]
  country_iso3 = "UGA"

  [visit.subject_id]
    field = "record_id"
    sensitive = true

  [visit.visit_id]
    field = "record_id"
    sensitive = true

  [visit.start_date]
    field = "hospitalization_date"

  [visit.pathogen_test_date]
    field = "oro_date"

  [visit.transfer_from_other_facility]
    field = "admission"
    values = { 4 = true }

  [visit.treatment_inotropes_vasopressors]
    field = "vasopressor"
    ref = "Y/N"

  [visit.treatment_oxygen_therapy]
    field = "daily_oxy"
    ref = "Y/N"

  [visit.treatment_antibiotics]
    field = "daily_antibiotic"
    ref = "Y/N"

  [visit.treatment_antibiotics_type]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "daily_antibiotic_type___1", values = { 1 = "Ceftriaxone" } },
      { field = "daily_antibiotic_type___2", values = { 1 = "Metronidazole" } },
      { field = "daily_antibiotic_type___3", values = { 1 = "Erythromycin" } },
      { field = "daily_antibiotic_type___4", values = { 1 = "Levofloxacin" } },
      { field = "daily_antibiotic_type___5", values = { 1 = "Cirofloxacin" } },
      { field = "daily_antibiotic_type___6", values = { 1 = "Gentamicin" } },
      { field = "daily_antibiotic_type___7", values = { 1 = "Co-trimoxazole" } },
      { field = "daily_antibiotic_type___8", values = { 1 = "Amoxacillin" } },
      { field = "daily_antibiotic_type___9", values = { 1 = "Penicillin" } },
      { field = "daily_antibiotic_type___10", values = { 1 = "Fluconazole" } },
      { field = "antibio_meds_oth" },
    ]

  [visit.treatment_antimalarial]
    combinedType = "any"
    excludeWhen = "none"
    fields = [
      { field = "daily_antimal", ref = "Y/N" },
      { field = "daily_antimal_typ___1", values = { 1 = true } },
      { field = "daily_antimal_typ___2", values = { 1 = true } },
      { field = "daily_antimal_typ___3", values = { 1 = true } },
    ]

  [visit.treatment_cardiovascular_support]
    combinedType = "any"
    fields = [{ field = "vasopressor", ref = "Y/N" }]

  [visit.treatment_antimalarial_type]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "daily_antimal_typ___1", values = { 1 = "Quinine" } },
      { field = "daily_antimal_typ___2", values = { 1 = "Coartem" } },
      { field = "daily_antimal_typ___3", values = { 1 = "Artesunate" } },
      { field = "daily_antimal_oth" },
    ]

  [visit.treatment_intravenous_fluids]
    field = "daily_iv_fluids"
    ref = "Y/N"

  [visit.outcome]
    field = "outcome"

    [visit.outcome.values]
      1 = "discharged"
      2 = "death"
      3 = "transferred"

[visit.date_outcome]
  field = "outcome_date"

  # OBSERVATION
  # required fields - phase, date, name

[[observation]]
  name = "avpu"
  date = { field = "vital_signs_date" }
  phase = "study"
  text = { field = "avpu", values = { 1 = "Alert", 2 = "Voice", 3 = "Pain", 4 = "Unresponsive" } }

[[observation]]
  name = "diastolic_blood_pressure_mmHg"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  value = { field = "diastol" }
  if.all = [{ diastol = { "!=" = "" } }, { diastol = { "!=" = 0 } }]

[[observation]]
  name = "diastolic_blood_pressure_mmHg"
  date = { field = "vital_signs_date" }
  phase = "study"
  value = { field = "diastol_iso" }
  if.all = [{ diastol_iso = { "!=" = "" } }, { diastol_iso = { "!=" = 0 } }]

[[observation]]
  name = "glasgow_coma_score"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  value = { field = "gcs" }
  if.all = [{ gcs = { "!=" = "" } }, { gcs = { "!=" = 0 } }]

[[observation]]
  name = "glasgow_coma_score"
  date = { field = "vital_signs_date" }
  phase = "study"
  value = { field = "mental" }
  if.all = [{ mental = { "!=" = "" } }, { mental = { "!=" = 0 } }]

[[observation]]
  name = "bleeding_haemorrhage"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "bleed", ref = "Y/N" }

[[observation]]
  name = "confusion"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "confused", ref = "Y/N" }

[[observation]]
  name = "cough"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "cof", ref = "Y/N" }

[[observation]]
  name = "diarrhoea"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "diarr", ref = "Y/N" }

[[observation]]
  name = "headache"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "head", ref = "Y/N" }

[[observation]]
  name = "history_of_fever"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "fever_hist", ref = "Y/N" }

[[observation]] # CHECK THIS!
  name = "inability_to_walk_scale"
  date = { field = "date_30" }
  phase = "followup"
  value = { field = "move_v2", values = { 1 = 1, 2 = 2, 3 = 4 } }
  context = ['walk around the home']

[[observation]] # CHECK THIS!
  name = "inability_to_walk_scale"
  date = { field = "date_30" }
  phase = "followup"
  value = { field = "walk_v2", values = { 1 = 1, 2 = 2, 3 = 4 } }
  context = ['walk on a flat surface for 20 mins']

[[observation]] # CHECK THIS!
  name = "inability_to_walk_scale"
  date = { field = "date_30" }
  phase = "followup"
  value = { field = "stairs_v2", values = { 1 = 1, 2 = 2, 3 = 4 } }
  context = ['walk up a hill']

[[observation]] # CHECK THIS!
  name = "inability_to_walk_scale"
  date = { field = "date_60" }
  phase = "followup"
  value = { field = "move_v60", values = { 1 = 1, 2 = 2, 3 = 4 } }
  context = ['walk around the home']

[[observation]] # CHECK THIS!
  name = "inability_to_walk_scale"
  date = { field = "date_60" }
  phase = "followup"
  value = { field = "walk_v60", values = { 1 = 1, 2 = 2, 3 = 4 } }
  context = ['walk on a flat surface for 20 mins']

[[observation]] # CHECK THIS!
  name = "inability_to_walk_scale"
  date = { field = "date_60" }
  phase = "followup"
  value = { field = "stairs_v60", values = { 1 = 1, 2 = 2, 3 = 4 } }
  context = ['walk up a hill']

[[observation]] # CHECK THIS!
  name = "inability_to_walk"
  date = { field = "vital_signs_date" }
  phase = "study"
  is_present = { field = "assist_study", ref = "Y/N" }
  context = ['requires assistance to walk/get out of bed']

[[observation]]
  name = "lower_chest_wall_indrawing"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "indraw", ref = "Y/N" }

[[observation]]
  name = "runny_nose"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "runny_nose", ref = "Y/N" }

[[observation]]
  name = "seizures"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "seizure", ref = "Y/N" }

[[observation]]
  name = "shortness_of_breath"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "breath", ref = "Y/N" }

[[observation]]
  name = "skin_rash"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "rash_skin", ref = "Y/N" }

[[observation]]
  name = "sore_throat"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "throat", ref = "Y/N" }

# data is mostly very short decimals (e.g. 0.01, 0.03...) possible data entry issues meaning 1, 3 seconds?
[[observation]] # SHOULD WE MAKE THIS A MIN OR MAX OF the recorded values? i.e., minimum(caps_1, caps_2, caps_3)
  name = "sternal_capillary_refill_time_greater_2s"
  date = { field = "vital_signs_date" }
  phase = "study"
  if.all = [{ caps_1 = { "!=" = "" } }, { caps_1 = { ">" = 2 } }]
  [observation.is_present]
    field = "caps_1"
    apply = { function = "isNotNull" }

[[observation]]
  name = "sternal_capillary_refill_time_greater_2s"
  date = { field = "vital_signs_date" }
  phase = "study"
  if.all = [{ caps_2 = { "!=" = "" } }, { caps_2 = { ">" = 2 } }]
  [observation.is_present]
    field = "caps_2"
    apply = { function = "isNotNull" }

[[observation]]
  name = "sternal_capillary_refill_time_greater_2s"
  date = { field = "vital_signs_date" }
  phase = "study"
  if.all = [{ caps_3 = { "!=" = "" } }, { caps_3 = { ">" = 2 } }]
  [observation.is_present]
    field = "caps_3"
    apply = { function = "isNotNull" }

[[observation]]
  name = "vomiting_nausea"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  is_present = { field = "vomi", ref = "Y/N" }

[[observation]]
  name = "heart_rate_bpm"
  date = { field = "vital_signs_date" }
  phase = "study"
  value = { field = "hr_study" }
  if.all = [{ hr_study = { "!=" = "" } }, { hr_study = { "!=" = 0 } }]

[[observation]]
  name = "heart_rate_bpm"
  date = { field = "vital_signs_date" }
  phase = "study"
  value = { field = "pulse_iso" }
  if.all = [{ pulse_iso = { "!=" = "" } }, { pulse_iso = { "!=" = 0 } }]

[[observation]]
  name = "mid_upper_arm_circumference_cm"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  value = { field = "muac" }
  if.all = [{ muac = { "!=" = "" } }, { muac = { "!=" = 0 } }]

[[observation]]
  name = "oxygen_o2hb"
  phase = "study"
  date = { field = "hospitalization_date" }
  value = { field = "heamogl" }

[[observation]]
  name = "oxygen_saturation_percent"
  date = { field = "hospitalization_date" }
  phase = "admission"
  value = { field = "oxy_satu" }
  if.all = [{ oxy_satu = { "!=" = "" } }, { oxy_satu = { "!=" = 0 } }]

  [observation.context]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "oxy_thpy", values = { 1 = "Room air", 2 = "Oxygen therapy" } },
    ]

[[observation]]
  name = "oxygen_saturation_percent"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  value = { field = "o2_satu" }
  if.all = [{ o2_satu = { "!=" = "" } }, { o2_satu = { "!=" = 0 } }]

  [observation.context]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "ox_type", values = { 1 = "Room air", 2 = "Oxygen therapy" } },
    ]

[[observation]]
  name = "respiratory_rate"
  date = { field = "vital_signs_date" }
  phase = "study"
  value = { field = "rr_iso" }
  if.all = [{ rr_iso = { "!=" = "" } }, { rr_iso = { "!=" = 0 } }]

[[observation]]
  name = "respiratory_rate"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  value = { field = "rr_study" }
  if.all = [{ rr_study = { "!=" = "" } }, { rr_study = { "!=" = 0 } }]

[[observation]]
  name = "systolic_blood_pressure_mmHg"
  date = { field = "vital_signs_date" }
  phase = "study"
  value = { field = "systol_iso" }
  if.all = [{ systol_iso = { "!=" = "" } }, { systol_iso = { "!=" = 0 } }]

[[observation]]
  name = "systolic_blood_pressure_mmHg"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  value = { field = "systol" }
  if.all = [{ systol = { "!=" = "" } }, { systol = { "!=" = 0 } }]

[[observation]]
  name = "temperature_celsius"
  date = { field = "outcome_date" }
  start_date = { field = "hospitalization_date" }
  duration_type = "event"
  phase = "study"
  value = { field = "temp_study" }
  if.all = [{ temp_study = { "!=" = "" } }, { temp_study = { "!=" = 0 } }]