isaric-followup-fr.toml

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

[adtl]
  name = "isairc-followup-fr"
  description = "French followup survey"

  [adtl.tables.subject]
    kind = "groupBy"
    groupBy = "subject_id"
    aggregation = "lastNotNull"
    schema = "../../schemas/dev/subject.schema.json"
    optional-fields = [
      "sex_at_birth",
      "sex",
      "ethnicity",
      "age",
      "date_of_birth",
      "dob_year",
      "enrolment_date",
    ]

  [adtl.tables.visit]
    kind = "groupBy"
    groupBy = "subject_id"
    aggregation = "lastNotNull"
    schema = "../../schemas/dev/visit.schema.json"
    optional-fields = ["country_iso3", "start_date", "outcome", "date_outcome"]

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

  [adtl.defs."Y/N".values]
    1 = true
    2 = false

    # SUBJECT
    # required fields - subject_id, admission_date, age, sex_at_birth, ethnicity, pathogen

[subject]
  pathogen = "COVID-19"

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

  [subject.earliest_admission_date]
    combinedType = "min"
    fields = [{ field = "ca_admission_date" }, { field = "ca_ni_hospdate" }]

  [subject.icu_admitted]
    field = "ca_ni_icu"
    ref = "Y/N"

  [subject.has_died]
    field = "ca_pat_alive"
    values = { 1 = false, 2 = true }

  [subject.date_death]
    field = "ca_death_date"


    # No visit table as data is followup only

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

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

  [visit.treatment_oxygen_therapy]
    field = "fio2_pao2"
    if = { fio2_pao2 = { ">" = 21 } }
    apply = { function = "isNotNull" }

  [visit.outcome]
    field = "ca_hospit"
    values = { 1 = "hospitalised" }
    if = { ca_same_hospit = 1 }

  [visit.date_outcome]
    field = "ca_date"
    if.all = [{ ca_hospit = 1 }, { ca_same_hospit = 1 }]

    # OBSERVATION


[[observation]]
  name = "glasgow_coma_score"
  date = { field = "ca_date" }
  phase = "followup"
  value = { field = "ca_glasgow", ref = "Y/N" }

[[observation]]
  name = "cough"
  date = { field = "ca_date" }
  phase = "followup"

  [observation.is_present]
    combinedType = "any"
    excludeWhen = "none"
    fields = [
      { field = "ca_cough", ref = "Y/N" },
      { field = "ca_coughsputum", ref = "Y/N" },
    ]

[[observation]]
  name = "cough_with_sputum_production"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_coughsputum", ref = "Y/N" }

[[observation]]
  name = "fatigue_malaise"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_fatigue", ref = "Y/N" }

[[observation]]
  name = "headache"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_headache", ref = "Y/N" }

[[observation]]
  name = "joint_pain"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_arthralgia", ref = "Y/N" }

[[observation]]
  name = "musculoskeletal_pain"
  phase = "followup"
  date = { field = "ca_date" }

  [observation.is_present]
    combinedType = "any"
    excludeWhen = "none"
    fields = [
      { field = "ca_myalgia", values = { 1 = true } },
      { field = "ca_arthralgia", values = { 1 = true } },
    ]

[[observation]]
  name = "loss_of_smell_or_taste"
  phase = "followup"
  date = { field = "ca_date" }

  [observation.is_present]
    combinedType = "any"
    fields = [
      { field = "ca_anosmia", ref = "Y/N" },
      { field = "ca_ageusia", ref = "Y/N" },
    ]

[[observation]]
  name = "loss_of_smell"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_anosmia", ref = "Y/N" }

[[observation]]
  name = "loss_of_taste"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_ageusia", ref = "Y/N" }

[[observation]]
  name = "muscle_aches"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_myalgia", ref = "Y/N" }

[[observation]]
  name = "shortness_of_breath"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_dyspnea", ref = "Y/N" }

[[observation]]
  name = "wheezing"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_wheezing", ref = "Y/N" }

[[observation]]
  name = "lung_sounds"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_crackles", ref = "Y/N" }

[[observation]]
  name = "cyanosis"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_cyanosis", ref = "Y/N" }

[[observation]]
  name = "sore_throat"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_sorethroat", ref = "Y/N" }

[[observation]]
  name = "temperature_celsius"
  phase = "followup"
  date = { field = "ca_date" }
  value = { field = "ca_temp" }

[[observation]]
  name = "diastolic_blood_pressure_mmHg"
  phase = "followup"
  date = { field = "ca_date" }
  value = { field = "ca_diasto" }

[[observation]]
  name = "systolic_blood_pressure_mmHg"
  phase = "followup"
  date = { field = "ca_date" }
  value = { field = "ca_systo" }

[[observation]]
  name = "heart_rate_bpm"
  phase = "followup"
  date = { field = "ca_date" }
  value = { field = "ca_hr" }

[[observation]]
  name = "respiratory_rate"
  phase = "followup"
  date = { field = "ca_date" }
  value = { field = "ca_rr" }

[[observation]]
  name = "oxygen_saturation_percent"
  phase = "followup"
  date = { field = "ca_date" }
  value = { field = "ca_o2" }

  [observation.context]
    combinedType = "set"
    excludeWhen = "none"
    fields = [
      { field = "ca_ambientair", values = { 1 = "on room air" } },
      { field = "ca_oxygentherapy", values = { 1 = "on oxygen therapy" } },
    ]

[[observation]]
  name = "hepatomegaly"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_hepatomegaly", ref = "Y/N" }

[[observation]]
  name = "lymphadenopathy"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_adenopathy", ref = "Y/N" }

[[observation]]
  name = "oxygen_o2hb"
  phase = "followup"
  date = { field = "ca_date" }
  value = { field = "ca_hb_lborres", unit = "g/dL", source_unit = { field = "ca_hb_lborresu", values = { 1 = "g/L", 2 = "g/dL", 3 = "mg/dl" } } } #, 4 = "mmol/L"

[[observation]]
  name = "fio2_percent"
  phase = "followup"
  date = { field = "abg_date" }
  value = { field = "fio2_pao2", unit = "%" }

[[observation]]
  name = "pao2_mmHg"
  phase = "followup"
  date = { field = "abg_date" }
  value = { field = "abg_pao2", source_unit = { field = "abg_pao2_unit", values = { 1 = "mmHg", 2 = "kPa" } }, unit = "mmHg" }
  context = ['arterial']

[[observation]]
  name = "pco2_mmHg"
  phase = "followup"
  date = { field = "abg_date" }
  value = { field = "abg_paco2", source_unit = { field = "abg_paco2_unit", values = { 1 = "mmHg", 2 = "kPa" } }, unit = "mmHg" }
  context = ['arterial']

[[observation]]
  name = "pH"
  phase = "followup"
  date = { field = "abg_date" }
  value = { field = "abg_ph" }
  context = ['arterial']

[[observation]]
  name = "runny_nose"
  phase = "followup"
  date = { field = "ca_date" }
  is_present = { field = "ca_runnynose", ref = "Y/N" }