Make checkbox fields explicit (#199)

isaric/parsers/ccp-ghana.toml

@@ -33,6 +33,7 @@
       common = { visit_id = { field = "record_id", sensitive = true } }
 
 [adtl.defs]
+  checkbox = { values = { 1 = true } }
   "Y/N/NK" = { values = { 0 = false, 1 = true } }
   uid = { field = "record_id", sensitive = true }
 
@@ -620,8 +621,8 @@
   excludeWhen = "none"
   fields = [
     { field = "daily_antimal_cmyn", description = "Antimalarial agent?", ref = "Y/N/NK" },
-    { field = "daily_exper_cmtype___1", values = { 1 = true } },
-    { field = "daily_exper_cmtype___2", values = { 1 = true } },
+    { field = "daily_exper_cmtype___1", ref = "checkbox" },
+    { field = "daily_exper_cmtype___2", ref = "checkbox" },
   ]
 
 [visit.treatment_antimalarial_type]
@@ -715,7 +716,7 @@
   excludeWhen = "none"
   fields = [
     { field = "can_oxy_ther", description = "High-flow nasal canula oxygen therapy", ref = "Y/N/NK" },
-    { field = "overall_oxygen_cmtype___2", description = "Oxygen therapy interface: HF nasal cannula", ref = "Y/N/NK" },
+    { field = "overall_oxygen_cmtype___2", description = "Oxygen therapy interface: HF nasal cannula", ref = "checkbox" },
     { field = "daily_oxygen_cmtype_1", description = "Oxygen therapy interface: HF nasal cannula", ref = "Y/N/NK" },
   ]
 
@@ -799,27 +800,27 @@
   [[visit.treatment_oxygen_therapy.fields]]
     field = "overall_oxygen_cmtype___1"
     description = "Oxygen therapy?"
-    values = { 1 = true }
+    ref = "checkbox"
 
   [[visit.treatment_oxygen_therapy.fields]]
     field = "overall_oxygen_cmtype___2"
     description = "Oxygen therapy?"
-    values = { 1 = true }
+    ref = "checkbox"
 
   [[visit.treatment_oxygen_therapy.fields]]
     field = "overall_oxygen_cmtype___3"
     description = "Oxygen therapy?"
-    values = { 1 = true }
+    ref = "checkbox"
 
   [[visit.treatment_oxygen_therapy.fields]]
     field = "overall_oxygen_cmtype___4"
     description = "Oxygen therapy?"
-    values = { 1 = true }
+    ref = "checkbox"
 
   [[visit.treatment_oxygen_therapy.fields]]
     field = "overall_oxygen_cmtype___5"
     description = "Oxygen therapy?"
-    values = { 1 = true }
+    ref = "checkbox"
 
   [[visit.treatment_oxygen_therapy.fields]]
     field = "daily_oxygen_cmtype_1"

isaric/parsers/ccp-guinea.toml

@@ -32,6 +32,7 @@
 
 [adtl.defs]
   "Y/N" = { values = { 1 = true, 2 = false } }
+  checkbox = { values = { 1 = true } }
 
   [adtl.defs.admissionDateHierarchy]
     combinedType = "firstNonNull"
@@ -552,8 +553,8 @@
   excludeWhen = "none"
   fields = [
     { field = "daily_antimal_cmyn", description = "Antimalarials?", values = { 1 = true, 0 = false } },
-    { field = "daily_exper_cmtype___1", values = { 1 = true } },
-    { field = "daily_exper_cmtype___2", values = { 1 = true } },
+    { field = "daily_exper_cmtype___1", ref = "checkbox" },
+    { field = "daily_exper_cmtype___2", ref = "checkbox" },
   ]
 
 [visit.treatment_antimalarial_type]

isaric/parsers/ccp-uganda-v2.toml

@@ -26,6 +26,9 @@
     1 = true
     0 = false
 
+  [adtl.defs.checkbox.values]
+    1 = true
+
 [adtl.defs.admissionDateHierarchy]
   combinedType = "firstNonNull"
   fields = [
@@ -598,7 +601,7 @@
     combinedType = "any"
     fields = [
       { field = "cof", ref = "Y/N" },
-      { field = "sick_symp___2", values = { 1 = true, 0 = false } },
+      { field = "sick_symp___2", ref = "checkbox" },
     ]
 
 [[observation]]
@@ -640,7 +643,7 @@
   ] } }
   duration_type = "event"
   phase = "admission"
-  is_present = { field = "sick_symp___3", values = { 1 = true, 0 = false } }
+  is_present = { field = "sick_symp___3", ref = "checkbox" }
 
 [[observation]]
   name = "diarrhoea"
@@ -674,7 +677,7 @@
   date = { field = "onset_date" }
   duration_type = "event"
   phase = "admission"
-  is_present = { field = "sick_symp___1", values = { 1 = true } }
+  is_present = { field = "sick_symp___1", ref = "checkbox" }
 
 [[observation]]
   name = "history_of_fever"

isaric/parsers/cocoa_pediatrics.toml

@@ -24,6 +24,7 @@
 
 [adtl.defs]
   "Y/N/NK" = { values = { 0 = false, 1 = true } }
+  checkbox = { values = { 1 = true } }
 
   [adtl.defs.admissionDateHierarchy]
     combinedType = "firstNonNull"
@@ -376,7 +377,7 @@
   name = "cough"
   phase = "followup"
   date = { field = "date" }
-  is_present = { field = "ongoing_symptoms___2", values = { 1 = true } }
+  is_present = { field = "ongoing_symptoms___2", ref = "checkbox" }
 
 [[observation]]
   name = "cough_dry"
@@ -414,7 +415,7 @@
   name = "diarrhoea"
   phase = "followup"
   date = { field = "date" }
-  is_present = { field = "ongoing_symptoms___10", values = { 1 = true } }
+  is_present = { field = "ongoing_symptoms___10", ref = "checkbox" }
 
 [[observation]]
   name = "diastolic_blood_pressure_mmHg"
@@ -440,7 +441,7 @@
   name = "hepatomegaly"
   phase = "admission"
   date = { field = "hostdat" }
-  is_present = { field = "cardiac_failure___4", values = { 1 = true } }
+  is_present = { field = "cardiac_failure___4", ref = "checkbox" }
 
 [[observation]]
   name = "history_of_fever"
@@ -454,7 +455,7 @@
   name = "history_of_fever"
   phase = "followup"
   date = { field = "date" }
-  is_present = { field = "ongoing_symptoms___1", values = { 1 = true } }
+  is_present = { field = "ongoing_symptoms___1", ref = "checkbox" }
 
 [[observation]]
   name = "fatigue_malaise"
@@ -480,7 +481,7 @@
   name = "feeding_intolerance_pediatrics"
   phase = "followup"
   date = { field = "date" }
-  is_present = { field = "ongoing_symptoms___11", values = { 1 = true } }
+  is_present = { field = "ongoing_symptoms___11", ref = "checkbox" }
 
 [[observation]]
   name = "inability_to_walk"
@@ -556,8 +557,8 @@
     combinedType = "any"
     excludeWhen = "none"
     fields = [
-      { field = "myalgia_ceoccur_v2", values = { 1 = true } },
-      { field = "jointpain_ceoccur_v2", values = { 1 = true } },
+      { field = "myalgia_ceoccur_v2", ref = "checkbox" },
+      { field = "jointpain_ceoccur_v2", ref = "checkbox" },
     ]
 
 [[observation]]
@@ -660,7 +661,7 @@
   name = "shortness_of_breath"
   phase = "followup"
   date = { field = "date" }
-  is_present = { field = "ongoing_symptoms___3", values = { 1 = true } }
+  is_present = { field = "ongoing_symptoms___3", ref = "checkbox" }
 
 [[observation]]
   name = "skin_rash"
@@ -674,7 +675,7 @@
   name = "skin_rash"
   phase = "followup"
   date = { field = "date" }
-  is_present = { field = "ongoing_symptoms___5", values = { 1 = true } }
+  is_present = { field = "ongoing_symptoms___5", ref = "checkbox" }
 
 [[observation]]
   name = "skin_ulcers"
@@ -740,7 +741,7 @@
   name = "vomiting_nausea"
   phase = "followup"
   date = { field = "date" }
-  is_present = { field = "ongoing_symptoms___9", values = { 1 = true } }
+  is_present = { field = "ongoing_symptoms___9", ref = "checkbox" }
 
 [[observation]]
   name = "blantyre_coma_score"

isaric/parsers/datcov-southafrica.toml

@@ -22,6 +22,9 @@
     1 = true
     0 = false
 
+  [adtl.defs.checkbox.values]
+    1 = true
+
 [adtl.defs.subjectId]
   combinedType = "firstNonNull"
   fields = [{ field = "PatientId" }, { field = "NICDCaseID" }]
@@ -135,35 +138,35 @@
   [subject.has_chronic_hematologic_disease]
     field = "flw_ongoing_chronic_list___12"
     description = "Diagnosed, ongoing condition before COVID-19 diagnosis: Blood disorder"
-    ref = "Y/N/NK"
+    ref = "checkbox"
 
   [subject.has_asplenia]
     field = "flw_ongoing_chronic_list___10"
-    ref = "Y/N/NK"
+    ref = "checkbox"
     description = "Asplenia"
 
   [subject.has_tuberculosis]
     combinedType = "any"
     fields = [
       { field = "Tuberculosis Active", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan]
-      { field = "flw_ongoing_chronic_list___20", ref = "Y/N/NK" },
+      { field = "flw_ongoing_chronic_list___20", ref = "checkbox" },
     ]
 
   [subject.has_dementia]
     field = "flw_ongoing_chronic_list___15"
-    ref = "Y/N/NK"
+    ref = "checkbox"
     description = "Dementia"
 
   [subject.has_rheumatologic_disorder]
     field = "flw_ongoing_chronic_list___13"
-    ref = "Y/N/NK"
+    ref = "checkbox"
     description = "Rhemumatologic disorder"
 
   [subject.has_hiv]
     combinedType = "any"
     fields = [
       { field = "HIV Positive", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', nan]}
-      { field = "flw_ongoing_chronic_list___16", ref = "Y/N/NK" },
+      { field = "flw_ongoing_chronic_list___16", ref = "checkbox" },
     ]
 
   [subject.has_obesity]
@@ -175,14 +178,14 @@
     combinedType = "any"
     fields = [
       { field = "Hypertension", values = { 'Yes' = true, 'No' = false } },
-      { field = "flw_ongoing_chronic_list___2", ref = "Y/N/NK" },
+      { field = "flw_ongoing_chronic_list___2", ref = "checkbox" },
     ]
 
   [subject.has_malignant_neoplasm]
     combinedType = "any"
     fields = [
       { field = "Malignancy", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'UNKNOWN', 'Yes', nan]
-      { field = "flw_ongoing_chronic_list___11", ref = "Y/N/NK" },
+      { field = "flw_ongoing_chronic_list___11", ref = "checkbox" },
     ]
 
   [subject.has_smoking]
@@ -196,30 +199,30 @@
     combinedType = "any"
     fields = [
       { field = "Asthma", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan]
-      { field = "flw_ongoing_chronic_list___3", ref = "Y/N/NK" },
+      { field = "flw_ongoing_chronic_list___3", ref = "checkbox" },
     ]
 
   [subject.has_chronic_cardiac_disease]
     combinedType = "any"
     fields = [
       { field = "Cardiac Disease", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'UNKNOWN', 'Yes', nan]
-      { field = "flw_ongoing_chronic_list___1", ref = "Y/N/NK" },
+      { field = "flw_ongoing_chronic_list___1", ref = "checkbox" },
     ]
 
   [subject.has_chronic_kidney_disease]
     combinedType = "any"
     fields = [
       { field = "Chronic Renal Failure", values = { 'Yes' = true, 'No' = false } }, # values = ['No', 'Unknown', 'UNKNOWN', 'Yes', nan] }
-      { field = "flw_ongoing_chronic_list___8", ref = "Y/N/NK" },
+      { field = "flw_ongoing_chronic_list___8", ref = "checkbox" },
     ]
 
   [subject.has_diabetes]
     combinedType = "any"
     fields = [
-      { field = "Diabetes", values = { 'Yes' = true, 'No' = false } },                                  # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan]
-      { field = "flw_ongoing_chronic_list___5", ref = "Y/N/NK", description = "Diabetes Type 1" },
-      { field = "flw_ongoing_chronic_list___6", ref = "Y/N/NK", description = "Diabetes Type 2" },
-      { field = "flw_ongoing_chronic_list___7", ref = "Y/N/NK", description = "Diabetes Gestational" },
+      { field = "Diabetes", values = { 'Yes' = true, 'No' = false } },                                    # values = ['No', 'Unknown', 'Yes', 'UNKNOWN', nan]
+      { field = "flw_ongoing_chronic_list___5", ref = "checkbox", description = "Diabetes Type 1" },
+      { field = "flw_ongoing_chronic_list___6", ref = "checkbox", description = "Diabetes Type 2" },
+      { field = "flw_ongoing_chronic_list___7", ref = "checkbox", description = "Diabetes Gestational" },
     ]
     # can we assume diabetes as a disease was there before COVID? and so the followup data applies here?
 
@@ -233,14 +236,9 @@
 
   [subject.has_liver_disease]
     field = "flw_ongoing_chronic_list___9"
-    ref = "Y/N/NK"
+    ref = "checkbox"
     description = "Liver disease"
 
-    # [subject.has_hiv_viral_suppression]
-    #   field = "HIV Viral Suppression"
-    #   values = { 'Yes' = true, 'No' = false }
-    #   # values = [nan, 'No', 'Unknown', 'Yes']
-
   [subject.has_tuberculosis_past]
     field = "Tuberculosis Past"
     values = { 'Yes' = true, 'No' = false }

isaric/parsers/isaric-ccpuk.toml

@@ -13,6 +13,9 @@
     1 = true
     2 = false
 
+  [adtl.defs.checkbox.values]
+    1 = true
+
 [adtl.defs.admissionDateHierarchy]
   combinedType = "firstNonNull"
   fields = [
@@ -445,7 +448,7 @@
 
   [visit.treatment_antimalarial]
     field = "antiviral_cmtrt___7"
-    values = { 1 = true }
+    ref = "checkbox"
 
   [visit.treatment_antimalarial_type]
     combinedType = "set"