Add fio2_percent and oxygen_flow_rate (#188)

Creates fio2_percent as an observation, transforms oxygen_flow_volume_max into oxygen_flow_rate to store L/min provision of oxygen. Uses presence of an oxygen flow rate as a input to treatment_oxygen_therapy.
globaldothealth · Nov 14, 2023 · ca0b877 · ca0b877
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diff --git a/docs/guide.rst b/docs/guide.rst
@@ -868,12 +868,16 @@ fields describing symptoms, here.
 
 **oxygen_o2hb**: Value (g/dL). Heamoglobin level, lab test.
 
-**oxygen_flow_volume_max**: Value. If the subject received O2 therapy,
-record the maximum flow volume.
+**oxygen_flow_rate**: Value (L/min). Flow rate of oxygen administered.
+Where possible, record the method of oxygen therapy being used, and whether
+this is a maximum or point value. Sometimes recorded in data as FiO2 (L/min).
 
 **oxygen_saturation_percent**: Value (20-100). Use context to note whether
 observation was made on room air, on while on oxygen.
 
+**fio2_percent**: Value (21-100): Fraction of inspired oxygen (concentration
+of oxygen in supplied gas mixture).
+
 **pao2_mmHg**: Value (25-150). Use context to record whether this is an arterial,
 venous or capillary measurement if data is provided. Use mmHg as the
 default unit.

diff --git a/isaric/parsers/ccp-cameroon.toml b/isaric/parsers/ccp-cameroon.toml
@@ -487,7 +487,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q30_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -529,7 +529,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q28_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -571,7 +571,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q37_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -613,7 +613,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q19_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -647,7 +647,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q33_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q33_signs_symptoms", description = "33) Conjunctivitis", ref = "Y/N" }
@@ -691,7 +691,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q12_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -728,7 +728,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q12_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q12_signs_symptoms", description = "12) Cough / Toux", ref = "Y/N" }
@@ -758,7 +758,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q13_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q13_signs_symptoms", description = "13) Cough - with sputum production", ref = "Y/N" }
@@ -788,7 +788,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q14_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q14_signs_symptoms", description = "14) Cough - bloodysputum", ref = "Y/N" }
@@ -818,7 +818,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q32_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q32_signs_symptoms", description = "32) Diarrhoea", ref = "Y/N" }
@@ -848,7 +848,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q6_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q6_signs_symptoms", source_unit = "mmHg", description = "6) Diastolic BP" }
@@ -878,7 +878,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q17_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q17_signs_symptoms", description = "17) Ear pain", ref = "Y/N" }
@@ -908,7 +908,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q22_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q22_signs_symptoms", description = "22) Fatigue , Malaise", ref = "Y/N" }
@@ -938,7 +938,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q27_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q27_signs_symptoms", description = "27) Headache", ref = "Y/N" }
@@ -968,7 +968,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q3_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q3_signs_symptoms", description = "3) HR/ Fréquence cardiaque" }
@@ -998,7 +998,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q11_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q11_signs_symptoms", description = "11) History of fever", ref = "Y/N" }
@@ -1028,7 +1028,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q21_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q21_signs_symptoms", description = "21) Joint pain (Arthralgia)", ref = "Y/N" }
@@ -1068,7 +1068,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q24_signs_symptoms = { "!=" = "" } },
   ]
   [observation.is_present]
@@ -1103,7 +1103,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q24_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q24_signs_symptoms", description = "24) Loss of sense of smell", ref = "Y/N" }
@@ -1133,7 +1133,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q25_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q25_signs_symptoms", description = "25) Loss of flavour", ref = "Y/N" }
@@ -1163,7 +1163,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q26_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q26_signs_symptoms", description = "26) Lower chest wall indrawing", ref = "Y/N" }
@@ -1193,7 +1193,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q36_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q36_signs_symptoms", description = "36) Lymphadenopathy", ref = "Y/N" }
@@ -1223,7 +1223,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q20_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q20_signs_symptoms", description = "20) Muscle aches (Myalgia)", ref = "Y/N" }
@@ -1334,7 +1334,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q9_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q9_signs_symptoms", description = "9) Oxygen saturation" }
@@ -1416,7 +1416,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q4_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q4_signs_symptoms", description = "4) RR / Fréquence Respiratoire" }
@@ -1446,7 +1446,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q16_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q16_signs_symptoms", description = "16) Runny nose (Rhinorrhoea)", ref = "Y/N" }
@@ -1476,7 +1476,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q29_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q29_signs_symptoms", description = "29) Seizures /Convulsions", ref = "Y/N" }
@@ -1519,7 +1519,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q7_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q7_signs_symptoms", description = "7) Severe dehydration", ref = "Y/N" }
@@ -1549,7 +1549,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q23_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q23_signs_symptoms", description = "23) Shortness of breath (Dyspnea)", ref = "Y/N" }
@@ -1579,7 +1579,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q34_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q34_signs_symptoms", description = "34) Skin rash / Eruption cutanée", ref = "Y/N" }
@@ -1609,7 +1609,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q35_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q35_signs_symptoms", description = "35) Skin ulcers", ref = "Y/N" }
@@ -1639,7 +1639,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q15_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q15_signs_symptoms", description = "15) Sore throat", ref = "Y/N" }
@@ -1673,7 +1673,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q8_signs_symptoms = { "!=" = "" } },
     { q8_signs_symptoms = { "!=" = 3 } },
   ]
@@ -1705,7 +1705,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q5_signs_symptoms = { "!=" = "" } },
   ]
   value = { field = "q5_signs_symptoms", description = "5) Systolic BP / Tension artérielle systolique", source_unit = "mmHg" }
@@ -1745,7 +1745,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q1_signs_symptoms = { "!=" = "" } },
   ]
 
@@ -1780,7 +1780,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q31_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q31_signs_symptoms", description = "31) Vomiting / Nausea", ref = "Y/N" }
@@ -1810,7 +1810,7 @@
   phase = "followup"
   date = { field = "q0_signs_symptoms" }
   if.all = [
-    { redcap_event_name = { "=~" = 'm*\d_arm_1' } },
+    { redcap_event_name = { "=~" = 'm\d_arm_1' } },
     { q18_signs_symptoms = { "!=" = "" } },
   ]
   is_present = { field = "q18_signs_symptoms", description = "18) Wheezing", ref = "Y/N" }