Integration of various profiling and indicator work (#64) (#28)

Co-authored-by: Piotr Mankowski <pmanko@uw.edu>

input/cql/HIVCommon.cql

@@ -146,7 +146,7 @@ define function ToDaily(frequency System.Integer, period System.Quantity):
     or end of period = maximum DateTime
 )
 
-  define function MedicationRequestPeriod(Request FHIR.MedicationRequest):
+  define fluent function MedicationRequestPeriod(Request MedicationRequest):
   Request R
     let
       dosage: singleton from R.dosageInstruction,
@@ -209,9 +209,36 @@ define function "DosesPerDay"(frequency Code):
   //dosage * Quantity { value: dosesPerDay, unit: '/d' }
 
 
+define fluent function dailyDose(Request "MedicationRequest"):
+  Request R
+    let
+      dosage: singleton from R.dosageInstruction,
+      doseAndRate: singleton from dosage.doseAndRate,
+      timing: dosage.timing,
+      frequency: Coalesce(timing.repeat.frequencyMax, timing.repeat.frequency),
+      period: System.Quantity { value: timing.repeat.period, unit: timing.repeat.periodUnit.value },
+      doseRange: doseAndRate.dose as Range,
+      doseQuantity: doseAndRate.dose as SimpleQuantity,
+      dose: Coalesce(doseRange.high, doseQuantity),
+      dosesPerDay: Coalesce(ToDaily(frequency, period), Count(timing.repeat.timeOfDay), 1.0),
+      quantity: R.dispenseRequest.quantity
+    return
+      quantity / (dose * dosesPerDay)
 
-
-
+define fluent function dailyDose(Dispense "MedicationDispense"):
+  Dispense D
+    let
+      dosage: singleton from D.dosageInstruction,
+      doseAndRate: singleton from dosage.doseAndRate,
+      timing: dosage.timing,
+      frequency: Coalesce(timing.repeat.frequencyMax, timing.repeat.frequency),
+      period: System.Quantity { value: timing.repeat.period, unit: timing.repeat.periodUnit.value },
+      doseRange: doseAndRate.dose as Range,
+      doseQuantity: doseAndRate.dose as SimpleQuantity,
+      dose: Coalesce(doseRange.high, doseQuantity),
+      dosesPerDay: Coalesce(ToDaily(frequency, period), Count(timing.repeat.timeOfDay), 1.0)
+    return
+      D.quantity / (dose * dosesPerDay)
 
 
 

input/cql/HIVConcepts.cql

@@ -1209,6 +1209,8 @@ code "Date injecting equipment provided": 'HIV.PRV.DE15' from "HIVConcepts" disp
 code "Date OAMT initiated": 'HIV.PRV.DE17' from "HIVConcepts" display 'Date OAMT initiated'
 code "Currently on OAMT": 'HIV.PRV.DE20' from "HIVConcepts" display 'Currently on OAMT'
 code "Retained on OAMT": 'HIV.PRV.DE21' from "HIVConcepts" display 'Retained on OAMT'
+code "Client being inducted on OAMT": 'HIV.PRV.DE22' from "HIVConcepts" display 'Client being inducted on OAMT'
+code "Client on reducing doses of OAMT": 'HIV.PRV.DE23' from "HIVConcepts" display 'Client on reducing doses of OAMT'
 code "Date of loss to follow-up or OAMT stopped": 'HIV.PRV.DE25' from "HIVConcepts" display 'Date of loss to follow-up or OAMT stopped'
 code "Date medications prescribed - HIV.PRV.DE27": 'HIV.PRV.DE27' from "HIVConcepts" display 'Date medications prescribed'
 code "Number of days prescribed - HIV.PRV.DE28": 'HIV.PRV.DE28' from "HIVConcepts" display 'Number of days prescribed'
@@ -1236,3 +1238,6 @@ code "Other priority populations": 'HIV.Config.DE19' from "HIVConcepts" display
 code "Reporting period end date": 'HIV.Config.DE20' from "HIVConcepts" display 'Reporting period end date'
 code "Reporting period start date": 'HIV.Config.DE21' from "HIVConcepts" display 'Reporting period start date'
 code "Reporting date": 'HIV.Config.DE22' from "HIVConcepts" display 'Reporting date'
+
+// Additional
+code "Live birth": 'HIV.E.DE48' from "HIVConcepts" display 'Live birth'

input/cql/HIVConceptsCustom.cql

@@ -4,6 +4,7 @@ codesystem "HIVConceptsCustom": 'http://smart.who.int/hiv/CodeSystem/HIVConcepts
 codesystem "ConditionCategoryCodes": 'http://terminology.hl7.org/CodeSystem/condition-category'
 codesystem "ConditionClinicalStatusCodes": 'http://terminology.hl7.org/CodeSystem/condition-clinical'
 codesystem "ObservationCategoryCodes": 'http://terminology.hl7.org/CodeSystem/observation-category'
+codesystem "missing concepts": 'missing concepts'
 codesystem "Devicestatement-status": 'http://hl7.org/fhir/device-statement-status'
 codesystem "SNOMEDCT:2018-03": 'urn:oid:2.16.840.1.113883.6.96' version 'urn:hl7:version:2018-03'
 codesystem "SNOMEDCT": 'urn:oid:2.16.840.1.113883.6.96'
@@ -63,19 +64,24 @@ code "Two to four times a day (qualifier value)": '396111001' from "SNOMEDCT" di
 code "HTS Visit": 'HTS Visit' from "HIVConceptsCustom"
 
 //not currently provided
-code "needle-syringe": 'needle syringe' from "HIVConceptsCustom"
-code "methadone": 'methadone' from "HIVConceptsCustom"
-code "buprenorphine": 'buprenorphine' from "HIVConceptsCustom"
-code "viral load test": 'viral load test' from "HIVConceptsCustom"
-code "delivery": 'delivery' from "HIVConceptsCustom"
-code "tb treatment": 'tb treatment' from "HIVConceptsCustom"
-code "ART medication": 'ART medication' from "HIVConceptsCustom"
-code "DSD ART eligibility assessed" : 'DSD ART eligibility assessed' from "HIVConceptsCustom"
-code "syphilis test" : 'syphilis test' from "HIVConceptsCustom"
-code "syphilis treatment" : 'syphilis treatment' from "HIVConceptsCustom"
-code "Gonorrhoea test" : 'gonorrhoea test' from "HIVConceptsCustom"
-code "Gonorrhoea treatment" : 'gonorrhoea treatment' from "HIVConceptsCustom"
-code "HBsAg test" : 'HBsAg test' from "HIVConceptsCustom"
-code "HCV viral load" : 'HCV viral load' from "HIVConceptsCustom"
+code "needle-syringe": 'needle syringe' from "missing concepts"
+code "methadone": 'methadone' from "missing concepts"
+code "buprenorphine": 'buprenorphine' from "missing concepts"
+code "viral load test": 'viral load test' from "missing concepts"
+code "delivery": 'delivery' from "missing concepts"
+code "tb treatment": 'tb treatment' from "missing concepts"
+code "ART medication": 'ART medication' from "missing concepts"
+code "DSD ART eligibility assessed" : 'DSD ART eligibility assessed' from "missing concepts"
+code "syphilis test" : 'syphilis test' from "missing concepts"
+code "HBsAg test" : 'HBsAg test' from "missing concepts"
+code "Gonorrhoea test" : 'Gonorrhoea test' from "missing concepts"
+code "syphilis treatment" : 'syphilis treatment' from "missing concepts"
+code "Gonorrhoea treatment" : 'Gonorrhoea treatment' from "missing concepts"
+code "HCV test" : 'HCV test' from "missing concepts"
+code "HCV viral load" : 'HCV viral load' from "missing concepts"
+code "cervical cancer screening test" : 'cervical cancer screening test' from "missing concepts"
+code "cervical precancer lesion treatment" : 'cervical precancer lesion treatment' from "missing concepts"
+code "Invasive cervical cancer treatment" : 'Invasive cervical cancer treatment' from "missing concepts"
+code "Antenatal care contact": 'Antenatal care contact' from "missing concepts"
+
 
-valueset "Antenatal care contact": 'http://fhir.org/guides/who/anc-cds/ValueSet/antenatal-care-contact'