Updates to Indicators, DT, profiling, and narrative (#20)

* 60-74 indicators done (#55) * Smart HIV DAK Business Processes Translation (#56) * L2 HIV testing and Treatment User scenarios Translations (#53) --------- Co-authored-by: Pprado23 <141263871+Pprado23@users.noreply.github.com> Co-authored-by: abertnamanya <abertnamanya@gmail.com>
I-TECH-UW · Oct 17, 2024 · 3843ac3 · 3843ac3
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diff --git a/input/cql/HIVConceptsCustom.cql b/input/cql/HIVConceptsCustom.cql
@@ -73,6 +73,9 @@ 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 "Gonorrhoea test" : 'Gonorrhoea test' from "missing concepts"
+code "syphilis treatment" : 'syphilis treatment' from "missing concepts"
+code "Gonorrhoea treatment" : 'Gonorrhoea treatment' from "missing concepts"
 
 
 valueset "Antenatal care contact": 'http://fhir.org/guides/who/anc-cds/ValueSet/antenatal-care-contact'
diff --git a/input/cql/HIVElements.cql b/input/cql/HIVElements.cql
@@ -552,13 +552,10 @@ define "Facility-level testing Observation":
 @activity: HIV.B6 Capture or update client history
 @description: Client is currently pregnant
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Currently pregnant B.DE29":
-  exists "Currently pregnant B.DE29 Observation"
-define "Currently pregnant B.DE29 Observation":
-  [Observation: Concepts."Currently pregnant - HIV.B.DE29"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value is true
+  [Condition: Concepts."Currently pregnant - HIV.B.DE29"] C
+  sort by start of prevalenceInterval() 
 /* End of Currently pregnant B.DE29 */
 
 /*
@@ -2800,38 +2797,32 @@ define "Inconclusive B.DE253":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Date of initiation of syphilis treatment
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Syphilis treatment start date B.DE254":
-  [Observation: Concepts."Syphilis treatment start date - HIV.B.DE254"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "Syphilis treatment start date B.DE254 Value":
-  "Syphilis treatment start date B.DE254" O
-  return O.value
+  [MedicationStatement] MS
+    where MS.status = 'completed'
+    and exists(MS.reasonCode C where C ~ ConceptsCustom."syphilis treatment")
 /* End of Syphilis treatment start date B.DE254 */
 
 /*
 @dataElement: HIV.B.DE255 - Gonorrhoea test date
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Date of Gonorrhoea test
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Gonorrhoea test date B.DE255":
-  [Observation: Concepts."Gonorrhoea test date - HIV.B.DE255"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "Gonorrhoea test date B.DE255 Value":
-  "Gonorrhoea test date B.DE255" O
-  return O.value
+  [Procedure] P
+  where P.status = 'completed'
+  and P.code ~ ConceptsCustom."Gonorrhoea test"
 /* End of Gonorrhoea test date B.DE255 */
 
 /*
 @dataElement: HIV.B.DE256 - Gonorrhoea test result
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Result from Gonorrhoea test
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Gonorrhoea test result B.DE256":
-  exists "Gonorrhoea test result B.DE256 Observation"
-define "Gonorrhoea test result B.DE256 Observation":
   [Observation: Concepts."Gonorrhoea test result - HIV.B.DE256"] O
     where O.status in { 'final', 'amended', 'corrected' }
 /* End of Gonorrhoea test result B.DE256 */
@@ -2841,64 +2832,45 @@ define "Gonorrhoea test result B.DE256 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Test result is positive for Neisseria gonorrhoeae
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Positive B.DE257":
-  exists "Positive B.DE257 Condition"
-    or exists "Positive B.DE257 Observation"
-define "Positive B.DE257 Condition":
-  [Condition: Concepts."Positive - HIV.B.DE257"]
-define "Positive B.DE257 Observation":
-  "Gonorrhoea test result B.DE256 Observation" O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value ~ Concepts."Positive - HIV.B.DE257"
+  "Gonorrhoea test result B.DE256" O
+  where O.value ~ Concepts."Positive - HIV.B.DE257"
 /* End of Positive B.DE257 */
 
 /*
 @dataElement: HIV.B.DE258 - Negative
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Test result is negative for Neisseria gonorrhoeae
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Negative B.DE258":
-  exists "Negative B.DE258 Condition"
-    or exists "Negative B.DE258 Observation"
-define "Negative B.DE258 Condition":
-  [Condition: Concepts."Negative - HIV.B.DE258"]
-define "Negative B.DE258 Observation":
-  "Gonorrhoea test result B.DE256 Observation" O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value ~ Concepts."Negative - HIV.B.DE258"
+  "Gonorrhoea test result B.DE256" O
+  where O.value ~ Concepts."Negative - HIV.B.DE258"
+
 /* End of Negative B.DE258 */
 
 /*
 @dataElement: HIV.B.DE259 - Inconclusive
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Test result is inconclusive
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Inconclusive B.DE259":
-  exists "Inconclusive B.DE259 Condition"
-    or exists "Inconclusive B.DE259 Observation"
-define "Inconclusive B.DE259 Condition":
-  [Condition: Concepts."Inconclusive - HIV.B.DE259"]
-define "Inconclusive B.DE259 Observation":
-  "Gonorrhoea test result B.DE256 Observation" O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value ~ Concepts."Inconclusive - HIV.B.DE259"
+  "Gonorrhoea test result B.DE256" O
+  where O.value ~ Concepts."Inconclusive - HIV.B.DE259"
 /* End of Inconclusive B.DE259 */
 
 /*
 @dataElement: HIV.B.DE260 - Gonorrhoea treatment start date
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Date of initiation of Gonorrhoea treatment
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Gonorrhoea treatment start date B.DE260":
-  [Observation: Concepts."Gonorrhoea treatment start date - HIV.B.DE260"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "Gonorrhoea treatment start date B.DE260 Value":
-  "Gonorrhoea treatment start date B.DE260" O
-  return O.value
+  [MedicationStatement] MS
+    where MS.status = 'completed'
+    and exists(MS.reasonCode C where C ~ ConceptsCustom."Gonorrhoea treatment")
 /* End of Gonorrhoea treatment start date B.DE260 */
 
 /*

diff --git a/input/cql/HIVIND60Logic.cql b/input/cql/HIVIND60Logic.cql
@@ -85,9 +85,9 @@ define "Initial Population":
  */
 
 define "Numerator":
-  First(HE."ANC contact date E.DE85") during "Measurement Period"
+  First(HIE."ANC within pregnancy").period.toInterval() during "Measurement Period"
   and exists(HE."Syphilis test date B.DE249" P
-    where start of P.performed.toInterval() = start of First(HE."ANC contact date E.DE85"))
+    where start of P.performed.toInterval() = start of First(HIE."ANC within pregnancy").period.toInterval())
 
 
 /**
@@ -98,7 +98,7 @@ define "Numerator":
  */
 
 define "Denominator":
-  First(HE."ANC contact date E.DE85") during "Measurement Period"
+  First(HIE."ANC within pregnancy").period.toInterval() during "Measurement Period"
 
 
 /* end Populations */

diff --git a/input/cql/HIVIND61Logic.cql b/input/cql/HIVIND61Logic.cql
@@ -79,13 +79,11 @@ define "Initial Population":
  * Calculation: COUNT of pregnant women with "ANC contact date" in reporting period AND "Syphilis test date" on ANY "ANC contact date" for this pregnancy
  */
 
-define "all anc dates":
-flatten{HE."ANC contact date E.DE85"}
 
 define "Numerator":
-  HIE."ANC contact date E.DE85"
+  exists(HIE."ANC within pregnancy within measurement period")
   and exists(HE."Syphilis test date B.DE249" P
-    where exists("all anc dates" t where duration in days of (t intersect P.performed.toInterval()) > 0)
+    where exists(HIE."all anc dates" t where duration in days of (t intersect P.performed.toInterval()) > 0)
   )
 
 
@@ -100,7 +98,7 @@ define "Numerator":
  */
 
 define "Denominator":
-  HIE."ANC contact date E.DE85"
+  exists(HIE."ANC within pregnancy within measurement period")
 
 
 /* end Populations */

diff --git a/input/cql/HIVIND64Logic.cql b/input/cql/HIVIND64Logic.cql
@@ -68,6 +68,9 @@ include HIVCommon version '0.0.1' called HIC
 include FHIRHelpers version '4.0.1'
 
 include WHOCommon called WCom
+include HIVElements called HE
+include HIVIndicatorElements called HIE
+include HIVConfig called Config
 
 // Indicator Definition
 parameter "Measurement Period" Interval<Date> default Interval[@2023-01-01, @2023-01-30]
@@ -89,8 +92,17 @@ define "Initial Population":
  * Calculation: COUNT of pregnant women with first "ANC contact date" for this pregnancy in the reporting period AND with "Syphilis test date" on first "ANC contact date" AND "Syphilis test result"='Positive'
  */
 
+
+
+
+
 define "Numerator":
-  true
+  First(HIE."ANC within pregnancy").period.toInterval() during "Measurement Period"
+  and exists(HE."Positive B.DE251" S
+  with HE."Syphilis test date B.DE249" P
+  such that S.partOf.references(P) and P.performed.toInterval() during "Measurement Period"
+  and start of P.performed.toInterval() = start of HIE."first anc date"
+  )
 
 
 /**
@@ -101,8 +113,30 @@ define "Numerator":
  */
 
 define "Denominator":
-  true
+  First(HIE."ANC within pregnancy").period.toInterval() during "Measurement Period"
+  and exists(HE."Syphilis test date B.DE249" P
+  where P.performed.toInterval() during "Measurement Period"
+  and start of P.performed.toInterval() = start of HIE."first anc date"
+  )
 
 
 /* end Populations */
 
+/*
+ * Disaggregators
+ */
+
+
+define "Age Stratifier":
+	HIE."By Age Stratifier 2"
+
+define "Geographic Region Stratifier":
+	HIE."By Geographic Region Stratifier"
+
+define "HIV Status":
+  HIE."HIV Status Stratifier"
+
+define "Stratification":
+HIE."By Age Stratifier 2"
++ ':' + HIE."By Geographic Region Stratifier"
++ ':' + HIE."HIV Status Stratifier".code 
diff --git a/input/cql/HIVIND65Logic.cql b/input/cql/HIVIND65Logic.cql
@@ -68,6 +68,9 @@ include HIVCommon version '0.0.1' called HIC
 include FHIRHelpers version '4.0.1'
 
 include WHOCommon called WCom
+include HIVElements called HE
+include HIVIndicatorElements called HIE
+include HIVConfig called Config
 
 // Indicator Definition
 parameter "Measurement Period" Interval<Date> default Interval[@2023-01-01, @2023-01-30]
@@ -89,8 +92,12 @@ define "Initial Population":
  * Calculation: COUNT of pregnant women with "ANC contact date" in reporting period AND with "Syphilis test date" on ANY "ANC contact date" for this pregnancy AND "Syphilis test result"='Positive'
  */
 
+
 define "Numerator":
-  true
+  exists(HIE."ANC within pregnancy within measurement period")
+  and exists(HE."Positive B.DE251" S
+  with HE."Syphilis test date B.DE249" P
+    such that S.partOf.references(P) and exists(HIE."all anc dates" t where duration in days of (t intersect P.performed.toInterval()) > 0))
 
 
 /**
@@ -101,8 +108,28 @@ define "Numerator":
  */
 
 define "Denominator":
-  true
+  exists(HIE."ANC within pregnancy within measurement period")
+  and exists(HE."Syphilis test date B.DE249" P
+    where exists(HIE."all anc dates" t where duration in days of (t intersect P.performed.toInterval()) > 0))
 
 
 /* end Populations */
 
+/*
+ * Disaggregators
+ */
+
+
+define "Age Stratifier":
+	HIE."By Age Stratifier 2"
+
+define "Geographic Region Stratifier":
+	HIE."By Geographic Region Stratifier"
+
+define "HIV Status":
+  HIE."HIV Status Stratifier"
+
+define "Stratification":
+HIE."By Age Stratifier 2"
++ ':' + HIE."By Geographic Region Stratifier"
++ ':' + HIE."HIV Status Stratifier".code 
diff --git a/input/cql/HIVIND66Logic.cql b/input/cql/HIVIND66Logic.cql
@@ -96,6 +96,9 @@ include HIVCommon version '0.0.1' called HIC
 include FHIRHelpers version '4.0.1'
 
 include WHOCommon called WCom
+include HIVElements called HE
+include HIVIndicatorElements called HIE
+include HIVConfig called Config
 
 // Indicator Definition
 parameter "Measurement Period" Interval<Date> default Interval[@2023-01-01, @2023-01-30]
@@ -118,7 +121,10 @@ define "Initial Population":
  */
 
 define "Numerator":
-  true
+  exists(HE."Positive B.DE251" S
+  with HE."Syphilis test date B.DE249" P
+  such that S.partOf.references(P) and P.performed.toInterval() during "Measurement Period")
+  and HIE."Syphilis treatment start date B.DE254"
 
 
 /**
@@ -129,8 +135,37 @@ define "Numerator":
  */
 
 define "Denominator":
-  true
+  exists(HE."Positive B.DE251" S
+  with HE."Syphilis test date B.DE249" P
+  such that S.partOf.references(P) and P.performed.toInterval() during "Measurement Period"
+  and exists (HE."Date accessed HIV prevention intervention" t where t = start of P.performed.toInterval()))
 
 
 /* end Populations */
 
+/*
+ * Disaggregators
+ */
+
+define "Administrative Gender Stratifier":
+	HIE."By Administrative Gender Stratifier"
+
+define "Age Stratifier":
+	HIE."By Age Stratifier 2"
+
+define "Geographic Region Stratifier":
+	HIE."By Geographic Region Stratifier"
+
+define "patientGroups Stratifier":
+	HIE."patientGroups"
+
+define "HIV Status":
+  HIE."HIV Status Stratifier"
+
+define "Stratification":
+ HIE."By Administrative Gender Stratifier".code 
+  + ':' + HIE."By Age Stratifier 2"
++ ':' + HIE."By Geographic Region Stratifier"
++ Combine(HIE.patientGroups, ':')
++ ':' + HIE."HIV Status Stratifier".code 
+