done with indicators 75-85 and adjusted tx curr (#59) (#21)

Co-authored-by: Patric Prado <pprado@caa.columbia.edu>

input/cql/HIVConceptsCustom.cql

@@ -73,9 +73,10 @@ 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" : 'Gonorrhoea treatment' from "missing concepts"
 
 valueset "Antenatal care contact": 'http://fhir.org/guides/who/anc-cds/ValueSet/antenatal-care-contact'

input/cql/HIVElements.cql

@@ -2592,9 +2592,11 @@ define "At elevated risk for HIV acquisition B.DE225":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Syndrome or STI for which client is diagnosed
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Syndrome/STI diagnosed B.DE226":
-  exists "Syndrome/STI diagnosed B.DE226 Observation"
+    "Urethral discharge syndrome B.DE227" or "Vaginal discharge syndrome B.DE228" or "Lower Abdominal pain  B.DE229" or "Genital ulcer disease syndrome B.DE230" or
+  "Anorectal discharge B.DE231"
+
 define "Syndrome/STI diagnosed B.DE226 Observation":
   [Observation: Concepts."Syndrome/STI diagnosed - HIV.B.DE226"] O
     where O.status in { 'final', 'amended', 'corrected' }
@@ -2605,7 +2607,7 @@ define "Syndrome/STI diagnosed B.DE226 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Client diagnosed with urethral discharge syndrome
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Urethral discharge syndrome B.DE227":
   exists "Urethral discharge syndrome B.DE227 Condition"
     or exists "Urethral discharge syndrome B.DE227 Observation"
@@ -2622,7 +2624,7 @@ define "Urethral discharge syndrome B.DE227 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Client diagnosed with vaginal discharge syndrome
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Vaginal discharge syndrome B.DE228":
   exists "Vaginal discharge syndrome B.DE228 Condition"
     or exists "Vaginal discharge syndrome B.DE228 Observation"
@@ -2639,12 +2641,10 @@ define "Vaginal discharge syndrome B.DE228 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Client diagnosed with lower abdominal pain
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Lower Abdominal pain  B.DE229":
-  exists "Lower Abdominal pain  B.DE229 Condition"
-    or exists "Lower Abdominal pain  B.DE229 Observation"
-define "Lower Abdominal pain  B.DE229 Condition":
-  [Condition: Concepts."Lower Abdominal pain  - HIV.B.DE229"]
+  exists "Lower Abdominal pain  B.DE229 Observation"
+
 define "Lower Abdominal pain  B.DE229 Observation":
   "Syndrome/STI diagnosed B.DE226 Observation" O
     where O.status in { 'final', 'amended', 'corrected' }
@@ -2656,7 +2656,7 @@ define "Lower Abdominal pain  B.DE229 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Client diagnosed with genital ulcer disease syndrome
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Genital ulcer disease syndrome B.DE230":
   exists "Genital ulcer disease syndrome B.DE230 Condition"
     or exists "Genital ulcer disease syndrome B.DE230 Observation"
@@ -2673,12 +2673,10 @@ define "Genital ulcer disease syndrome B.DE230 Observation":
 @activity: HIV.B23 Offer sexual and reproductive health services
 @description: Client diagnosed with anorectal discharge
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Anorectal discharge B.DE231":
-  exists "Anorectal discharge B.DE231 Condition"
-    or exists "Anorectal discharge B.DE231 Observation"
-define "Anorectal discharge B.DE231 Condition":
-  [Condition: Concepts."Anorectal discharge - HIV.B.DE231"]
+  exists "Anorectal discharge B.DE231 Observation"
+
 define "Anorectal discharge B.DE231 Observation":
   "Syndrome/STI diagnosed B.DE226 Observation" O
     where O.status in { 'final', 'amended', 'corrected' }
@@ -6189,24 +6187,22 @@ define "STI testing and treatment D.DE160 Observation":
 @activity: HIV.D12 Determine recommended screenings and tests
 @description: Date client was tested for hepatitis B virus (HBV)
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "HBsAg test date D.DE161":
-  [Observation: Concepts."HBsAg test date - HIV.D.DE161"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "HBsAg test date D.DE161 Value":
-  "HBsAg test date D.DE161" O
-  return O.value
+  [Procedure] P
+  where P.status = 'completed'
+  and P.code ~ ConceptsCustom."HBsAg test"
+
 /* End of HBsAg test date D.DE161 */
 
+
 /*
 @dataElement: HIV.D.DE162 - HBsAg test result
 @activity: HIV.D12 Determine recommended screenings and tests
 @description: Hepatitis B virus test result (HBsAg)
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "HBsAg test result D.DE162":
-  exists "HBsAg test result D.DE162 Observation"
-define "HBsAg test result D.DE162 Observation":
   [Observation: Concepts."HBsAg test result - HIV.D.DE162"] O
     where O.status in { 'final', 'amended', 'corrected' }
 /* End of HBsAg test result D.DE162 */
@@ -6216,50 +6212,34 @@ define "HBsAg test result D.DE162 Observation":
 @activity: HIV.D12 Determine recommended screenings and tests
 @description: HBsAg test result was positive
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Positive D.DE163":
-  exists "Positive D.DE163 Condition"
-    or exists "Positive D.DE163 Observation"
-define "Positive D.DE163 Condition":
-  [Condition: Concepts."Positive - HIV.D.DE163"]
-define "Positive D.DE163 Observation":
-  "HBsAg test result D.DE162 Observation" O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value ~ Concepts."Positive - HIV.D.DE163"
+  "HBsAg test result D.DE162" O
+  where O.value ~ Concepts."Positive - HIV.D.DE163"
+
 /* End of Positive D.DE163 */
 
 /*
 @dataElement: HIV.D.DE164 - Negative
 @activity: HIV.D12 Determine recommended screenings and tests
 @description: HBsAg test result was negative
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Negative D.DE164":
-  exists "Negative D.DE164 Condition"
-    or exists "Negative D.DE164 Observation"
-define "Negative D.DE164 Condition":
-  [Condition: Concepts."Negative - HIV.D.DE164"]
-define "Negative D.DE164 Observation":
-  "HBsAg test result D.DE162 Observation" O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value ~ Concepts."Negative - HIV.D.DE164"
+  "HBsAg test result D.DE162" O
+  where O.value ~ Concepts."Negative - HIV.D.DE164"
+
 /* End of Negative D.DE164 */
 
 /*
 @dataElement: HIV.D.DE165 - Indeterminate
 @activity: HIV.D12 Determine recommended screenings and tests
 @description: HBsAg test result was indeterminate
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Indeterminate D.DE165":
-  exists "Indeterminate D.DE165 Condition"
-    or exists "Indeterminate D.DE165 Observation"
-define "Indeterminate D.DE165 Condition":
-  [Condition: Concepts."Indeterminate - HIV.D.DE165"]
-define "Indeterminate D.DE165 Observation":
-  "HBsAg test result D.DE162 Observation" O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value ~ Concepts."Indeterminate - HIV.D.DE165"
+    "HBsAg test result D.DE162" O
+  where O.value ~ Concepts."Indeterminate - HIV.D.DE165"
 /* End of Indeterminate D.DE165 */
 
 /*
@@ -6281,13 +6261,12 @@ define "HBV treatment TDF start date Value":
 @activity: HIV.D12 Determine recommended screenings and tests
 @description: Date client was tested for hepatitis C virus (HCV antibody, HCV RNA or HCV core antigen)
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "HCV test date D.DE169":
-  [Observation: Concepts."HCV test date - HIV.D.DE169"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-define "HCV test date D.DE169 Value":
-  "HCV test date D.DE169" O
-  return O.value
+  [Procedure] P
+  where P.status = 'completed'
+  and P.code ~ ConceptsCustom."HCV test"
+
 /* End of HCV test date D.DE169 */
 
 /*
@@ -14760,13 +14739,11 @@ define "ART start date SRV.DE6 Value":
 @activity: HIV.B6 Capture or update client history
 @description: Client is currently pregnant
 */
-// TODO: Replace placeholder with relevant CQL logic
+
 define "Currently pregnant SRV.DE7":
-  exists "Currently pregnant SRV.DE7 Observation"
-define "Currently pregnant SRV.DE7 Observation":
-  [Observation: Concepts."Currently pregnant - HIV.SRV.DE7"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and O.value is true
+  exists "Currently pregnant SRV.DE7 Condition"
+define "Currently pregnant SRV.DE7 Condition":
+  [Condition: Concepts."Currently pregnant - HIV.SRV.DE7"]
 /* End of Currently pregnant SRV.DE7 */
 
 /*

input/cql/HIVIND27Logic.cql

@@ -71,6 +71,8 @@ include FHIRHelpers version '4.0.1'
 include WHOCommon called WCom
 include HIVElements called HE
 include HIVIndicatorElements called HIE
+include HIVConfig called Config
+include HIVConcepts called Concepts
 
 // Indicator Definition
 parameter "Measurement Period" Interval<Date> default Interval[@2023-01-01, @2023-01-30]
@@ -84,10 +86,24 @@ context Patient
 
 define "Measure Population":
    HIE."Has HIV-positive Status"
-   and HIE."On ART H.DE47"
+   and exists(HE."On ART H.DE47" A
+    with [EpisodeOfCare] EOC
+      such that A.context.references(EOC) and 
+      //Not Transferred out
+      not (exists(EOC.type T where T ~ Concepts."On ART - HIV.H.DE47")
+      and EOC.status = 'finished' and EOC.period.toInterval() ends during "Measurement Period")
+      and not exists (
+      EOC.statusHistory H
+      where H.status = 'finished'
+      and H.period.toInterval() ends during "Measurement Period")
+      //On ART for at least one day in measurement period
+    where A.effective.toInterval() starts before end of "Measurement Period"
+    and A.effective.toInterval() ends after start of "Measurement Period"
+    //Not Lost to follow up
+	and (A.effective.toInterval() ends after (end of "Measurement Period" - Config."LTFU Days"))
+   )
    and not HIE."Has death documented"
-   and not HIE."Has transferred out"
-   and not HIE."Is lost to follow-up"
+
 
 /*
  * As defined by Member States

input/cql/HIVIND70Logic.cql

@@ -133,6 +133,7 @@ define "Initial Population":
 
 define "Numerator":
   HIE."Gonorrhoea test date B.DE255"
+  and HIE."Date accessed HIV prevention intervention"
 
 
 /**

input/cql/HIVIND75Logic.cql

@@ -82,6 +82,9 @@ 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]
@@ -104,7 +107,12 @@ define "Initial Population":
  */
 
 define "Numerator":
-  true
+HIE."Has HIV-positive Status"
+  and exists(HE."Positive B.DE257" G
+  with HE."Gonorrhoea test date B.DE255" P
+  such that G.partOf.references(P) and P.performed.toInterval() during "Measurement Period")
+  and HIE."Gonorrhoea treatment start date B.DE260"
+
 
 
 /**
@@ -115,8 +123,32 @@ define "Numerator":
  */
 
 define "Denominator":
-  true
+  HIE."Has HIV-positive Status"
+  and exists(HE."Positive B.DE257" G
+  with HE."Gonorrhoea test date B.DE255" P
+  such that G.partOf.references(P) and P.performed.toInterval() during "Measurement Period")
 
 
 /* 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 "Stratification":
+ HIE."By Administrative Gender Stratifier".code 
+  + ':' + HIE."By Age Stratifier 2"
++ ':' + HIE."By Geographic Region Stratifier"
++ Combine(HIE.patientGroups, ':')

input/cql/HIVIND76Logic.cql

@@ -97,6 +97,9 @@ 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]
@@ -119,7 +122,9 @@ define "Initial Population":
  */
 
 define "Numerator":
-  true
+  exists(HE."Syndrome/STI diagnosed B.DE226 Observation" O
+    where O.effective.toInterval() during "Measurement Period" 
+  and exists (HE."Date accessed HIV prevention intervention" t where t = start of O.effective.toInterval()))
 
 
 /**
@@ -130,8 +135,42 @@ define "Numerator":
  */
 
 define "Denominator":
-  true
+  HIE."Date accessed HIV prevention intervention"
 
 
 /* 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 prevention intervention":
+	HIE."HIV prevention intervention"
+
+  define "STI syndrome":
+	HIE."STI syndrome"
+
+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, ':')
++ Combine(HIE."HIV prevention intervention", ':')
++ ':' + HIE."HIV Status Stratifier".code 
++ Combine(HIE."STI syndrome", ':')