Updated naming and fixed some errors (#40)

input/cql/HIVCommon.cql

@@ -28,6 +28,10 @@ define "HIV Positive Condition":
     where C.clinicalStatus ~ HCC."active"
     and exists(C.category CC where CC ~ HCC."encounter-diagnosis")
     and C.code ~ HC."HIV-positive - HIV.B.DE116"
+    sort by start of onset.toInterval()
+
+define "First HIV Positive Condition":
+  First("HIV Positive Condition")
 
 define "HIV Positive Observation":
 [Observation] O
@@ -53,12 +57,10 @@ define "HIV test resulted":
     and O.code ~ HC."Rapid diagnostic test for HIV - HIV.B.DE82"
 
 define "HIV Treatment Active":
-[MedicationStatement] MS
-Sort by MS.effective
+  [MedicationStatement] MS
     where MS.status = 'completed'
     and exists(MS.reasonCode C where C ~ HC."On ART - HIV.H.DE47")
-
-
+    sort by effective
 
 define "HIV PREP Active":
 [MedicationStatement] MS
@@ -121,15 +123,15 @@ define "HIV Test Positive After PEP Prescribed during Measurement Period":
 
 define "Needle Syringe Dispensed":  
   [DeviceUseStatement] DUS
-  with [Observation: HC."Key population member* - HIV.E.DE113"] O
+  with [Observation: HC."Key population member - HIV.E.DE113"] O
       such that DUS.reasonReference.references(O) 
         and O.status in { 'final', 'amended', 'corrected' }
         and exists(O.category OC where OC ~ HCC."social-history")
         and O.value ~ HC."People who inject drugs - HIV.B.DE54"
   where DUS.status = 'completed'
 
 define PWID_person:
-  [Observation: HC."Key population member* - HIV.E.DE113"] O
+  [Observation: HC."Key population member - HIV.E.DE113"] O
   where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."People who inject drugs - HIV.B.DE54"
@@ -301,39 +303,39 @@ define "HIV Status":
 
  define SW:
   exists (
-    [Observation: HC."Key population member* - HIV.E.DE113"] O
+    [Observation: HC."Key population member - HIV.E.DE113"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."Sex worker - HIV.B.DE51"
   )
 
  define MSM:
   exists (
-    [Observation: HC."Key population member* - HIV.E.DE113"] O
+    [Observation: HC."Key population member - HIV.E.DE113"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."Men who have sex with men"
   )
 
   define Trans:
   exists (
-    [Observation: HC."Key population member* - HIV.E.DE113"] O
+    [Observation: HC."Key population member - HIV.E.DE113"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."Trans and gender-diverse people - HIV.B.DE53"
   )
 
   define PWID:
   exists (
-    [Observation: HC."Key population member* - HIV.E.DE113"] O
+    [Observation: HC."Key population member - HIV.E.DE113"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."People who inject drugs - HIV.B.DE54"
   )
 
   define Prisoner:
   exists (
-    [Observation: HC."Key population member* - HIV.E.DE113"] O
+    [Observation: HC."Key population member - HIV.E.DE113"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."People living in prisons and other closed settings"
@@ -360,23 +362,23 @@ define "HIV Status":
 
 define Exposure_Occupational:
   exists (
-    [Observation: HC."HIV exposure type*"] O
+    [Observation: HC."HIV exposure type"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."Occupational"
   )
 
 define Exposure_Non_Occupational_violent:
   exists (
-    [Observation: HC."HIV exposure type*"] O
+    [Observation: HC."HIV exposure type"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."Non-occupational violent"
   )
 
 define Exposure_Non_Occupational_consensual_sex:
   exists (
-    [Observation: HC."HIV exposure type*"] O
+    [Observation: HC."HIV exposure type"] O
     where O.status in { 'final', 'amended', 'corrected' }
     and exists(O.category OC where OC ~ HCC."social-history")
     and O.value ~ HC."Non-occupational consensual sex"
@@ -831,9 +833,9 @@ define "VMMC_adverse_event_Postoperative":
 
   define "Time to start ART":
     case 
-        when difference in days between "First HIV Treatment".effective and "HIV Positive Condition".onset <= 7 then HC."Within 7 days of HIV diagnosis"
-        when difference in days between "First HIV Treatment".effective and "HIV Positive Condition".onset <= 30 then HC."Within 30 days of HIV diagnosis"
-        when difference in days between "First HIV Treatment".effective and "HIV Positive Condition".onset <= 90 then HC."Within 90 days of HIV diagnosis"
+        when difference in days between start of "First HIV Treatment".effective.toInterval() and start of "First HIV Positive Condition".onset.toInterval() <= 7 then HC."Within 7 days of HIV diagnosis"
+        when difference in days between start of "First HIV Treatment".effective.toInterval() and start of "First HIV Positive Condition".onset.toInterval() <= 30 then HC."Within 30 days of HIV diagnosis"
+        when difference in days between start of "First HIV Treatment".effective.toInterval() and start of "First HIV Positive Condition".onset.toInterval() <= 90 then HC."Within 90 days of HIV diagnosis"
     else null
     end
 
@@ -876,28 +878,28 @@ define "VMMC_adverse_event_Postoperative":
 //(including PrEP, OAMT, NSP, STI services, VMMC) 
   define "HIV prevention intervention":
   List<String>{
-    if "HIV PREP Active" then 'PrEP' else null,
+    if exists("HIV PREP Active") then 'PrEP' else null,
     if OAMT_initiated then 'OAMT' else null,
-    if "Needle Syringe Dispensed" then 'NSP' else null,
-    if STI_testing then 'STI services' else null,
-    if VMMC_done then 'VMMC' else null
+    if exists("Needle Syringe Dispensed") then 'NSP' else null,
+    if exists(STI_testing) then 'STI services' else null,
+    if exists(VMMC_done) then 'VMMC' else null
   }
 
 define "Negative Tests within Measurement Period":
-HIC."HIV Negative Observation" O
-    with HIC."Client is at elevated risk for HIV acquisition" HIV
+"HIV Negative Observation" O
+    with "Client is at elevated risk for HIV acquisition" HIV
     such that O.hasMember.references(HIV)
     and O.issued after start of "Measurement Period"
     and O.issued before end of "Measurement Period"
-Sort by O.issued
+    sort by issued
 
 define "First Negative Test within Measurement Period":
 ( First("Negative Tests within Measurement Period"))
 
 define "Negative Tests after First Negative Test":
-HIC."HIV Negative Observation" O
-    with HIC."Client is at elevated risk for HIV acquisition" HIV
-    such that O.hasMember.references(HIV)
-    and O.issued after "First Negative Test within Measurement Period"
-    and O.issued before ("First Negative Test within Measurement Period" + "Testing Interval")
-Sort by O.issued
+  "HIV Negative Observation" O
+    with "Client is at elevated risk for HIV acquisition" HIV
+      such that O.hasMember.references(HIV)
+    where O.issued after "First Negative Test within Measurement Period".issued
+      and O.issued before ("First Negative Test within Measurement Period".issued + "Testing Interval")
+    sort by issued

input/cql/HIVConcepts.cql

@@ -10,14 +10,14 @@
 library HIVConcepts
 codesystem "HIVConcepts": 'http://smart.who.int/hiv/CodeSystem/HIVConcepts'
 
-valueset "Gender* Choices": 'http://smart.who.int/hiv/ValueSet/HIV.A.DE18'
+valueset "Gender Choices": 'http://smart.who.int/hiv/ValueSet/HIV.A.DE18'
 valueset "Reason for visit - HIV.B.DE1 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE1'
 valueset "Referred through partner services Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE5'
 valueset "Type of contact or partner for partner services Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE8'
 valueset "Testing entry point Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE15'
 valueset "Partner HIV status reported Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE33'
-valueset "Key population member type* - HIV.B.DE50 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE50'
-valueset "HIV exposure type* Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE61'
+valueset "Key population member type - HIV.B.DE50 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE50'
+valueset "HIV exposure type Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE61'
 valueset "HIV test type - HIV.B.DE81 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE81'
 valueset "Assay number in testing strategy - HIV.B.DE88 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE88'
 valueset "Test result of HIV assay 1 - HIV.B.DE94 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE94'
@@ -26,7 +26,7 @@ valueset "Test result of HIV assay 3 - HIV.B.DE102 Choices": 'http://smart.who.i
 valueset "Test result of HIV assay 1 repeated - HIV.B.DE106 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE106'
 valueset "HIV test result - HIV.B.DE111 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE111'
 valueset "HIV status Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE115'
-valueset "Probable route of transmission* Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE121'
+valueset "Probable route of transmission Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE121'
 valueset "Counselling provided Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE142'
 valueset "Prevention services offered and referrals - HIV.B.DE149 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE149'
 valueset "Sexual and reproductive health integrated services - HIV.B.DE158 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.B.DE158'
@@ -117,7 +117,7 @@ valueset "TPT regimen type Choices": 'http://smart.who.int/hiv/ValueSet/HIV.D.DE
 valueset "TB preventive treatment TPT status Choices": 'http://smart.who.int/hiv/ValueSet/HIV.D.DE1034'
 valueset "Timing of ART initiation Choices": 'http://smart.who.int/hiv/ValueSet/HIV.E.DE41'
 valueset "Place of delivery Choices": 'http://smart.who.int/hiv/ValueSet/HIV.E.DE67'
-valueset "Key population member type* - HIV.E.DE114 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.E.DE114'
+valueset "Key population member type - HIV.E.DE114 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.E.DE114'
 valueset "Signs of substantial risk of HIV infection - HIV.E.DE155 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.E.DE155'
 valueset "HIV test type - HIV.E.DE168 Choices": 'http://smart.who.int/hiv/ValueSet/HIV.E.DE168'
 valueset "Maternal and child health service visit Choices": 'http://smart.who.int/hiv/ValueSet/HIV.E.DE173'
@@ -153,7 +153,7 @@ valueset "Other priority populations Choices": 'http://smart.who.int/hiv/ValueSe
 code "Visit date - HIV.A.DE3": 'HIV.A.DE3' from "HIVConcepts" display 'Visit date'
 code "Estimated age": 'HIV.A.DE16' from "HIVConcepts" display 'Estimated age'
 code "Age": 'HIV.A.DE17' from "HIVConcepts" display 'Age'
-code "Gender*": 'HIV.A.DE18' from "HIVConcepts" display 'Gender*'
+code "Gender": 'HIV.A.DE18' from "HIVConcepts" display 'Gender*'
 code "Female": 'HIV.A.DE19' from "HIVConcepts" display 'Female'
 code "Male": 'HIV.A.DE20' from "HIVConcepts" display 'Male'
 code "Transgender male": 'HIV.A.DE21' from "HIVConcepts" display 'Transgender male'
@@ -181,15 +181,15 @@ code "Partner HIV status reported": 'HIV.B.DE33' from "HIVConcepts" display 'Par
 code "HIV-positive - HIV.B.DE34": 'HIV.B.DE34' from "HIVConcepts" display 'HIV-positive'
 code "HIV-negative - HIV.B.DE35": 'HIV.B.DE35' from "HIVConcepts" display 'HIV-negative'
 code "Unknown - HIV.B.DE36": 'HIV.B.DE36' from "HIVConcepts" display 'Unknown'
-code "Key population member* - HIV.B.DE49": 'HIV.B.DE49' from "HIVConcepts" display 'Key population member*'
-code "Key population member type* - HIV.B.DE50": 'HIV.B.DE50' from "HIVConcepts" display 'Key population member type*'
+code "Key population member - HIV.B.DE49": 'HIV.B.DE49' from "HIVConcepts" display 'Key population member*'
+code "Key population member type - HIV.B.DE50": 'HIV.B.DE50' from "HIVConcepts" display 'Key population member type*'
 code "Sex worker - HIV.B.DE51": 'HIV.B.DE51' from "HIVConcepts" display 'Sex worker'
 code "Men who have sex with men": 'HIV.B.DE52' from "HIVConcepts" display 'Men who have sex with men'
 code "Trans and gender-diverse people - HIV.B.DE53": 'HIV.B.DE53' from "HIVConcepts" display 'Trans and gender-diverse people'
 code "People who inject drugs - HIV.B.DE54": 'HIV.B.DE54' from "HIVConcepts" display 'People who inject drugs'
 code "People living in prisons and other closed settings": 'HIV.B.DE55' from "HIVConcepts" display 'People living in prisons and other closed settings'
 code "Date HIV test results returned": 'HIV.B.DE60' from "HIVConcepts" display 'Date HIV test results returned'
-code "HIV exposure type*": 'HIV.B.DE61' from "HIVConcepts" display 'HIV exposure type*'
+code "HIV exposure type": 'HIV.B.DE61' from "HIVConcepts" display 'HIV exposure type*'
 code "Occupational": 'HIV.B.DE62' from "HIVConcepts" display 'Occupational'
 code "Non-occupational violent": 'HIV.B.DE63' from "HIVConcepts" display 'Non-occupational violent'
 code "Non-occupational consensual sex": 'HIV.B.DE64' from "HIVConcepts" display 'Non-occupational consensual sex'
@@ -234,7 +234,7 @@ code "HIV status": 'HIV.B.DE115' from "HIVConcepts" display 'HIV status'
 code "HIV-positive - HIV.B.DE116": 'HIV.B.DE116' from "HIVConcepts" display 'HIV-positive'
 code "HIV-negative - HIV.B.DE117": 'HIV.B.DE117' from "HIVConcepts" display 'HIV-negative'
 code "Unknown - HIV.B.DE118": 'HIV.B.DE118' from "HIVConcepts" display 'Unknown'
-code "Probable route of transmission*": 'HIV.B.DE121' from "HIVConcepts" display 'Probable route of transmission*'
+code "Probable route of transmission": 'HIV.B.DE121' from "HIVConcepts" display 'Probable route of transmission*'
 code "Heterosexual sex": 'HIV.B.DE122' from "HIVConcepts" display 'Heterosexual sex'
 code "Sex between men": 'HIV.B.DE123' from "HIVConcepts" display 'Sex between men'
 code "Unprotected intercourse during sex work": 'HIV.B.DE124' from "HIVConcepts" display 'Unprotected intercourse during sex work'
@@ -935,8 +935,8 @@ code "ANC contact date - HIV.E.DE85": 'HIV.E.DE85' from "HIVConcepts" display 'A
 code "Infant date of birth": 'HIV.E.DE87' from "HIVConcepts" display 'Infant date of birth'
 code "Age of infant": 'HIV.E.DE90' from "HIVConcepts" display 'Age of infant'
 code "HIV-exposed infant or child - HIV.E.DE112": 'HIV.E.DE112' from "HIVConcepts" display 'HIV-exposed infant or child'
-code "Key population member* - HIV.E.DE113": 'HIV.E.DE113' from "HIVConcepts" display 'Key population member*'
-code "Key population member type* - HIV.E.DE114": 'HIV.E.DE114' from "HIVConcepts" display 'Key population member type*'
+code "Key population member - HIV.E.DE113": 'HIV.E.DE113' from "HIVConcepts" display 'Key population member*'
+code "Key population member type - HIV.E.DE114": 'HIV.E.DE114' from "HIVConcepts" display 'Key population member type*'
 code "Sex worker - HIV.E.DE115": 'HIV.E.DE115' from "HIVConcepts" display 'Sex worker'
 code "People who inject drugs - HIV.E.DE116": 'HIV.E.DE116' from "HIVConcepts" display 'People who inject drugs'
 code "Trans and gender-diverse people - HIV.E.DE117": 'HIV.E.DE117' from "HIVConcepts" display 'Trans and gender-diverse people'