Implement B9 DT and B2 DT (#47)

* Start decision table logic for HIVB9DT; format HIVB7DTLogic

* Two HIV B decision tables

* Update HIVB2DTLogic.cql

* Fix sushi error

---------

Co-authored-by: Mutesasira Moses <[email protected]>

input/cql/HIVB2DTLogic.cql

@@ -21,7 +21,7 @@ library HIVB2DTLogic
 using FHIR version '4.0.1'
 
 include HIVCommon version '0.0.1' called HIC
-include HIVConcepts called HCx
+include HIVConcepts called Concepts
 include HIVEncounterElements called Elements
 include FHIRHelpers version '4.0.1'
 
@@ -47,9 +47,10 @@ define "Age under 10":
  @output: "Immediately take action or refer for care if a client is having this issue"
  */
 define "Immediately take action or refer for care if a client is having this issue":
-  exists(Elements."Signs of serious illness" O
-    where "Age 10 or older" 
-      and O.value ~ HCx."Tachycardia")
+  "Age 10 or older" and exists(
+    Elements."Signs of serious illness Observation" O
+      where O.value ~ Concepts."Tachycardia"
+  )
 
 /*
  @output "Immediately take action or refer for care if client is showing this sign of a serious illness."
@@ -69,45 +70,51 @@ define "Use clinical judgement and consider local epidemiology to determine if s
 define "Guidance":
   case 
   when "Immediately take action or refer for care if a client is having this issue" 
-    then "Immediately take action or refer for care if a client is having this issue."
+    then 'Immediately take action or refer for care if a client is having this issue.'
   when "Immediately take action or refer for care if client is showing this sign of a serious illness" and "Age 10 or older"
-    then "Immediately take action or refer for care if client is showing this sign of a serious illness."
+    then 'Immediately take action or refer for care if client is showing this sign of a serious illness.'
   when "Immediately take action or refer for care if client is showing this sign of a serious illness" and "Age under 10"
-    then """This is a sign and/or symptom of a serious health condition.
+    then '''This is a sign and/or symptom of a serious health condition.
   
-Immediately take action or refer for care if client is showing this sign of a serious illness."""
+Immediately take action or refer for care if client is showing this sign of a serious illness.'''
   else null
   end
 
 /*
  Supporting Logic
 */
 define "Signs of serious illness age 10 or older":
-  "Age 10 or older" and Elements."Signs of serious illness" O
-    where
-      O.value ~ HCx."Tachypnea" or
-      O.value ~ HCx."Unable to walk unaided"
+  "Age 10 or older" and exists(
+    Elements."Signs of serious illness Observation" O
+      where
+        O.value ~ Concepts."Tachypnea" or
+        O.value ~ Concepts."Unable to walk unaided"
+  )
 
 define "Signs of serious illness age under 10":
-  "Age under 10" and Elements."Signs of serious illness" O
-    where 
-      O.value in {
-        HCx."Lethargy - HIV.D.DE22",
-        HCx."Unconsciousness",
-        HCx."Convulsions",
-        HCx."Unable to breastfeed",
-        HCx."Unable to drink",
-        HCx."Repeated vomiting"
-      } 
-  
+  "Age under 10" and exists(
+    Elements."Signs of serious illness Observation" O
+      where
+        O.value ~ Concepts."Lethargy - HIV.D.DE22" or
+        O.value ~ Concepts."Unconsciousness" or
+        O.value ~ Concepts."Convulsions" or
+        O.value ~ Concepts."Unable to breastfeed" or
+        O.value ~ Concepts."Unable to drink" or
+        O.value ~ Concepts."Repeated vomiting"
+    )
+
 define "Signs of serious illness requiring clinical judgement age 10 or older":
-  "Age 10 or older" and Elements."Signs of serious illness" O
-    where
-      O.value ~ HCx."Fever of 39 C or greater" or
-      O.value ~ HCx."Other sign of serious illness"
-
+  "Age 10 or older" and exists(
+    Elements."Signs of serious illness Observation" O
+      where
+        O.value ~ Concepts."Fever of 39 C or greater" or
+        O.value ~ Concepts."Other sign of serious illness"
+  )
+
 define "Signs of serious illness requiring clinical judgement age under 10":
-  "Age under 10" and Elements."Signs of serious illness" O
-    where 
-      O.value ~ HCx."Fever of 39 C or greater" or
-      O.value ~ HCx."Other sign of serious illness"
+  "Age under 10" and exists(
+    Elements."Signs of serious illness Observation" O
+      where
+        O.value ~ Concepts."Fever of 39 C or greater" or
+        O.value ~ Concepts."Other sign of serious illness"
+  )

input/cql/HIVB9DTLogic.cql

@@ -35,7 +35,6 @@ include WHOCommon called WCom
 include WHOConcepts called WCx
 include WHOEncounterElements called WElm
 
-
 context Patient
 
  /*

input/cql/HIVConceptsCustom.cql

@@ -10,6 +10,7 @@ codesystem "SNOMEDCT:2018-03": 'urn:oid:2.16.840.1.113883.6.96' version 'urn:hl7
 codesystem "SNOMEDCT": 'urn:oid:2.16.840.1.113883.6.96'
 codesystem "AdverseEventSeverity": 'http://terminology.hl7.org/CodeSystem/adverse-event-severity'
 codesystem "RoleCode": 'http://terminology.hl7.org/CodeSystem/v3-RoleCode'
+
 code "encounter-diagnosis": 'encounter-diagnosis' from "ConditionCategoryCodes" display 'Encounter Diagnosis'
 
 // Related Person

input/fsh/libraries/HIVB2DTLogic.fsh

@@ -1,7 +1,7 @@
 Instance: HIVB2DTLogic
 InstanceOf: Library
 Title: "HIV.B2.DT Logic"
-Description: "Description not yet available for HIV.B2.DT Logic."
+Description: "HIV.B2.DT Signs of Serious Illness Logic"
 Usage: #definition
 * meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablelibrary"
 * meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablelibrary"

input/fsh/libraries/HIVB9DTLogic.fsh

@@ -1,7 +1,7 @@
 Instance: HIVB9DTLogic
 InstanceOf: Library
 Title: "HIV.B9.DT Logic"
-Description: "Description not yet available for HIV.B9.DT Logic."
+Description: "HIV.B9.DT Re-test Recommendations Logic"
 Usage: #definition
 * meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareablelibrary"
 * meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishablelibrary"

input/fsh/plandefinition/HIVB2DT.fsh

@@ -0,0 +1,33 @@
+Instance: HIVB2DT
+InstanceOf: http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-recommendationdefinition
+Title: "HIV.B2.DT Check for signs of serious illness"
+Description: "Check for signs of serious illness"
+Usage: #definition
+* meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-shareableplandefinition"
+* meta.profile[+] = "http://hl7.org/fhir/uv/crmi/StructureDefinition/crmi-publishableplandefinition"
+* library = Canonical(HIVB2DTLogic)
+* extension[+]
+  * url = "http://hl7.org/fhir/StructureDefinition/cqf-knowledgeCapability"
+  * valueCode = #computable
+* url = "http://smart.who.int/hiv/PlanDefinition/HIVB2DT"
+* name = "HIVB2DT"
+* status = #draft
+* experimental = true
+* publisher = "World Health Organization (WHO)"
+* relatedArtifact[+]
+  * type = #citation
+  * citation = "Consolidated Guidelines on HIV Testing Services (2019)"
+* action[+]
+  * textEquivalent = "Check for signs of serious illness"
+  * action[+]
+    * textEquivalent = "Take appropriate action for client showing signs of serious illness"
+    * condition[+]
+      * kind = #applicability
+      * expression
+        * language = #text/cql
+        * expression = "exists(Guidance)"
+    * dynamicValue[+]
+      * path = "description"
+      * expression
+        * language = #text/cql-identifier
+        * expression = "Guidance"