Add in updates for Hepatitis B and Polio into the main branch

.gitignore

@@ -7,3 +7,5 @@ bundles
 *.jar
 .DS_Store
 **/tests-*-bundle.json
+node_modules/
+outputs/*

input/cql/IMMZCommon.cql

@@ -96,9 +96,19 @@ define "Preterm":
     return O.value
 
 //Observed Preterm birth
+/*
 define "Preterm Birth":
   [Observation] O
     where (O.value as CodeableConcept) in IMMZc.PretermBirth
+*/
+
+define "Preterm Birth Observation":
+  [Observation: IMMZc."Preterm Birth"] O
+    where O.value as FHIR.boolean = true
+    sort by issued desc
+
+define "Preterm Birth":
+  exists("Preterm Birth Observation")
 
 //@dataElement Adverse Event:
 define "Adverse Event":
@@ -152,18 +162,24 @@ define "Symptomatic HIV Infection Condition":
 define "Severely immunocompromised Condition":
   [Condition: IMMZc."Severely immunocompromised"]
 
+define "Immunodeficiency syndromes Condition":
+  [Condition: IMMZc."Immunodeficiency syndromes"]
+
 define "Breastfeeding Condition":
   [Condition: IMMZc."Breastfeeding"]
 
 /******************************
  * Test Results
  */
 
-
+/*
 define "Patient birth weight observation value":
 [Observation: code in IMMZc."Patient birth weight observation value"] O
   return O.value as FHIR.Quantity
-
+*/
+define "Patient birth weight in grams":
+  First([Observation: IMMZc."Birth Weight in Grams"] O
+    sort by issued desc).value as FHIR.integer
 /** 
  * @dataElement Patient age in years
  */

input/cql/IMMZConcepts.cql

@@ -23,8 +23,8 @@ valueset "WHO ATC": 'http://hl7.org/fhir/uv/ips/ValueSet/whoatc-uv-ips'
 valueset "Negative Result": 'http://smart.who.int/ig/smart-immunizations/ValueSet/Negativetestresult-values'
 valueset "Positive Result": 'http://smart.who.int/ig/smart-immunizations/ValueSet/PositiveTestResult-values'
 valueset "Immunocompromised": 'http://smart.who.int/ig/smart-immunizations/ValueSet/Immunocompromised-values'
-valueset "Patient birth weight observation value": 'http://smart.who.int/ig/smart-immunizations/ValueSet/Birthweight-values'
-valueset "PretermBirth": 'http://smart.who.int/ig/smart-immunizations/ValueSet/Preterm-values'
+//valueset "Patient birth weight observation value": 'http://smart.who.int/ig/smart-immunizations/ValueSet/Birthweight-values'
+//valueset "PretermBirth": 'http://smart.who.int/ig/smart-immunizations/ValueSet/Preterm-values'
 valueset "Live Attenuated": 'http://smart.who.int/ig/smart-immunizations/ValueSet/LiveAttenuatedVaccines'
 
 //valueset "Target Disease": 'http://hl7.org/fhir/ValueSet/immunization-target-disease'
@@ -40,6 +40,10 @@ valueset "ARV Drugs": 'http://smart.who.int/ig/smart-immunizations/ValueSet/ARVD
 valueset "MCV Vaccine": 'http://smart.who.int/ig/smart-immunizations/ValueSet/IMMZ.Z.DE9'
 valueset "Yellow Fever Vaccine": 'http://smart.who.int/ig/smart-immunizations/ValueSet/IMMZ.Z.DE23'
 valueset "Polio Vaccine": 'http://smart.who.int/ig/smart-immunizations/ValueSet/IMMZ.Z.DE14'
+valueset "Polio Vaccine - bOPV": 'http://smart.who.int/ig/smart-immunizations/ValueSet/IMMZ.Z.DE14.bOPV'
+valueset "Polio Vaccine - IPV": 'http://smart.who.int/ig/smart-immunizations/ValueSet/IMMZ.Z.DE14.IPV'
+valueset "Hepatitis B Vaccine": 'http://smart.who.int/ig/smart-immunizations/ValueSet/IMMZ.Z.DE6'
+
 
 /*
 // Plugin is complaining about not finding these so that should be resolved, but here until it can be fixed
@@ -48,6 +52,9 @@ valueset "Cholera Vaccine": 'http://smart.who.int/ig/smart-immunizations/ValueSe
 */
 
 
+code "Birth Weight in Grams": 'DE29' from "IMMZ.D1" display 'Birth Weight in Grams'
+code "Preterm Birth": 'DE15' from "IMMZ.D1" display 'Preterm Birth'
+
 code "Adverse Event Severity": '246112005' from "SNOMED-CT" display 'Severity (attribute)'
 code "Adverse Event Manifestation": '246112005' from "SNOMED-CT" display 'Severity (attribute)'
 
@@ -56,5 +63,6 @@ code "Severely immunosuppressed": 'DE165' from "IMMZ.D" display 'Severely immuno
 code "History of anaphylactic reactions": 'DE166' from "IMMZ.D" display 'History of anaphylactic reactions'
 code "Severe allergic reactions": 'DE167' from "IMMZ.D" display 'Severe allergic reactions'
 code "Symptomatic HIV infection": 'DE168' from "IMMZ.D" display 'Symptomatic HIV infection'
+code "Immunodeficiency syndromes": 'DE187' from "IMMZ.D" display 'Immunodeficiency syndromes'
 code "Severely immunocompromised": 'DE200' from "IMMZ.D" display 'Severely immunocompromised'
 code "Breastfeeding": 'DE191' from "IMMZ.D" display 'Breastfeeding'

input/cql/IMMZD2DTHepatitisB3Delayed.cql

@@ -0,0 +1,164 @@
+
+/*
+ * Library: IMMZD2DTHepatitisB3Delayed (IMMZ.D2.DT.Hepatitis B.Delayed start)
+ * Rule: Determine if the client is due for a hepatitis B vaccination according to the national immunization schedule
+ * Decision Table: 3-dose schedule (no birth dose + 3 doses), delayed start
+ * Trigger: IMMZ.D2 Determine required vaccination(s) if any
+ */
+library IMMZD2DTHepatitisB3Delayed
+// Start Skeleton CQL
+using FHIR version '4.0.1'
+include FHIRHelpers version '4.0.1'
+include IMMZCommon called IMMZCom
+include IMMZConcepts called IMMZc
+include IMMZConfig called IMMZCon
+include IMMZVaccineLibrary called IMMZvl
+include FHIRCommon called FC
+include IMMZD2DTHepatitisBInput called input
+
+// End Skeleton CQL
+context Patient
+
+
+
+/*
+@dynamicValue: Guidance
+*/
+define "Guidance":
+  case
+    when "Client is due for hepatitis B vaccination" then "Client is due for hepatitis B vaccination Guidance"
+    when "Client is not due for a hepatitis B vaccination" then "Client is not due for a hepatitis B vaccination Guidance"
+    when "Client is due for a hepatitis B vaccination" then "Client is due for a hepatitis B vaccination Guidance"
+    when "Hepatitis B immunization schedule is complete" then "Hepatitis B immunization schedule is complete Guidance"
+    else ''
+  end
+
+/*
+@output: Client is due for hepatitis B vaccination
+@pseudocode: "Immunization recommendation status" = "Due"
+*/
+define "Client is due for hepatitis B vaccination":
+  input."No hepatitis B doses were administered"
+    and input."Client's age is more than {Member States defined upper limit}"
+
+/*
+@output: Client is due for hepatitis B vaccination Guidance
+@guidance: Should vaccinate client for first hepatitis B dose as hepatitis B birth dose was not administered. The first hepatitis B dose should be administered as soon as possible.  Check for contraindications.
+*/
+define "Client is due for hepatitis B vaccination Guidance":
+  'Should vaccinate client for first hepatitis B dose as hepatitis B birth dose was not administered. The first hepatitis B dose should be administered as soon as possible.  Check for contraindications.'
+
+/*
+@output: Client is not due for a hepatitis B vaccination Case 1
+@pseudocode: "Immunization recommendation status" = "Not due"
+*/
+define "Client is not due for a hepatitis B vaccination Case 1":
+  input."One hepatitis B dose was administered"
+    and input."The latest hepatitis B dose was administered less than 4 weeks ago"
+
+/*
+@output: Client is not due for a hepatitis B vaccination Case 2
+@pseudocode: "Immunization recommendation status" = "Not due"
+*/
+define "Client is not due for a hepatitis B vaccination Case 2":
+  input."Two hepatitis B doses were administered"
+    and input."The latest hepatitis B dose was administered less than 4 weeks ago"
+
+/*
+@output: Client is not due for a hepatitis B vaccination Case 3
+@pseudocode: "Immunization recommendation status" = "Not due"
+*/
+define "Client is not due for a hepatitis B vaccination Case 3":
+  input."Two hepatitis B doses were administered"
+    and input."The latest hepatitis B dose was administered more than 4 weeks ago"
+    and input."The first hepatitis B dose was administered less than 6 months ago"
+
+/*
+@output: Client is not due for a hepatitis B vaccination
+@pseudocode: "Immunization recommendation status" = "Not due"
+*/
+define "Client is not due for a hepatitis B vaccination":
+  "Client is not due for a hepatitis B vaccination Case 1"
+    or "Client is not due for a hepatitis B vaccination Case 2"
+    or "Client is not due for a hepatitis B vaccination Case 3"
+
+/*
+@output: Client is not due for a hepatitis B vaccination Guidance
+@guidance: Should not vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.
+@guidance: Should not vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Two hepatitis B doses have been administered to the client. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.
+@guidance: Should not vaccinate client for third hepatitis B dose as the first hepatitis B dose was administered less than 6 months ago. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.
+*/
+define "Client is not due for a hepatitis B vaccination Guidance":
+  case
+    when "Client is not due for a hepatitis B vaccination Case 1" then 'Should not vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.'
+    when "Client is not due for a hepatitis B vaccination Case 2" then 'Should not vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Two hepatitis B doses have been administered to the client. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.'
+    when "Client is not due for a hepatitis B vaccination Case 3" then 'Should not vaccinate client for third hepatitis B dose as the first hepatitis B dose was administered less than 6 months ago. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.'
+    else ''
+  end
+
+/*
+@output: Client is due for a hepatitis B vaccination Case 1
+@pseudocode: "Immunization recommendation status" = "Due"
+*/
+define "Client is due for a hepatitis B vaccination Case 1":
+  input."One hepatitis B dose was administered"
+    and input."The latest hepatitis B dose was administered more than 4 weeks ago"
+
+/*
+@output: Client is due for a hepatitis B vaccination Case 2
+@pseudocode: "Immunization recommendation status" = "Due"
+*/
+define "Client is due for a hepatitis B vaccination Case 2":
+  input."Two hepatitis B doses were administered"
+    and input."The latest hepatitis B dose was administered more than 4 weeks ago"
+    and input."The first hepatitis B dose was administered more than 6 months ago"
+
+/*
+@output: Client is due for a hepatitis B vaccination
+@pseudocode: "Immunization recommendation status" = "Due"
+*/
+define "Client is due for a hepatitis B vaccination":
+  "Client is due for a hepatitis B vaccination Case 1"
+    or "Client is due for a hepatitis B vaccination Case 2"
+
+/*
+@output: Client is due for a hepatitis B vaccination Guidance
+@guidance: Should vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Check for contraindications.
+@guidance: Should vaccinate client for third hepatitis B dose as the first hepatitis B dose was administered more than 6 months ago and the latest hepatitis B dose was administered more than 4 weeks ago. Check for contraindications.
+*/
+define "Client is due for a hepatitis B vaccination Guidance":
+  case
+    when "Client is due for a hepatitis B vaccination Case 1" then 'Should vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Check for contraindications.'
+    when "Client is due for a hepatitis B vaccination Case 2" then 'Should vaccinate client for third hepatitis B dose as the first hepatitis B dose was administered more than 6 months ago and the latest hepatitis B dose was administered more than 4 weeks ago. Check for contraindications.'
+    else ''
+  end
+
+/*
+@output: Hepatitis B immunization schedule is complete
+@pseudocode: 
+*/
+define "Hepatitis B immunization schedule is complete":
+  input."Three hepatitis B doses were administered"
+
+/*
+@output: Hepatitis B immunization schedule is complete Guidance
+@guidance: Hepatitis B immunization schedule is complete. Three hepatitis B primary series doses were administered. Check for any other vaccines due.
+*/
+define "Hepatitis B immunization schedule is complete Guidance":
+  'Hepatitis B immunization schedule is complete. Three hepatitis B primary series doses were administered. Check for any other vaccines due.'
+
+
+/*
+@test: Test expected results based on example patients
+*/
+define "Test Validation":
+  case
+    when Patient.id = '54.D0Amt4w' then "Client is due for hepatitis B vaccination" and "Guidance" = 'Should vaccinate client for first hepatitis B dose as hepatitis B birth dose was not administered. The first hepatitis B dose should be administered as soon as possible.  Check for contraindications.'
+    when Patient.id = '55.D1Hlt4w' then "Client is not due for a hepatitis B vaccination Case 1" and "Guidance" = 'Should not vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.'
+    when Patient.id = '56.D1Hgt4w' then "Client is due for a hepatitis B vaccination Case 1" and "Guidance" = 'Should vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Check for contraindications.'
+    when Patient.id = '57.D2Hlt4w' then "Client is not due for a hepatitis B vaccination Case 2" and "Guidance" = 'Should not vaccinate client for second hepatitis B dose as the latest hepatitis B dose was administered less than 4 weeks ago. Two hepatitis B doses have been administered to the client. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.'
+    when Patient.id = '58.D2Hgt4wFlt6m' then "Client is not due for a hepatitis B vaccination Case 3" and "Guidance" = 'Should not vaccinate client for third hepatitis B dose as the first hepatitis B dose was administered less than 6 months ago. Check for any other vaccines due, and inform the caregiver of when to come back for the next dose.'
+    when Patient.id = '59.D2Hgt4wFgt6m' then "Client is due for a hepatitis B vaccination Case 2" and "Guidance" = 'Should vaccinate client for third hepatitis B dose as the first hepatitis B dose was administered more than 6 months ago and the latest hepatitis B dose was administered more than 4 weeks ago. Check for contraindications.'
+    when Patient.id = '60.D3' then "Hepatitis B immunization schedule is complete" and "Guidance" = 'Hepatitis B immunization schedule is complete. Three hepatitis B primary series doses were administered. Check for any other vaccines due.'
+    else 'No test case set'
+  end