Fix ind

_refresh.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+#DO NOT EDIT WITH WINDOWS
+tooling_jar=tooling-cli-2.4.0.jar
+input_cache_path=./input-cache
+ig_ini_path=$PWD/ig.ini
+
+set -e
+echo Checking internet connection...
+wget -q --spider tx.fhir.org
+
+if [ $? -eq 0 ]; then
+	echo "Online"
+	fsoption=""
+else
+	echo "Offline"
+	fsoption=""
+fi
+
+echo "$fsoption"
+
+tooling=$input_cache_path/$tooling_jar
+if test -f "$tooling"; then
+	java -jar $tooling -RefreshIG -ini="$ig_ini_path" -d -p -t $fsoption
+else
+	tooling=../$tooling_jar
+	echo $tooling
+	if test -f "$tooling"; then
+		java -jar $tooling -RefreshIG -ini="$ig_ini_path" -d -p -t $fsoption
+	else
+		echo IG Refresh NOT FOUND in input-cache or parent folder.  Please run _updateCQFTooling.  Aborting...
+	fi
+fi

input/cql/IMMZCommon.cql

@@ -1,11 +1,11 @@
-library IMMZCommon
+library IMMZCommon version '4.0.1'
 
 using FHIR version '4.0.1'
 
 include WHOCommon called WCom
 include WHOConcepts called Wcon
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
+include FHIRCommon version '4.0.1' called FC
 include IMMZConcepts called IMMZc
 
 
@@ -241,21 +241,32 @@ define function Only(protocols List<FHIR.Immunization.ProtocolApplied>):
  */
 define function ToDate(choice Choice<FHIR.date, FHIR.string>):
   case
+    when choice is null then null//should not happend
 	  when choice is FHIR.date then
     	choice as FHIR.date
-		else
-      Message(null as FHIR.date, true, '1', 'Error', 'Cannot compute a date from a String value')
+		when choice is FHIR.string and ConvertsToDate(choice) then
+      FHIRHelpers.ToDate(choice)
+    when choice is FHIR.string then
+      Message(null as FHIR.date, true, '1', 'Error', 'Cannot compute a date from a the string' + choice)
+    else
+      Message(null as FHIR.date, true, '1', 'Error', 'Cannot compute a datetime from the source' )//should not happend
 	end
 
 /**
  * @description Takes the date choice of a date/string choice (for Immunization date)
  */
 define function ToDateTime(choice Choice<FHIR.dateTime, FHIR.string>):
   case
+    when choice is null then null//should not happend
 	  when choice is FHIR.dateTime then
     	choice as FHIR.dateTime
-		else
-      Message(null as FHIR.dateTime, true, '1', 'Error', 'Cannot compute a date from a String value')
+		when choice is FHIR.string and ConvertsToDateTime(choice) then
+      FHIRHelpers.ToDateTime(choice)
+    when choice is FHIR.string then
+      Message(null as FHIR.dateTime, true, '1', 'Error', 'Cannot compute a datetime from a the string' + choice)
+    else
+      Message(null as FHIR.dateTime, true, '1', 'Error', 'Cannot compute a datetime from the source' )//should not happend
+
 	end
 
 

input/cql/IMMZConcepts.cql

@@ -7,7 +7,7 @@ codesystem "SNOMED-CT": 'http://snomed.info/sct'
 codesystem "LOINC": 'http://loinc.org'
 codesystem "RxNorm": 'http://www.nlm.nih.gov/research/umls/rxnorm'
 codesystem "CIEL": 'http://hl7.org/fhir/sid/ciel'
-codesystem "ICD-11": 'http://hl7.org/fhir/sid/icd-11'
+codesystem "ICD-11": 'http://hl7.org/fhir/sid/icd-11/mms'
 codesystem "ICHI": 'https://mitel.dimi.uniud.it/ichi/#http://id.who.int/ichi'
 codesystem "ICF": 'http://hl7.org/fhir/sid/icf-nl'
 codesystem "Extended Codes CodeSystem codes": 'http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom-codes'
@@ -25,7 +25,7 @@ valueset "Positive Result": 'http://smart.who.int/ig/smart-immunizations-measles
 valueset "Immunocompromised": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/Immunocompromised-values'
 valueset "Patient birth weight observation value": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/Birthweight-values'
 valueset "PretermBirth": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/Preterm-values'
-valueset "Live Attenuated": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/LiveAttenduatedVaccines'
+valueset "Live Attenuated": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/LiveAttenuatedVaccines'
 
 //valueset "Target Disease": 'http://hl7.org/fhir/ValueSet/immunization-target-disease'
 
@@ -37,7 +37,7 @@ valueset "ARV Drugs": 'http://smart.who.int/ig/smart-immunizations-measles/Value
 
 // Vaccine Value Sets
 
-valueset "MCV Vaccine": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/IMMZ.A1.DE9'
+valueset "MCV Vaccine": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/IMMZ.Z.DE9'
 
 // Plugin is complaining about not finding these so that should be resolved, but here until it can be fixed
 valueset "BCG Vaccine": 'http://smart.who.int/ig/smart-immunizations-measles/ValueSet/IMMZ.A1.DE1'

input/cql/IMMZD2DTMeasles.cql → input/cql/IMMZD2DTMeaslesLogic.cql

@@ -1,17 +1,16 @@
 /*
- * Library: IMMZD2DTMeasles (IMMZ.D2.DT.Measles)
+ * Library: IMMZD2DTMeaslesLogic (IMMZ.D2.DT.Measles)
  * Rule: If the child or patient has not been given MCV1 (at 9 months) and MCV2 (between 15-18 months) vaccination 
  * Trigger: Patient has never received measles vaccination
  */
-library IMMZD2DTMeasles
+library IMMZD2DTMeaslesLogic
 // 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
 
 parameter "Individual is at high risk of contracting measles" Boolean default false
 parameter "Individual is travelling to a country experiencing measles outbreaks" Boolean default false

input/cql/IMMZDT08.cql

@@ -11,7 +11,6 @@ include IMMZCommon called IMMZCom
 include IMMZConcepts called IMMZc
 include IMMZConfig called IMMZCon
 include IMMZVaccineLibrary called IMMZvl
-include FHIRCommon called FC
 
 parameter "Individual is at high risk of contracting measles" Boolean default false
 parameter "Individual is travelling to a country experiencing measles outbreaks" Boolean default false

input/cql/IMMZIND08.cql

@@ -27,7 +27,6 @@ include IMMZConcepts called IMMZc
 include IMMZConfig called IMMZCon
 include IMMZIndicatorCommon called IMMZIndCom
 include IMMZVaccineLibrary called IMMZvl
-include FHIRCommon called FC
 // End Skeleton CQL
 parameter "Measurement Period" Interval<Date>
 

input/cql/IMMZINDMeasles.cql

@@ -26,52 +26,59 @@ include IMMZCommon called IMMZCom
 include IMMZConcepts called IMMZc
 include IMMZConfig called IMMZCon
 include IMMZIndicatorCommon called IMMZIndCom
-include IMMZVaccineLibrary called IMMZvl
-include FHIRCommon called FC
-include IMMZD2DTMeasles called Measles
 // End Skeleton CQL
-parameter "Measurement Period" Interval<Date>
+parameter "Measurement Period" Interval<DateTime> default Interval[@2019-03-01T00:00:00.0, @2019-04-01T00:00:00.0 )
 
 context Patient
 
-/*
-define "MCV Doses Administered to Patient During Measurement Period":
-    Measles."MCV Doses Administered to Patient" I 
-    where IMMZCom.ToDate(I.occurrence) during "Measurement Period"
-*/
+define  getPatientImmunisationMeasles:
+  [Immunization] I
+    where I.status = 'completed'
+	and  I.vaccineCode in IMMZc."MCV Vaccine"
+    sort by date from (occurrence as FHIR.dateTime) desc
+
+define  getFirstDose:
+  getPatientImmunisationMeasles I
+    where Coalesce(First(I.protocolApplied pa where pa.doseNumber is not null).doseNumber.value as Integer,1) = 1 
+	sort by date from (occurrence as FHIR.dateTime) desc
+
+define getSecondDose:
+
+  getPatientImmunisationMeasles I
+	 where Coalesce(First(I.protocolApplied pa where pa.doseNumber is not null).doseNumber.value as Integer,1) = 2 
+	 or (   I.occurrence after (First(getFirstDose).occurrence + 4 weeks  ))
+	sort by date from (occurrence as FHIR.dateTime) desc
 
-define function "Measure Observation" (Patient "Patient"):
-  1
 
 /*
  * Target population for first dose: Any one over 9 (in high transmission area) or 12 (in low transmission area) months old
  */ 
-define "Initial Population 05":
-	Measles."First MCV Dose Administered to Patient" I where IMMZCom.ToDate(I.occurrence) during "Measurement Period"
+define "Measure Population 05":
+	(getFirstDose I where  I.occurrence during "Measurement Period")
+
 
 /*
  * Numerator for first dose: Anyone having received the first dose
  */
-define "Measure Population 05":
-	"Initial Population 05"
+define "Initial Population 05":
+	(getFirstDose)
 
 /*
  * Target population for second dose: Any one over 15 months
  */ 
 define "Initial Population 40":
-	Measles."Second MCV Dose Administered to Patient" I where IMMZCom.ToDate(I.occurrence) during "Measurement Period"
+	(getSecondDose)
 
 /*
  * Numerator for second dose: Anyone having received the first dose
  */
 define "Measure Population 40":
-	"Initial Population 40"
+	(getSecondDose I where ( I.occurrence) during "Measurement Period")
 
 
 /*
  * Combined stratifiers
  */
 define "Stratification":
-		IMMZIndCom."By Administrative Gender Stratifier".code + ':' + IMMZIndCom."Toddler By Age Stratifier".code + ':' + IMMZIndCom."By Geographic Region Stratifier"
-
+		Patient.gender.value 
 

input/cql/IMMZIndicatorCommon.cql

@@ -7,7 +7,7 @@ library IMMZIndicatorCommon
 using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
+include FHIRCommon version '4.0.1' called FC
 include IMMZCommon called IMMZCom
 include IMMZConcepts called IMMZc
 include WHOCommon called WCom

input/cql/IMMZVaccineLibrary.cql

@@ -4,7 +4,6 @@ using FHIR version '4.0.1'
 include WHOCommon called WCom
 include WHOConcepts called Wcon
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
 include IMMZConcepts called IMMZc
 include IMMZCommon called IMMZcom
 

input/cql/WHOCommon.cql

@@ -4,7 +4,7 @@ using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
 
-include FHIRCommon called FC
+include FHIRCommon version '4.0.1' called FC
 
 context Patient
 

input/cql/WHOConcepts.cql

@@ -6,7 +6,7 @@ codesystem "SNOMED-CT": 'http://snomed.info/sct'
 codesystem "LOINC": 'http://loinc.org'
 codesystem "RxNorm": 'http://www.nlm.nih.gov/research/umls/rxnorm'
 codesystem "CIEL": 'http://hl7.org/fhir/sid/ciel'
-codesystem "ICD-11": 'http://id.who.int/icd11/mms'
+codesystem "ICD-11": 'http://hl7.org/fhir/sid/icd-11/mms'
 codesystem "ICHI": 'https://mitel.dimi.uniud.it/ichi/#http://id.who.int/ichi'
 codesystem "ICF": 'http://hl7.org/fhir/sid/icf-nl'
 codesystem "Extended Codes CodeSystem codes": 'http://fhir.org/guides/who/anc-cds/CodeSystem/anc-custom-codes'

input/fsh/Aliases.fsh

@@ -1,9 +1,10 @@
 Alias: $SCT = http://snomed.info/sct
 Alias: $LNC = http://loinc.org
-Alias: $ICD11 = http://id.who.int/icd11/mms
+Alias: $ICD11 = http://hl7.org/fhir/sid/icd-11/mms
 Alias: $ICD10 = http://hl7.org/fhir/sid/icd-10
 Alias: $CVX = http://hl7.org/fhir/sid/cvx 
 Alias: $GENDER = http://hl7.org/fhir/administrative-gender
 
+Alias: $library-type = http://terminology.hl7.org/CodeSystem/library-type
 Alias: $measure-scoring = http://terminology.hl7.org/CodeSystem/measure-scoring
 Alias: $measure-population = http://terminology.hl7.org/CodeSystem/measure-population

input/fsh/activitydefinitions/IMMZD2DTMeaslesEval.fsh

@@ -26,4 +26,4 @@ Usage: #definition
   * expression
     * description = "Measles Code"
     * language = #text/cql
-    * expression = "Code { system: 'http://hl7.org/fhir/sid/icd-11', code: 'XM28X5' }"
+    * expression = "Code { system: 'http://hl7.org/fhir/sid/icd-11/mms', code: 'XM28X5' }"

input/fsh/libraries/FHIRCommon.fsh

@@ -0,0 +1,16 @@
+Instance: FHIRCommon
+InstanceOf: Library
+Title: "FHIRCommon"
+Description: "This library defines terminologies and functions commonly used in FHIR-based CQL artifacts"
+Usage: #definition
+* url = "http://smart.who.int/ig/smart-immunizations-measles/Library/FHIRCommon"
+* extension[+]
+  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * valueCode = #computable
+* version = "0.1.0"
+* name = "FHIRCommon"
+* status = #draft
+* experimental = false
+* publisher = "World Health Organization (WHO)"
+* type = $library-type#logic-library
+* content.id = "ig-loader-FHIRCommon.cql"

input/fsh/libraries/FHIRHelpers.fsh

@@ -0,0 +1,17 @@
+Instance: FHIRHelpers
+InstanceOf: Library
+Title: "FHIRHelpers"
+Description: "	
+This library defines functions to convert between FHIR data types and CQL system-defined types, as well as functions to support FHIRPath implementation. For more information, the FHIRHelpers wiki page: https://github.com/cqframework/clinical_quality_language/wiki/FHIRHelpers"
+Usage: #definition
+* url = "http://smart.who.int/ig/smart-immunizations-measles/Library/FHIRHelpers"
+* extension[+]
+  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * valueCode = #computable
+* version = "0.1.0"
+* name = "FHIRHelpers"
+* status = #draft
+* experimental = false
+* publisher = "World Health Organization (WHO)"
+* type = $library-type#logic-library
+* content.id = "ig-loader-FHIRHelpers.cql"

input/fsh/libraries/IMMZCommon.fsh

@@ -0,0 +1,16 @@
+Instance: IMMZCommon
+InstanceOf: Library
+Title: "IMMZCommon"
+Description: "This library defines common terminologies and functions used throughout the Immunization CPG"
+Usage: #definition
+* url = "http://smart.who.int/ig/smart-immunizations-measles/Library/IMMZCommon"
+* extension[+]
+  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * valueCode = #computable
+* version = "0.1.0"
+* name = "IMMZCommon"
+* status = #draft
+* experimental = false
+* publisher = "World Health Organization (WHO)"
+* type = $library-type#logic-library
+* content.id = "ig-loader-IMMZCommon.cql"

input/fsh/libraries/IMMZCommonIzDataElements.fsh

@@ -0,0 +1,16 @@
+Instance: IMMZCommonIzDataElements
+InstanceOf: Library
+Title: "IMMZCommonIzDataElements"
+Description: "This library defines common terminologies and functions used throughout the Immunization CPG"
+Usage: #definition
+* url = "http://smart.who.int/ig/smart-immunizations-measles/Library/IMMZCommonIzDataElements"
+* extension[+]
+  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * valueCode = #computable
+* version = "0.1.0"
+* name = "IMMZCommonIzDataElements"
+* status = #draft
+* experimental = false
+* publisher = "World Health Organization (WHO)"
+* type = $library-type#logic-library
+* content.id = "ig-loader-IMMZCommonIzDataElements.cql"

input/fsh/libraries/IMMZConcepts.fsh

@@ -0,0 +1,16 @@
+Instance: IMMZConcepts
+InstanceOf: Library
+Title: "IMMZConcepts"
+Description: "This library defines concepts used throughout the Immunization CPG"
+Usage: #definition
+* url = "http://smart.who.int/ig/smart-immunizations-measles/Library/IMMZConcepts"
+* extension[+]
+  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * valueCode = #computable
+* version = "0.1.0"
+* name = "IMMZConcepts"
+* status = #draft
+* experimental = false
+* publisher = "World Health Organization (WHO)"
+* type = $library-type#logic-library
+* content.id = "ig-loader-IMMZConcepts.cql"

input/fsh/libraries/IMMZConfig.fsh

@@ -0,0 +1,16 @@
+Instance: IMMZConfig
+InstanceOf: Library
+Title: "IMMZConfig"
+Description: "This library defines configuration points for the Immunization CPG"
+Usage: #definition
+* url = "http://smart.who.int/ig/smart-immunizations-measles/Library/IMMZConfig"
+* extension[+]
+  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * valueCode = #computable
+* version = "0.1.0"
+* name = "IMMZConfig"
+* status = #draft
+* experimental = false
+* publisher = "World Health Organization (WHO)"
+* type = $library-type#logic-library
+* content.id = "ig-loader-IMMZConfig.cql"