Updated some vocabulary references to fix some errors in processing C…

…QL with the vscode plugin. Standardized the ids for vocabulary. Added in intial IMMZS01 CQL and resources.
opensrp · Feb 27, 2023 · 44612cb · 44612cb
1 parent dd77c13
commit 44612cb
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diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@ temp/
 fsh-generated
 bundles/
 template/
+input/vocabulary/valueset/fromfsh
diff --git a/_autoPublish.bat b/_autoPublish.bat
@@ -1,5 +1,5 @@
 @ECHO off
-SET tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+SET tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
 SET input_cache_path=%~dp0input-cache
 SET resources_path=%~dp0input/resources
 SET ig_resource_path=input/core.xml
@@ -29,4 +29,4 @@ SET ini_file=ig.ini
 
 REM TODO - PUBLISH to "web site"  copy output dir to another location
     ECHO [94m Done with publish to web site
-    ECHO [0m
+    ECHO [0m
diff --git a/_gencontinuous.sh b/_gencontinuous.sh
diff --git a/_genonce.bat b/_genonce.bat
@@ -17,9 +17,9 @@ SET txoption=
 SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8
 
 IF EXIST "%input_cache_path%\%publisher_jar%" (
-	JAVA -Xmx2048M -jar "%input_cache_path%\%publisher_jar%" -ig . %txoption% %*
+	JAVA -jar "%input_cache_path%\%publisher_jar%" -ig . %txoption% %*
 ) ELSE If exist "..\%publisher_jar%" (
-	JAVA -Xmx2048M -jar "..\%publisher_jar%" -ig . %txoption% %*
+	JAVA -jar "..\%publisher_jar%" -ig . %txoption% %*
 ) ELSE (
 	ECHO IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
 )

diff --git a/_genonce.sh b/_genonce.sh
@@ -14,14 +14,16 @@ fi
 
 echo "$txoption"
 
+export JAVA_TOOL_OPTIONS="$JAVA_TOOL_OPTIONS -Dfile.encoding=UTF-8"
+
 publisher=$input_cache_path/$publisher_jar
 if test -f "$publisher"; then
 	java -jar $publisher -ig . $txoption $*
 
 else
 	publisher=../$publisher_jar
 	if test -f "$publisher"; then
-		java -Xmx2048M -jar $publisher -ig . $txoption $*
+		java -jar $publisher -ig . $txoption $*
 	else
 		echo IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
 	fi

diff --git a/_processDataDictionary.bat b/_processDataDictionary.bat
@@ -1,5 +1,5 @@
 @ECHO off
-SET tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+SET tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
 SET input_cache_path=%~dp0input-cache
 SET datadictionary_directory=input/datadictionary/
 SET datadictionary_filename=%datadictionary_directory%\IMZDAKDataDictionaryDRAFT.xlsx

diff --git a/_processDataDictionary.sh b/_processDataDictionary.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 #DO NOT EDIT WITH WINDOWS
-tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
 input_cache_path=./input-cache
 datadictionary_filename="IMZDAKDataDictionaryDRAFT.xlsx"
 datadictionary_sheetname="Master-1.0"

diff --git a/_refresh.sh b/_refresh.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 #DO NOT EDIT WITH WINDOWS
-tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
 input_cache_path=./input-cache
 resources_path=$PWD/input/resources
 ig_ini_path=./ig.ini

diff --git a/_testMagick.sh b/_testMagick.sh
diff --git a/_updateCQFTooling.bat b/_updateCQFTooling.bat
@@ -2,8 +2,8 @@
 
 SETLOCAL
 
-SET dlurl=https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots^&g=org.opencds.cqf^&a=tooling^&v=1.3.1-SNAPSHOT^&c=jar-with-dependencies
-SET tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+SET dlurl=https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots^&g=org.opencds.cqf^&a=tooling^&v=1.4.1-SNAPSHOT^&c=jar-with-dependencies
+SET tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
 SET input_cache_path=%~dp0input-cache\
 SET skipPrompts=false
 IF "%~1"=="/f" SET skipPrompts=true

diff --git a/_updateCQFTooling.sh b/_updateCQFTooling.sh
@@ -5,15 +5,15 @@
 r=snapshots
 g=org.opencds.cqf
 a=tooling
-v=1.3.1-SNAPSHOT
+v=1.4.1-SNAPSHOT
 c=jar-with-dependencies
 
 dlurl='https://oss.sonatype.org/service/local/artifact/maven/redirect?r='${r}'&g='${g}'&a='${a}'&v='${v}'&c='${c}''
 
 echo ${dlurl}
 
 input_cache_path=./input-cache/
-tooling_jar=tooling-1.3.1-SNAPSHOT-jar-with-dependencies.jar
+tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar
 
 set -e
 if ! type "curl" > /dev/null; then

diff --git a/input/cql/IMMZConcepts.cql b/input/cql/IMMZConcepts.cql
@@ -16,29 +16,29 @@ codesystem "Extended Codes CodeSystem codes": 'http://fhir.org/guides/who/anc-cd
 valueset "WHO ATC": 'http://hl7.org/fhir/uv/ips/ValueSet/whoatc-uv-ips'
 
 // General use ValueSets 
-valueset "Negative Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Negativetestresultvalues'
-valueset "Positive Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/PositiveTestResultvalues'
-valueset "CD4% Test Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/CD4percentageTestvalues'
-valueset "CD4 Count Test Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/CD4CountTestResultvalues'
-valueset "Immunocompromised": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Immunocompromisedvalues'
-valueset "Patient birth weight observation value": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Birthweightvalues'
-valueset "Seronegative": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Seronegativevalues'
-valueset "PretermBirth": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Pretermvalues'
+valueset "Negative Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Negativetestresult-values'
+valueset "Positive Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/PositiveTestResult-values'
+valueset "CD4% Test Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/CD4percentageTest-values'
+valueset "CD4 Count Test Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/CD4CountTestResult-values'
+valueset "Immunocompromised": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Immunocompromised-values'
+valueset "Patient birth weight observation value": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Birthweight-values'
+valueset "Seronegative": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Seronegative-values'
+valueset "PretermBirth": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Preterm-values'
 
 // TODO : Adapt from ANC
-valueset "HIV status": 'http://fhir.org/guides/who/smart-immunization/ValueSet/HIVstatusvalues'
+valueset "HIV status": 'http://fhir.org/guides/who/smart-immunization/ValueSet/HIVstatus-values'
 valueset "HIV status - HIV positive Choices": 'http://fhir.org/guides/who/anc-cds/ValueSet/anc-b9-de46'
 valueset "HIV status - HIV negative Choices": 'http://fhir.org/guides/who/anc-cds/ValueSet/anc-b9-de47'
 
 // Vaccine specific ValueSets
 //BCG specific ValuSets
 valueset "TST Test Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/TSTTestResult-values'
-valueset "IGRA Test Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/IGRATestResultvalues'
-valueset "ARV Drugs": 'http://fhir.org/guides/who/smart-immunization/ValueSet/ARVDrugsvalues'
-valueset "VNA levels": 'http://fhir.org/guides/who/smart-immunization/ValueSet/VNAlevelsRAbiesvalues'
+valueset "IGRA Test Result": 'http://fhir.org/guides/who/smart-immunization/ValueSet/IGRATestResult-values'
+valueset "ARV Drugs": 'http://fhir.org/guides/who/smart-immunization/ValueSet/ARVDrugs-values'
+valueset "VNA levels": 'http://fhir.org/guides/who/smart-immunization/ValueSet/VNAlevelsRabies-values'
 
 // JE Classification 
-valueset "Inactivated Vero cell-derived Japanese Encephalitis vaccines": 'http://fhir.org/guides/who/smart-immunization/ValueSet/InactivatedJEvalues'
+valueset "Inactivated Vero cell-derived Japanese Encephalitis vaccines": 'http://fhir.org/guides/who/smart-immunization/ValueSet/InactivatedJE-values'
 
 //valueset "Target Disease": 'http://hl7.org/fhir/ValueSet/immunization-target-disease'
 
@@ -93,4 +93,4 @@ valueset "FSME-Immun Class TBE Vaccine": 'http://fhir.org/guides/who/smart-immun
 valueset "TBE-Moscow Class TBE Vaccine": 'http://fhir.org/guides/who/smart-immunization/ValueSet/TBEMoscowClassTBEVaccinevalues'
 valueset "EnceVir Class TBE Vaccine": 'http://fhir.org/guides/who/smart-immunization/ValueSet/EnceVirClassTBEVaccinevalues'
 valueset "Encepur Class TBE Vaccine": 'http://fhir.org/guides/who/smart-immunization/ValueSet/EncepurClassTBEVaccinevalues'
-valueset "Intussusception": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Intussusceptionvalues'
+valueset "Intussusception": 'http://fhir.org/guides/who/smart-immunization/ValueSet/Intussusceptionvalues'
diff --git a/input/cql/IMMZS01.cql b/input/cql/IMMZS01.cql
@@ -0,0 +1,33 @@
+/*
+ * Library: IMMZS01 (IMMZ.S.01.BCG)
+ * Rule: If child or person has not been vaccinated, give BCG vaccine as soon as possible after birth 
+ * Trigger: Patient has never had BCG vaccination
+ */
+library IMMZS01
+// Start Skeleton CQL
+using FHIR version '4.0.1'
+include FHIRHelpers version '4.0.1'
+include IMMZCommon called IMMZCom
+include IMMZConcepts called IMMZc
+include IMMZVaccineLibrary called IMMZvl
+include IMMZConfig called IMMZConf
+// End Skeleton CQL
+context Patient
+
+/*
+ * Rule: Provision of the BCG dose
+ * Create Condition:
+ *   - BCG dose should be provided if the patient has not received any BCG doses, and is in a High incidence of TB and/or high leprosy burden, and TST-negative and IGRA-negative
+ * 
+ * Completion:
+ *   - "BCG Dose 1 provided" = TRUE
+ *
+ * References:
+ * 	- WHO recommendations for routine immunization - summary tables: https://www.who.int/teams/immunization-vaccines-and-biologicals/policies/who-recommendations-for-routine-immunization---summary-tables
+ * 	 
+ */
+define "Provision of the BCG dose":
+	IMMZCom."No BCG Doses Administered to Patient" and
+		IMMZConf."High incidence of TB and/or high leprosy burden" = true and 
+		Coalesce((IMMZCom."Most Recent TST Test Result" in IMMZc."Negative Result"), false) and 
+		Coalesce((IMMZCom."Most Recent IGRA Test Result" in IMMZc."Negative Result"), false) 
diff --git a/input/cql/cql-options.json b/input/cql/cql-options.json
@@ -6,7 +6,7 @@
       "DisableListPromotion"
    ],
    "formats":[
-     "JXSON"
+     "JSON"
    ],
    "validateUnits":true,
    "verifyOnly":false,

diff --git a/input/fsh/ValueSet_ARVDrugs.fsh b/input/fsh/ValueSet_ARVDrugs.fsh
@@ -1,9 +1,9 @@
 ValueSet: ARVDrugsvalues
-Id: ARVDrugsvalues
+Id: ARVDrugs-values
 Title: "ARV Drugs values"
 Description: "Codes representing ARV Drugs values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#713540004 "Substance with antiretroviral mechanism of action (substance)"
-* SCT#788075003 "Medicinal product acting as antiretroviral agent (product)"
+* SCT#788075003 "Medicinal product acting as antiretroviral agent (product)"
diff --git a/input/fsh/ValueSet_CD4CountTestResult.fsh b/input/fsh/ValueSet_CD4CountTestResult.fsh
@@ -1,9 +1,9 @@
 ValueSet: CD4CountTestResultvalues
-Id: CD4CountTestResultvalues
+Id: CD4CountTestResult-values
 Title: "CD4 Count Test Result"
 Description: "Codes representing CD4 Count Test Result values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#313660005 "Absolute CD4 count procedure (procedure)"
-* ICD11#XH7EL2 "Primary cutaneous CD4-positive small/medium T-cell lymphoma"
+* ICD11#XH7EL2 "Primary cutaneous CD4-positive small/medium T-cell lymphoma"
diff --git a/input/fsh/ValueSet_CD4percentageTest.fsh b/input/fsh/ValueSet_CD4percentageTest.fsh
@@ -1,7 +1,7 @@
 //Example Valuset you can use as a template to create new ones
 //change ValueSet name, Id, Title, Description
 ValueSet: CD4percentageTestvalues
-Id: CD4percentageTestvalues
+Id: CD4percentageTest-values
 Title: "CD4 Percentage Test"
 Description: "Codes representing CD4 Percentage Test values"
 //don't touch status, experimental, immutable
@@ -11,4 +11,4 @@ Description: "Codes representing CD4 Percentage Test values"
 //fill in codes, check AL_CodeSystems.fsh for the short names of the codesystem
 * SCT#313938009 "CD4 percent count (procedure)"
 * SCT#413069009 "Percentage CD4 (T4 cells) count (procedure)"
-* LNC#80223-1 "CD4 cells/100 lymphocytes in Specimen"
+* LNC#80223-1 "CD4 cells/100 lymphocytes in Specimen"
diff --git a/input/fsh/ValueSet_EnceVirClassTBEVaccine.fsh b/input/fsh/ValueSet_EnceVirClassTBEVaccine.fsh
@@ -1,9 +1,9 @@
 ValueSet: EnceVirClassTBEVaccinevalues
-Id: EnceVirClassTBEVaccinevalues
+Id: EnceVirClassTBEVaccine-values
 Title: "EnceVir Class TBE Vaccine values"
 Description: "Codes representing EnceVir Class TBE Vaccine values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#871719005  "Vaccine product containing only Tick-borne encephalitis virus antigen (medicinal product)"
-* SCT#836403007 "Vaccine product containing Tick-borne encephalitis virus antigen (medicinal product)"
+* SCT#836403007 "Vaccine product containing Tick-borne encephalitis virus antigen (medicinal product)"
diff --git a/input/fsh/ValueSet_EncepurClassTBEVaccine.fsh b/input/fsh/ValueSet_EncepurClassTBEVaccine.fsh
@@ -1,9 +1,9 @@
 ValueSet: EncepurClassTBEVaccinevalues
-Id: EncepurClassTBEVaccinevalues
+Id: EncepurClassTBEVaccine-values
 Title: "Encepur Class TBE Vaccine values"
 Description: "Codes representing Encepur Class TBE Vaccine values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#871719005  "Vaccine product containing only Tick-borne encephalitis virus antigen (medicinal product)"
-* SCT#836403007 "Vaccine product containing Tick-borne encephalitis virus antigen (medicinal product)"
+* SCT#836403007 "Vaccine product containing Tick-borne encephalitis virus antigen (medicinal product)"
diff --git a/input/fsh/ValueSet_FSME-ImmunClassTBEVaccine.fsh b/input/fsh/ValueSet_FSME-ImmunClassTBEVaccine.fsh
@@ -1,9 +1,9 @@
 ValueSet: FSMEImmunClassTBEVaccinevalues
-Id: FSMEImmunClassTBEVaccinevalues
+Id: FSMEImmunClassTBEVaccine-values
 Title: "FSME-Immun Class TBE Vaccine values"
 Description: "Codes representing FSME-Immun Class TBE Vaccine values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#871719005  "Vaccine product containing only Tick-borne encephalitis virus antigen (medicinal product)"
-* SCT#836403007 "Vaccine product containing Tick-borne encephalitis virus antigen (medicinal product)"
+* SCT#836403007 "Vaccine product containing Tick-borne encephalitis virus antigen (medicinal product)"
diff --git a/input/fsh/ValueSet_HIVstatus.fsh b/input/fsh/ValueSet_HIVstatus.fsh
@@ -1,7 +1,7 @@
 //Example Valuset you can use as a template to create new ones
 //change ValueSet name, Id, Title, Description
 ValueSet: HIVstatusvalues
-Id: HIVstatusvalues
+Id: HIVstatus-values
 Title: "HIV status values"
 Description: "Codes representing HIV status values"
 //don't touch status, experimental, immutable
@@ -11,4 +11,4 @@ Description: "Codes representing HIV status values"
 //fill in codes, check AL_CodeSystems.fsh for the short names of the codesystem
 * SCT#278977008 "Human immunodeficiency virus status (observable entity)"
 * ICD11#1C62.Z "Human immunodeficiency virus disease without mention of associated disease or condition, clinical stage unspecified"
-* ICD11#MA14.0 "Laboratory evidence of human immunodeficiency virus"
+* ICD11#MA14.0 "Laboratory evidence of human immunodeficiency virus"
diff --git a/input/fsh/ValueSet_IGRATestResult.fsh b/input/fsh/ValueSet_IGRATestResult.fsh
@@ -1,9 +1,9 @@
 ValueSet: IGRATestResultvalues
-Id: IGRATestResultvalues
+Id: IGRATestResult-values
 Title: "IGRA Test Result values"
 Description: "Codes representing IGRA Test Result values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#458561000124101 "Screening for tuberculosis using gamma interferon assay"
-* SCT#35140007 "Interferon gamma assay (procedure)"
+* SCT#35140007 "Interferon gamma assay (procedure)"
diff --git a/input/fsh/ValueSet_Immunocompromised.fsh b/input/fsh/ValueSet_Immunocompromised.fsh
@@ -1,9 +1,9 @@
 ValueSet: Immunocompromisedvalues
-Id: Immunocompromisedvalues
+Id: Immunocompromised-values
 Title: "Immunocompromised valueset"
 Description: "Codes representing Immunocompromised values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#370388006 "Patient immunocompromised"
-* SCT#370391006 "Patient immunosuppressed"
+* SCT#370391006 "Patient immunosuppressed"
diff --git a/input/fsh/ValueSet_InactivatedJE.fsh b/input/fsh/ValueSet_InactivatedJE.fsh
@@ -1,9 +1,9 @@
 ValueSet: InactivatedJEvalues
-Id: InactivatedJEvalues
+Id: InactivatedJE-values
 Title: "Inactivated Vero cell-derived Japanese Encephalitis vaccines valueset"
 Description: "Codes representing Inactivated Vero cell-derived Japanese Encephalitis vaccines values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 //fill in codes, check AL_CodeSystems.fsh for the short names of the codesystem
-* SCT#871725009 "Vaccine product containing only inactivated whole Japanese encephalitis virus antigen (medicinal product)"
+* SCT#871725009 "Vaccine product containing only inactivated whole Japanese encephalitis virus antigen (medicinal product)"
diff --git a/input/fsh/ValueSet_Intussusception.fsh b/input/fsh/ValueSet_Intussusception.fsh
@@ -1,9 +1,9 @@
 ValueSet: Intussusceptionvalues
-Id: Intussusceptionvalues
+Id: Intussusception-values
 Title: "Intussusception valueset"
 Description: "Codes representing Intussuception values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 * SCT#41444002 "Invagination (morphologic abnormality)"
-* ICD11#DA91.0 "Intussusception of small intestine"
+* ICD11#DA91.0 "Intussusception of small intestine"
diff --git a/input/fsh/ValueSet_MenAconjugatevaccine.fsh b/input/fsh/ValueSet_MenAconjugatevaccine.fsh
@@ -1,5 +1,5 @@
 ValueSet: MenAconjugatevaccinevalues
-Id: MenAconjugatevaccinevalues
+Id: MenAconjugatevaccine-values
 Title: "MenA conjugate vaccine values"
 Description: "Codes representing MenA conjugate vaccine values"
 * ^status = #draft
@@ -8,4 +8,4 @@ Description: "Codes representing MenA conjugate vaccine values"
 * ICD11#XM2WV4 "Meningococcal vaccines"
 * ICD11#XM2280 "Meningococcus A, purified polysaccharides antigen conjugated"
 * ICD11#XM37L5 "Meningococcus A, purified polysaccharides antigen"
-* SCT#259839009 "Meningococcal polysaccharide group A antibody (substance)"
+* SCT#259839009 "Meningococcal polysaccharide group A antibody (substance)"
diff --git a/input/fsh/ValueSet_NegTestResult.fsh b/input/fsh/ValueSet_NegTestResult.fsh
@@ -1,12 +1,12 @@
 //Example Valuset you can use as a template to create new ones
 //change ValueSet name, Id, Title, Description
 ValueSet: Negativetestresultvalues
-Id: Negativetestresultvalues
+Id: Negativetestresult-values
 Title: "Negative Test Results"
 Description: "Codes representing negative test result values"
 //don't touch status, experimental, immutable
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
 //fill in codes, check AL_CodeSystems.fsh for the short names of the codesystem
-* SCT#260385009 "Negative (qualifier value)"
+* SCT#260385009 "Negative (qualifier value)"
diff --git a/input/fsh/ValueSet_PosTestResult.fsh b/input/fsh/ValueSet_PosTestResult.fsh
@@ -1,8 +1,8 @@
 ValueSet: PositiveTestResultvalues
-Id: PositiveTestResultvalues
+Id: PositiveTestResult-values
 Title: "Positive Test Result valuest"
 Description: "Codes representing Positive Test Result values"
 * ^status = #draft
 * ^experimental = false
 * ^immutable = true
-* SCT#10828004 "Positive (qualifier value)"
+* SCT#10828004 "Positive (qualifier value)"