Bump CQL Translator/Evaluator to 2.4

benchmark/build.gradle.kts

@@ -73,9 +73,32 @@ configurations {
     exclude(module = "javax.json")
     exclude(module = "jcl-over-slf4j")
     exclude(group = "org.apache.httpcomponents")
-    // Remove this after this issue has been fixed:
-    // https://github.com/cqframework/clinical_quality_language/issues/799
-    exclude(module = "antlr4")
+
+    // Removes newer versions of caffeine and manually imports 2.9
+    // Removes newer versions of hapi and keeps on 6.0.1
+    // (newer versions don't work on Android)
+    resolutionStrategy {
+      force(Dependencies.HapiFhir.caffeine)
+      force(Dependencies.HapiFhir.fhirBase)
+      force(Dependencies.HapiFhir.fhirClient)
+      force(Dependencies.HapiFhir.structuresDstu2)
+      force(Dependencies.HapiFhir.structuresDstu3)
+      force(Dependencies.HapiFhir.structuresR4)
+      force(Dependencies.HapiFhir.structuresR5)
+      force(Dependencies.HapiFhir.validation)
+      force(Dependencies.HapiFhir.validationDstu3)
+      force(Dependencies.HapiFhir.validationR4)
+      force(Dependencies.HapiFhir.validationR5)
+
+      force(Dependencies.HapiFhir.fhirCoreDstu2)
+      force(Dependencies.HapiFhir.fhirCoreDstu2016)
+      force(Dependencies.HapiFhir.fhirCoreDstu3)
+      force(Dependencies.HapiFhir.fhirCoreR4)
+      force(Dependencies.HapiFhir.fhirCoreR4b)
+      force(Dependencies.HapiFhir.fhirCoreR5)
+      force(Dependencies.HapiFhir.fhirCoreUtils)
+      force(Dependencies.HapiFhir.fhirCoreConvertors)
+    }
   }
 }
 

buildSrc/src/main/kotlin/Dependencies.kt

@@ -34,10 +34,6 @@ object Dependencies {
     const val openCdsGroup = "org.opencds.cqf.cql"
     const val translatorGroup = "info.cqframework"
 
-    // Remove this after this issue has been fixed:
-    // https://github.com/cqframework/clinical_quality_language/issues/799
-    const val antlr4Runtime = "org.antlr:antlr4-runtime:${Versions.Cql.antlr}"
-
     const val engine = "$openCdsGroup:engine:${Versions.Cql.engine}"
     const val engineJackson = "$openCdsGroup:engine.jackson:${Versions.Cql.engine}"
 
@@ -54,8 +50,32 @@ object Dependencies {
   }
 
   object HapiFhir {
+    const val fhirBase = "ca.uhn.hapi.fhir:hapi-fhir-base:${Versions.hapiFhir}"
+    const val fhirClient = "ca.uhn.hapi.fhir:hapi-fhir-client:${Versions.hapiFhir}"
+    const val structuresDstu2 = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:${Versions.hapiFhir}"
+    const val structuresDstu3 = "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3:${Versions.hapiFhir}"
     const val structuresR4 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${Versions.hapiFhir}"
+    const val structuresR4b = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4b:${Versions.hapiFhir}"
+    const val structuresR5 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r5:${Versions.hapiFhir}"
+
     const val validation = "ca.uhn.hapi.fhir:hapi-fhir-validation:${Versions.hapiFhir}"
+    const val validationDstu3 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:${Versions.hapiFhir}"
+    const val validationR4 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:${Versions.hapiFhir}"
+    const val validationR5 =
+      "ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r5:${Versions.hapiFhir}"
+
+    const val fhirCoreDstu2 = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu2016 =
+      "ca.uhn.hapi.fhir:org.hl7.fhir.dstu2016may:${Versions.hapiFhirCore}"
+    const val fhirCoreDstu3 = "ca.uhn.hapi.fhir:org.hl7.fhir.dstu3:${Versions.hapiFhirCore}"
+    const val fhirCoreR4 = "ca.uhn.hapi.fhir:org.hl7.fhir.r4:${Versions.hapiFhirCore}"
+    const val fhirCoreR4b = "ca.uhn.hapi.fhir:org.hl7.fhir.r4b:${Versions.hapiFhirCore}"
+    const val fhirCoreR5 = "ca.uhn.hapi.fhir:org.hl7.fhir.r5:${Versions.hapiFhirCore}"
+    const val fhirCoreUtils = "ca.uhn.hapi.fhir:org.hl7.fhir.utilities:${Versions.hapiFhirCore}"
+    const val fhirCoreConvertors =
+      "ca.uhn.hapi.fhir:org.hl7.fhir.convertors:${Versions.hapiFhirCore}"
 
     // Runtime dependency that is required to run FhirPath (also requires minSDK of 26).
     // Version 3.0 uses java.lang.System.Logger, which is not available on Android
@@ -64,9 +84,19 @@ object Dependencies {
   }
 
   object Jackson {
-    const val annotations = "com.fasterxml.jackson.core:jackson-annotations:${Versions.jackson}"
-    const val core = "com.fasterxml.jackson.core:jackson-core:${Versions.jackson}"
-    const val databind = "com.fasterxml.jackson.core:jackson-databind:${Versions.jackson}"
+    const val mainGroup = "com.fasterxml.jackson"
+    const val coreGroup = "$mainGroup.core"
+    const val dataformatGroup = "$mainGroup.dataformat"
+    const val datatypeGroup = "$mainGroup.datatype"
+    const val moduleGroup = "$mainGroup.module"
+
+    const val annotations = "$coreGroup:jackson-annotations:${Versions.jackson}"
+    const val bom = "$mainGroup:jackson-bom:${Versions.jackson}"
+    const val core = "$coreGroup:jackson-core:${Versions.jackson}"
+    const val databind = "$coreGroup:jackson-databind:${Versions.jackson}"
+    const val dataformatXml = "$dataformatGroup:jackson-dataformat-xml:${Versions.jackson}"
+    const val jaxbAnnotations = "$moduleGroup:jackson-module-jaxb-annotations:${Versions.jackson}"
+    const val jsr310 = "$datatypeGroup:jackson-datatype-jsr310:${Versions.jackson}"
   }
 
   object Kotlin {
@@ -188,9 +218,9 @@ object Dependencies {
 
     object Cql {
       const val antlr = "4.10.1"
-      const val engine = "2.1.0"
-      const val evaluator = "2.1.0"
-      const val translator = "2.2.0"
+      const val engine = "2.4.0"
+      const val evaluator = "2.4.0"
+      const val translator = "2.4.0"
     }
 
     object Kotlin {
@@ -205,8 +235,9 @@ object Dependencies {
     const val fhirUcum = "1.0.3"
     const val guava = "28.2-android"
     const val hapiFhir = "6.0.1"
+    const val hapiFhirCore = "5.6.36"
     const val http = "4.9.1"
-    const val jackson = "2.12.2"
+    const val jackson = "2.14.1"
     const val jsonToolsPatch = "1.13"
     const val jsonAssert = "1.5.1"
     const val kotlinPoet = "1.9.0"

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -100,10 +100,6 @@ fun Project.configureLicensee() {
     allowDependency("org.antlr", "antlr4-runtime", "4.10.1") {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
-    // ANTLR 4
-    allowDependency("org.antlr", "antlr4", "4.10.1") {
-      because("BSD 3-clause. http://www.antlr.org/license.html")
-    }
 
     // Utilities
     // https://developers.google.com/android/reference/com/google/android/gms/common/package-summary

workflow-testing/build.gradle.kts

@@ -18,6 +18,43 @@ android {
   kotlinOptions { jvmTarget = Java.kotlinJvmTarget.toString() }
 }
 
+configurations {
+  all {
+    exclude(module = "xpp3")
+    exclude(module = "xpp3_min")
+    exclude(module = "xmlpull")
+    exclude(module = "javax.json")
+    exclude(module = "jcl-over-slf4j")
+    exclude(group = "org.apache.httpcomponents")
+
+    // Removes newer versions of caffeine and manually imports 2.9
+    // Removes newer versions of hapi and keeps on 6.0.1
+    // (newer versions don't work on Android)
+    resolutionStrategy {
+      force(Dependencies.HapiFhir.caffeine)
+      force(Dependencies.HapiFhir.fhirBase)
+      force(Dependencies.HapiFhir.fhirClient)
+      force(Dependencies.HapiFhir.structuresDstu2)
+      force(Dependencies.HapiFhir.structuresDstu3)
+      force(Dependencies.HapiFhir.structuresR4)
+      force(Dependencies.HapiFhir.structuresR5)
+      force(Dependencies.HapiFhir.validation)
+      force(Dependencies.HapiFhir.validationDstu3)
+      force(Dependencies.HapiFhir.validationR4)
+      force(Dependencies.HapiFhir.validationR5)
+
+      force(Dependencies.HapiFhir.fhirCoreDstu2)
+      force(Dependencies.HapiFhir.fhirCoreDstu2016)
+      force(Dependencies.HapiFhir.fhirCoreDstu3)
+      force(Dependencies.HapiFhir.fhirCoreR4)
+      force(Dependencies.HapiFhir.fhirCoreR4b)
+      force(Dependencies.HapiFhir.fhirCoreR5)
+      force(Dependencies.HapiFhir.fhirCoreUtils)
+      force(Dependencies.HapiFhir.fhirCoreConvertors)
+    }
+  }
+}
+
 dependencies {
   compileOnly(Dependencies.Cql.engine)
   compileOnly(Dependencies.Cql.evaluator)
@@ -28,6 +65,16 @@ dependencies {
   compileOnly(Dependencies.Cql.translatorElm)
   compileOnly(Dependencies.Cql.translatorModel)
 
+  // Forces the most recent version of jackson, ignoring what dependencies use.
+  // Remove these lines when HAPI 6.4 becomes available.
+  compileOnly(Dependencies.Jackson.annotations)
+  compileOnly(Dependencies.Jackson.bom)
+  compileOnly(Dependencies.Jackson.core)
+  compileOnly(Dependencies.Jackson.databind)
+  compileOnly(Dependencies.Jackson.dataformatXml)
+  compileOnly(Dependencies.Jackson.jaxbAnnotations)
+  compileOnly(Dependencies.Jackson.jsr310)
+
   compileOnly(Dependencies.junit)
   compileOnly(Dependencies.jsonAssert)
   compileOnly(Dependencies.woodstox)

workflow-testing/src/main/java/com/google/android/fhir/workflow/testing/PlanDefinition.kt

@@ -21,7 +21,6 @@ import ca.uhn.fhir.context.FhirVersionEnum
 import org.hl7.fhir.instance.model.api.IBaseBundle
 import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.model.Bundle
-import org.hl7.fhir.r4.model.CarePlan
 import org.hl7.fhir.r4.model.Coding
 import org.hl7.fhir.r4.model.Endpoint
 import org.hl7.fhir.r4.model.IdType
@@ -49,7 +48,7 @@ import org.opencds.cqf.cql.evaluator.fhir.adapter.r4.AdapterFactory
 import org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal
 import org.opencds.cqf.cql.evaluator.library.CqlFhirParametersConverter
 import org.opencds.cqf.cql.evaluator.library.LibraryProcessor
-import org.opencds.cqf.cql.evaluator.plandefinition.r4.OperationParametersParser
+import org.opencds.cqf.cql.evaluator.plandefinition.OperationParametersParser
 import org.opencds.cqf.cql.evaluator.plandefinition.r4.PlanDefinitionProcessor
 import org.skyscreamer.jsonassert.JSONAssert
 
@@ -218,7 +217,7 @@ object PlanDefinition : Loadable() {
     }
   }
 
-  class GeneratedCarePlan(val carePlan: CarePlan) {
+  class GeneratedCarePlan(val carePlan: IBaseResource) {
     fun isEqualsTo(expectedCarePlanAssetName: String) {
       try {
         JSONAssert.assertEquals(
@@ -229,6 +228,9 @@ object PlanDefinition : Loadable() {
       } catch (e: JSONException) {
         e.printStackTrace()
         fail("Unable to compare Jsons: " + e.message)
+      } catch (e: AssertionError) {
+        println("Actual: " + jsonParser.encodeResourceToString(carePlan))
+        throw e
       }
     }
   }

workflow-testing/src/main/resources/plan-definition/child-routine-visit/child_routine_visit_careplan.json

@@ -1,66 +1,90 @@
 {
 	"resourceType": "CarePlan",
-	"contained": [ {
-		"resourceType": "RequestGroup",
-		"id": "1",
-		"status": "draft",
-		"intent": "proposal",
-		"action": [ {
-			"title": "Child Monthly Routine Visit",
-			"description": "This action will performed every month for a patient < 5 years old. The start date with be next month after registration while the end date will be the 60th week after birth.",
-			"timingTiming": {
-				"repeat": {
-					"countMax": 59,
-					"duration": 2,
-					"durationMax": 4,
-					"durationUnit": "h",
-					"frequency": 1,
-					"frequencyMax": 1,
-					"period": 1,
-					"periodMax": 1,
-					"periodUnit": "mo"
+	"contained": [
+		{
+			"resourceType": "RequestGroup",
+			"id": "ChildRoutineVisit-PlanDefinition-1.0.0",
+			"instantiatesCanonical": [ "http://fhir.org/guides/cdc/opioid-cds/PlanDefinition/ChildRoutineVisit-PlanDefinition-1.0.0" ],
+			"status": "draft",
+			"intent": "proposal",
+			"subject": {
+				"reference": "Patient/ChildRoutine-Reportable"
+			},
+			"action": [
+				{
+					"title": "Child Monthly Routine Visit",
+					"description": "This action will performed every month for a patient < 5 years old. The start date with be next month after registration while the end date will be the 60th week after birth.",
+					"timingTiming": {
+						"repeat": {
+							"countMax": 59,
+							"duration": 2,
+							"durationMax": 4,
+							"durationUnit": "h",
+							"frequency": 1,
+							"frequencyMax": 1,
+							"period": 1,
+							"periodMax": 1,
+							"periodUnit": "mo"
+						}
+					},
+					"resource": {
+						"reference": "https://fhir.labs.smartregister.org/fhir/Questionnaire/105056"
+					}
+				}
+			]
+		},
+		{
+			"resourceType": "Goal",
+			"id": "1",
+			"category": [
+				{
+					"coding": [
+						{
+							"system": "https://www.hl7.org/fhir/codesystem-goal-category.html",
+							"code": "nursing",
+							"display": "Nursing"
+						}
+					]
 				}
+			],
+			"priority": {
+				"coding": [
+					{
+						"system": "https://www.hl7.org/fhir/codesystem-goal-priority.html",
+						"code": "high-priority",
+						"display": "High Priority"
+					}
+				]
 			},
-			"resource": {
-				"reference": "https://fhir.labs.smartregister.org/fhir/Questionnaire/105056"
+			"startCodeableConcept": {
+				"coding": [
+					{
+						"system": "http://www.snomed.org/",
+						"code": "32485007",
+						"display": "Admission to hospital"
+					}
+				]
 			}
-		} ]
-	}, {
-		"resourceType": "Goal",
-		"id": "2",
-		"category": [ {
-			"coding": [ {
-				"system": "https://www.hl7.org/fhir/codesystem-goal-category.html",
-				"code": "nursing",
-				"display": "Nursing"
-			} ]
-		} ],
-		"priority": {
-			"coding": [ {
-				"system": "https://www.hl7.org/fhir/codesystem-goal-priority.html",
-				"code": "high-priority",
-				"display": "High Priority"
-			} ]
-		},
-		"startCodeableConcept": {
-			"coding": [ {
-				"system": "http://www.snomed.org/",
-				"code": "32485007",
-				"display": "Admission to hospital"
-			} ]
 		}
-	} ],
-	"instantiatesCanonical": [ "ChildRoutineVisit-PlanDefinition-1.0.0" ],
+	],
+	"instantiatesCanonical": [
+		"http://fhir.org/guides/cdc/opioid-cds/PlanDefinition/ChildRoutineVisit-PlanDefinition-1.0.0"
+	],
 	"status": "draft",
+	"intent": "proposal",
 	"subject": {
 		"reference": "Patient/ChildRoutine-Reportable"
 	},
-	"goal": [ {
-		"reference": "#2"
-	} ],
-	"activity": [ {
-		"reference": {
+	"goal": [
+		{
 			"reference": "#1"
 		}
-	} ]
+	],
+	"activity": [
+		{
+			"reference": {
+				"reference": "#ChildRoutineVisit-PlanDefinition-1.0.0"
+			}
+		}
+	]
 }

workflow-testing/src/main/resources/plan-definition/child-routine-visit/child_routine_visit_plan_definition.json

@@ -7,6 +7,7 @@
       "resource": {
         "resourceType": "PlanDefinition",
         "id": "ChildRoutineVisit-PlanDefinition-1.0.0",
+        "url": "http://fhir.org/guides/cdc/opioid-cds/PlanDefinition/ChildRoutineVisit-PlanDefinition-1.0.0",
         "name": "Child Routine visit PlanDefinition",
         "title": "Child Routine visit PlanDefinition",
         "status": "active",