Migrates engine to HAPI 6.8 while forcing Workflow to stay on 6.0 (#2245

)

* Migrates engine to HAPI 6.8 while forcing Workflow to stay on 6.0

* comment

buildSrc/build.gradle.kts

@@ -18,6 +18,6 @@ dependencies {
 
   implementation("com.spotify.ruler:ruler-gradle-plugin:1.2.1")
 
-  implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.0.1")
+  implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.8.0")
   implementation("com.squareup:kotlinpoet:1.12.0")
 }

buildSrc/src/main/kotlin/Dependencies.kt

@@ -88,6 +88,7 @@ object Dependencies {
     // Version 3.0 uses java.lang.System.Logger, which is not available on Android
     // Replace for Guava when this PR gets merged: https://github.com/hapifhir/hapi-fhir/pull/3977
     const val caffeine = "com.github.ben-manes.caffeine:caffeine:${Versions.caffeine}"
+    const val guavaCaching = "ca.uhn.hapi.fhir:hapi-fhir-caching-guava:${Versions.hapiFhir}"
   }
 
   object Jackson {
@@ -99,7 +100,7 @@ object Dependencies {
 
     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 core = "$coreGroup:jackson-core:${Versions.jacksonCore}"
     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}"
@@ -243,30 +244,28 @@ object Dependencies {
       const val stdlib = "1.8.20"
     }
 
-    const val androidFhirCommon = "0.1.0-alpha04"
+    const val androidFhirCommon = "0.1.0-alpha05"
     const val androidFhirEngine = "0.1.0-beta03"
     const val androidFhirKnowledge = "0.1.0-alpha01"
     const val apacheCommonsCompress = "1.21"
     const val desugarJdkLibs = "2.0.3"
     const val caffeine = "2.9.1"
     const val fhirUcum = "1.0.3"
     const val gson = "2.9.1"
-    const val guava = "28.2-android"
+    const val guava = "32.1.2-android"
 
-    // Hapi FHIR and HL7 Core Components are interlinked.
-    // Newer versions of HapiFhir don't work on Android due to the use of Caffeine 3+
-    // Wait for this to release (6.3): https://github.com/hapifhir/hapi-fhir/pull/4196
-    const val hapiFhir = "6.0.1"
-
-    // Newer versions don't work on Android due to Apache Commons Codec:
-    // Wait for this fix: https://github.com/hapifhir/org.hl7.fhir.core/issues/1046
-    const val hapiFhirCore = "5.6.36"
+    const val hapiFhir = "6.8.0"
+    const val hapiFhirCore = "6.0.22"
 
     const val http = "4.11.0"
 
-    // Maximum version that supports Android API Level 24:
+    // Maximum Jackson libraries (excluding core) version that supports Android API Level 24:
     // https://github.com/FasterXML/jackson-databind/issues/3658
     const val jackson = "2.13.5"
+
+    // Maximum Jackson Core library version that supports Android API Level 24:
+    const val jacksonCore = "2.15.2"
+
     const val jsonToolsPatch = "1.13"
     const val jsonAssert = "1.5.1"
     const val material = "1.9.0"
@@ -312,13 +311,22 @@ object Dependencies {
     exclude(group = "org.apache.httpcomponents")
   }
 
+  fun Configuration.forceGuava() {
+    // Removes caffeine
+    exclude(module = "hapi-fhir-caching-caffeine")
+    exclude(group = "com.github.ben-manes.caffeine", module = "caffeine")
+
+    resolutionStrategy {
+      force(guava)
+      force(HapiFhir.guavaCaching)
+    }
+  }
+
   fun Configuration.forceHapiVersion() {
     // 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(HapiFhir.caffeine)
-
       force(HapiFhir.fhirBase)
       force(HapiFhir.fhirClient)
       force(HapiFhir.fhirCoreConvertors)

buildSrc/src/main/kotlin/FirebaseTestLabConfig.kt

@@ -33,7 +33,6 @@ fun Project.configureFirebaseTestLabForLibraries() {
         "clearPackageData" to "true",
       ),
     )
-    flakyTestAttempts.set(3)
     devices.set(
       listOf(
         mapOf(
@@ -43,7 +42,7 @@ fun Project.configureFirebaseTestLabForLibraries() {
           "locale" to "en_US",
         ),
         mapOf(
-          "model" to "panther",
+          "model" to "MediumPhone.arm",
           "version" to "${project.extensions.getByType(LibraryExtension::class.java).compileSdk}",
           "locale" to "en_US",
         ),
@@ -64,8 +63,6 @@ fun Project.configureFirebaseTestLabForMicroBenchmark() {
         "clearPackageData" to "true",
       ),
     )
-    // some of the benchmark tests get timed-out in the default 15m
-    testTimeout.set("45m")
     devices.set(
       listOf(
         mapOf(
@@ -86,7 +83,9 @@ private fun FlankGradleExtension.commonConfigurationForFirebaseTestLab(project:
     },
   )
   useOrchestrator.set(true)
-  maxTestShards.set(20)
+  flakyTestAttempts.set(1)
+  maxTestShards.set(10)
+  testTimeout.set("45m")
   directoriesToPull.set(listOf("/sdcard/Download"))
   resultsBucket.set("android-fhir-build-artifacts")
   resultsDir.set(

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -39,6 +39,10 @@ fun Project.configureLicensee() {
     ignoreDependencies("org.jacoco", "org.jacoco.agent") {
       because("JaCoCo is used in tests only, so it is not distributed with our library")
     }
+    allowDependency("org.javassist", "javassist", "3.29.0-GA") {
+      because("Multi-licensed under Apache. https://github.com/jboss-javassist/javassist")
+    }
+    // Remove once Evaluator 3 migration is over
     allowDependency("org.javassist", "javassist", "3.20.0-GA") {
       because("Multi-licensed under Apache. https://github.com/jboss-javassist/javassist")
     }

catalog/build.gradle.kts

@@ -1,3 +1,5 @@
+import Dependencies.forceGuava
+
 plugins {
   id(Plugins.BuildPlugins.application)
   id(Plugins.BuildPlugins.kotlinAndroid)
@@ -40,6 +42,8 @@ android {
   kotlin { jvmToolchain(11) }
 }
 
+configurations { all { forceGuava() } }
+
 dependencies {
   androidTestImplementation(Dependencies.AndroidxTest.extJunit)
   androidTestImplementation(Dependencies.Espresso.espressoCore)

contrib/barcode/build.gradle.kts

@@ -1,3 +1,5 @@
+import Dependencies.forceGuava
+
 plugins {
   id(Plugins.BuildPlugins.androidLib)
   id(Plugins.BuildPlugins.kotlinAndroid)
@@ -44,7 +46,12 @@ android {
   kotlin { jvmToolchain(11) }
 }
 
-configurations { all { exclude(module = "xpp3") } }
+configurations {
+  all {
+    exclude(module = "xpp3")
+    forceGuava()
+  }
+}
 
 dependencies {
   androidTestImplementation(Dependencies.AndroidxTest.core)

datacapture/build.gradle.kts

@@ -1,3 +1,6 @@
+import Dependencies.forceGuava
+import Dependencies.forceHapiVersion
+import Dependencies.forceJacksonVersion
 import java.net.URL
 
 plugins {
@@ -52,7 +55,15 @@ android {
 
 afterEvaluate { configureFirebaseTestLabForLibraries() }
 
-configurations { all { exclude(module = "xpp3") } }
+configurations {
+  all {
+    exclude(module = "xpp3")
+    exclude(group = "net.sf.saxon", module = "Saxon-HE")
+    forceGuava()
+    forceHapiVersion()
+    forceJacksonVersion()
+  }
+}
 
 dependencies {
   androidTestImplementation(Dependencies.AndroidxTest.core)
@@ -77,10 +88,10 @@ dependencies {
   implementation(Dependencies.Androidx.coreKtx)
   implementation(Dependencies.Androidx.fragmentKtx)
   implementation(Dependencies.Glide.glide)
+  implementation(Dependencies.HapiFhir.guavaCaching)
   implementation(Dependencies.HapiFhir.validation) {
     exclude(module = "commons-logging")
     exclude(module = "httpclient")
-    exclude(group = "net.sf.saxon", module = "Saxon-HE")
   }
   implementation(Dependencies.Kotlin.kotlinCoroutinesCore)
   implementation(Dependencies.Kotlin.stdlib)

datacapture/src/main/java/com/google/android/fhir/datacapture/fhirpath/FHIRPathEngineHostServices.kt

@@ -25,8 +25,12 @@ import org.hl7.fhir.r4.utils.FHIRPathEngine
  * Resolves constants defined in the fhir path expressions beyond those defined in the specification
  */
 internal object FHIRPathEngineHostServices : FHIRPathEngine.IEvaluationContext {
-  override fun resolveConstant(appContext: Any?, name: String?, beforeContext: Boolean): Base? =
-    (appContext as? Map<*, *>)?.get(name) as? Base
+  override fun resolveConstant(
+    appContext: Any?,
+    name: String?,
+    beforeContext: Boolean,
+  ): List<Base>? =
+    ((appContext as? Map<*, *>)?.get(name) as? Base)?.let { listOf(it) } ?: emptyList()
 
   override fun resolveConstantType(appContext: Any?, name: String?): TypeDetails {
     throw UnsupportedOperationException()
@@ -59,15 +63,15 @@ internal object FHIRPathEngineHostServices : FHIRPathEngine.IEvaluationContext {
     throw UnsupportedOperationException()
   }
 
-  override fun resolveReference(appContext: Any?, url: String?): Base {
+  override fun resolveReference(appContext: Any?, url: String?, refContext: Base?): Base? {
     throw UnsupportedOperationException()
   }
 
   override fun conformsToProfile(appContext: Any?, item: Base?, url: String?): Boolean {
     throw UnsupportedOperationException()
   }
 
-  override fun resolveValueSet(appContext: Any?, url: String?): ValueSet {
+  override fun resolveValueSet(appContext: Any?, url: String?): ValueSet? {
     throw UnsupportedOperationException()
   }
 }

datacapture/src/main/java/com/google/android/fhir/datacapture/mapping/ResourceMapper.kt

@@ -775,13 +775,21 @@ private fun Base.asExpectedReferenceType(): Type {
       this@asExpectedReferenceType as Resource
       Reference().apply {
         reference =
-          "${this@asExpectedReferenceType.resourceType}/${this@asExpectedReferenceType.logicalId}"
+          if (this@asExpectedReferenceType.resourceType != null) {
+            "${this@asExpectedReferenceType.resourceType}/${this@asExpectedReferenceType.logicalId}"
+          } else {
+            this@asExpectedReferenceType.logicalId
+          }
       }
     }
     this is IdType ->
       Reference().apply {
         reference =
-          "${this@asExpectedReferenceType.resourceType}/${this@asExpectedReferenceType.idPart}"
+          if (this@asExpectedReferenceType.resourceType != null) {
+            "${this@asExpectedReferenceType.resourceType}/${this@asExpectedReferenceType.idPart}"
+          } else {
+            this@asExpectedReferenceType.idPart
+          }
       }
     else -> throw FHIRException("Expression supplied does not evaluate to IdType.")
   }

datacapture/src/test/java/com/google/android/fhir/datacapture/QuestionnaireViewModelTest.kt

@@ -4400,7 +4400,7 @@ class QuestionnaireViewModelTest {
                 Extension(
                   "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-answerExpression",
                   Expression().apply {
-                    this.expression = "Observation?subject={{%patient.id}}"
+                    this.expression = "Observation?subject=Patient/{{%patient.id}}"
                     this.language = Expression.ExpressionLanguage.APPLICATION_XFHIRQUERY.toCode()
                   },
                 ),

datacapture/src/test/java/com/google/android/fhir/datacapture/fhirpath/FHIRPathEngineHostServicesTest.kt

@@ -30,28 +30,28 @@ class FHIRPathEngineHostServicesTest {
   fun testFHIRPathHostServices_resolveConstantKeyNotPresent_returnsNull() {
     val answer = FHIRPathEngineHostServices.resolveConstant(mapOf("A" to IntegerType(1)), "B", true)
 
-    assertThat(answer).isNull()
+    assertThat(answer).isEmpty()
   }
 
   @Test
   fun testFHIRPathHostServices_resolveConstantKeyAndValuePresent_returnsNotNull() {
     val answer = FHIRPathEngineHostServices.resolveConstant(mapOf("A" to IntegerType(1)), "A", true)
 
-    assertThat((answer as Type).asStringValue()).isEqualTo("1")
+    assertThat((answer?.first() as Type).asStringValue()).isEqualTo("1")
   }
 
   @Test
   fun testFHIRPathHostServices_resolveConstantKeyPresentAndValueNotPresent_returnsNull() {
     val answer = FHIRPathEngineHostServices.resolveConstant(mapOf("A" to null), "A", true)
 
-    assertThat(answer).isNull()
+    assertThat(answer).isEmpty()
   }
 
   @Test
   fun testFHIRPathHostServices_resolveConstantNullAppContext_returnsNull() {
     val answer = FHIRPathEngineHostServices.resolveConstant(null, "A", true)
 
-    assertThat(answer).isNull()
+    assertThat(answer).isEmpty()
   }
 
   @Test
@@ -97,7 +97,7 @@ class FHIRPathEngineHostServicesTest {
   @Test
   fun testFHIRPathHostServices_resolveReference_throwsUnsupportedOperationException() {
     assertThrows(UnsupportedOperationException::class.java) {
-      FHIRPathEngineHostServices.resolveReference(mapOf<Any, Any>(), "")
+      FHIRPathEngineHostServices.resolveReference(mapOf<Any, Any>(), "", null)
     }
   }
 

datacapture/src/test/java/com/google/android/fhir/datacapture/mapping/ResourceMapperTest.kt

@@ -1564,7 +1564,7 @@ class ResourceMapperTest {
       val questionnaireResponse = ResourceMapper.populate(questionnaire, patient)
 
       assertThat((questionnaireResponse.item[0].answer[0].value as Reference).reference)
-        .isEqualTo(patient.id)
+        .isEqualTo(patient.idPart)
     }
 
   @Test

demo/build.gradle.kts

@@ -1,3 +1,5 @@
+import Dependencies.forceGuava
+
 plugins {
   id(Plugins.BuildPlugins.application)
   id(Plugins.BuildPlugins.kotlinAndroid)
@@ -38,6 +40,8 @@ android {
   kotlin { jvmToolchain(11) }
 }
 
+configurations { all { forceGuava() } }
+
 dependencies {
   androidTestImplementation(Dependencies.AndroidxTest.extJunit)
   androidTestImplementation(Dependencies.Espresso.espressoCore)

engine/benchmark/build.gradle.kts

@@ -1,3 +1,4 @@
+import Dependencies.forceGuava
 import Dependencies.forceHapiVersion
 import Dependencies.forceJacksonVersion
 import Dependencies.removeIncompatibleDependencies
@@ -50,6 +51,7 @@ afterEvaluate { configureFirebaseTestLabForMicroBenchmark() }
 configurations {
   all {
     removeIncompatibleDependencies()
+    forceGuava()
     forceHapiVersion()
     forceJacksonVersion()
   }

engine/build.gradle.kts

@@ -1,3 +1,6 @@
+import Dependencies.forceGuava
+import Dependencies.forceHapiVersion
+import Dependencies.forceJacksonVersion
 import codegen.GenerateSearchParamsTask
 import java.net.URL
 
@@ -84,6 +87,10 @@ configurations {
     exclude(module = "jakarta.activation-api")
     exclude(module = "javax.activation")
     exclude(module = "jakarta.xml.bind-api")
+
+    forceGuava()
+    forceHapiVersion()
+    forceJacksonVersion()
   }
 }
 
@@ -98,6 +105,17 @@ dependencies {
 
   api(Dependencies.HapiFhir.structuresR4) { exclude(module = "junit") }
 
+  // We have removed the dependency on Caffeine from HAPI due to conflicts with android
+  // Guave Caching must be individually loaded instead.
+  implementation(Dependencies.HapiFhir.guavaCaching)
+
+  // Validation to load system types into FhirPath's Context
+  // The loading happens via a ResourceStream in XML and thus
+  // XML parsers are also necessary.
+  implementation(Dependencies.HapiFhir.validationR4)
+  implementation(Dependencies.woodstox)
+  implementation(Dependencies.xerces)
+
   coreLibraryDesugaring(Dependencies.desugarJdkLibs)
 
   implementation(Dependencies.Androidx.datastorePref)