Merge branch 'master' into fix-sync-state-excepiton

Signed-off-by: Elly Kitoto <junkmailstoelly@gmail.com>

CODEOWNERS

@@ -1,5 +1,2 @@
 # Owners of the repository
-* @aditya-07 @deepankarb @jingtang10 @jjtswan @kevinmost @ktarasenko @omarismail94 @stevenckngaa @vvikramraj @wantingzhang77 @yigit
-# Owners of SDC library and catalog app
-catalog/ @aditya-07 @deepankarb @jingtang10 @jjtswan @joiskash @kevinmost @ktarasenko @omarismail94 @santosh-pingle @stevenckngaa @vvikramraj @wantingzhang77 @yigit
-datacapture/ @aditya-07 @deepankarb @jingtang10 @jjtswan @joiskash @kevinmost @ktarasenko @omarismail94 @santosh-pingle @stevenckngaa @vvikramraj @wantingzhang77 @yigit
+* @google/android-fhir @santosh-pingle

benchmark/build.gradle.kts

@@ -24,10 +24,7 @@ android {
     targetSdk = Sdk.targetSdk
 
     testInstrumentationRunner = "androidx.benchmark.junit4.AndroidBenchmarkRunner"
-    // Runs only once
-    testInstrumentationRunnerArguments["androidx.benchmark.dryRunMode.enable"] = "true"
-    // Includes Startup time
-    testInstrumentationRunnerArguments["androidx.benchmark.startupMode.enable"] = "true"
+    testInstrumentationRunnerArguments["androidx.benchmark.output.enable"] = "true"
   }
 
   testBuildType = "release"
@@ -68,6 +65,8 @@ android {
   }
 }
 
+afterEvaluate { configureFirebaseTestLabForMicroBenchmark() }
+
 configurations {
   all {
     removeIncompatibleDependencies()
@@ -85,8 +84,13 @@ dependencies {
   androidTestImplementation(Dependencies.junit)
   androidTestImplementation(Dependencies.Kotlin.kotlinCoroutinesAndroid)
   androidTestImplementation(Dependencies.truth)
+  androidTestImplementation(Dependencies.Androidx.workRuntimeKtx)
+  androidTestImplementation(Dependencies.AndroidxTest.workTestingRuntimeKtx)
+  androidTestImplementation(Dependencies.mockWebServer)
+  androidTestImplementation(Dependencies.Retrofit.coreRetrofit)
 
   androidTestImplementation(project(":engine"))
+  androidTestImplementation(project(":knowledge"))
   androidTestImplementation(project(":workflow"))
   androidTestImplementation(project(":workflow-testing"))
 }

benchmark/src/androidTest/AndroidManifest.xml

@@ -13,9 +13,12 @@
     -->
     <application
         android:debuggable="false"
+        android:usesCleartextTraffic="true"
         tools:ignore="HardcodedDebugMode"
         tools:replace="android:debuggable"
+        android:requestLegacyExternalStorage="true"
     >
         <profileable android:shell="true" />
     </application>
+    <uses-permission android:name="android.permission.INTERNET" />
 </manifest>

benchmark/src/androidTest/java/com/google/android/fhir/benchmark/D_FhirJsonParserBenchmark.kt

@@ -43,7 +43,7 @@ class D_FhirJsonParserBenchmark {
   fun parseLightFhirBundle() {
     benchmarkRule.measureRepeated {
       val jsonParser = runWithTimingDisabled {
-        var fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
+        val fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
         fhirContext.newJsonParser()
       }
 
@@ -60,16 +60,14 @@ class D_FhirJsonParserBenchmark {
   fun parseLightFhirLibrary() {
     benchmarkRule.measureRepeated {
       val jsonParser = runWithTimingDisabled {
-        var fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
+        val fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
         fhirContext.newJsonParser()
       }
 
-      val library = runWithTimingDisabled { open("/immunity-check/ImmunityCheck.json") }
-
-      val libraryBundle = jsonParser.parseResource(library) as Bundle
-
-      val immunityCheckLibrary = libraryBundle.entry[0].resource as Library
-      val fhirHelpersLibrary = libraryBundle.entry[1].resource as Library
+      val immunityCheckJson = runWithTimingDisabled { open("/immunity-check/ImmunityCheck.json") }
+      val immunityCheckLibrary = jsonParser.parseResource(immunityCheckJson) as Library
+      val fhirHelpersJson = runWithTimingDisabled { open("/immunity-check/FhirHelpers.json") }
+      val fhirHelpersLibrary = jsonParser.parseResource(fhirHelpersJson) as Library
 
       assertThat(immunityCheckLibrary.id).isEqualTo("Library/ImmunityCheck-1.0.0")
       assertThat(immunityCheckLibrary.content[0].data.size).isEqualTo(575)

benchmark/src/androidTest/java/com/google/android/fhir/benchmark/E_ElmJsonLibraryLoaderBenchmark.kt

@@ -24,7 +24,6 @@ import ca.uhn.fhir.context.FhirVersionEnum
 import com.google.common.truth.Truth.assertThat
 import java.io.InputStream
 import java.io.StringReader
-import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.Library
 import org.junit.Rule
 import org.junit.Test
@@ -43,13 +42,12 @@ class E_ElmJsonLibraryLoaderBenchmark {
   @Test
   fun parseImmunityCheckCqlFromFhirLibrary() {
     benchmarkRule.measureRepeated {
-      val libraryBundle = runWithTimingDisabled {
-        var fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
+      val immunityCheckLibrary = runWithTimingDisabled {
+        val fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
         val jsonParser = fhirContext.newJsonParser()
-        jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Bundle
+        jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Library
       }
 
-      val immunityCheckLibrary = libraryBundle.entry[0].resource as Library
       val jsonLib = immunityCheckLibrary.content.first { it.contentType == "application/elm+json" }
 
       val immunityCheckCqlLibrary = JsonCqlLibraryReader().read(StringReader(String(jsonLib.data)))
@@ -61,13 +59,12 @@ class E_ElmJsonLibraryLoaderBenchmark {
   @Test
   fun parseFhirHelpersCqlFromFhirLibrary() {
     benchmarkRule.measureRepeated {
-      val libraryBundle = runWithTimingDisabled {
-        var fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
+      val fhirHelpersLibrary = runWithTimingDisabled {
+        val fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
         val jsonParser = fhirContext.newJsonParser()
-        jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Bundle
+        jsonParser.parseResource(open("/immunity-check/FhirHelpers.json")) as Library
       }
 
-      val fhirHelpersLibrary = libraryBundle.entry[1].resource as Library
       val jsonLib = fhirHelpersLibrary.content.first { it.contentType == "application/elm+json" }
 
       val fhirHelpersCqlLibrary = JsonCqlLibraryReader().read(StringReader(String(jsonLib.data)))

benchmark/src/androidTest/java/com/google/android/fhir/benchmark/F_EngineDatabaseBenchmark.kt

@@ -22,12 +22,15 @@ import androidx.test.core.app.ApplicationProvider
 import androidx.test.ext.junit.runners.AndroidJUnit4
 import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
+import com.google.android.fhir.FhirEngineConfiguration
 import com.google.android.fhir.FhirEngineProvider
 import com.google.common.truth.Truth.assertThat
 import java.io.InputStream
 import kotlinx.coroutines.runBlocking
 import org.hl7.fhir.r4.model.Bundle
 import org.hl7.fhir.r4.model.ResourceType
+import org.junit.AfterClass
+import org.junit.BeforeClass
 import org.junit.Rule
 import org.junit.Test
 import org.junit.runner.RunWith
@@ -63,4 +66,18 @@ class F_EngineDatabaseBenchmark {
       }
     }
   }
+
+  companion object {
+
+    @JvmStatic
+    @BeforeClass
+    fun oneTimeSetup() {
+      FhirEngineProvider.init(FhirEngineConfiguration(testMode = true))
+    }
+    @JvmStatic
+    @AfterClass
+    fun oneTimeTearDown() {
+      FhirEngineProvider.cleanup()
+    }
+  }
 }

benchmark/src/androidTest/java/com/google/android/fhir/benchmark/G_CqlEvaluatorBenchmark.kt

@@ -16,19 +16,26 @@
 
 package com.google.android.fhir.benchmark
 
+import android.content.Context
 import androidx.benchmark.junit4.BenchmarkRule
 import androidx.benchmark.junit4.measureRepeated
 import androidx.test.core.app.ApplicationProvider
 import androidx.test.ext.junit.runners.AndroidJUnit4
 import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
+import com.google.android.fhir.FhirEngineConfiguration
 import com.google.android.fhir.FhirEngineProvider
-import com.google.android.fhir.workflow.FhirOperator
+import com.google.android.fhir.knowledge.KnowledgeManager
+import com.google.android.fhir.workflow.FhirOperatorBuilder
 import com.google.common.truth.Truth.assertThat
+import java.io.File
 import java.io.InputStream
 import kotlinx.coroutines.runBlocking
 import org.hl7.fhir.r4.model.Bundle
+import org.hl7.fhir.r4.model.Library
 import org.hl7.fhir.r4.model.Parameters
+import org.junit.AfterClass
+import org.junit.BeforeClass
 import org.junit.Rule
 import org.junit.Test
 import org.junit.runner.RunWith
@@ -48,20 +55,30 @@ class G_CqlEvaluatorBenchmark {
       val fhirOperator = runWithTimingDisabled {
         val fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
         val jsonParser = fhirContext.newJsonParser()
+        val context: Context = ApplicationProvider.getApplicationContext()
 
         val patientImmunizationHistory =
           jsonParser.parseResource(open("/immunity-check/ImmunizationHistory.json")) as Bundle
         val fhirEngine = FhirEngineProvider.getInstance(ApplicationProvider.getApplicationContext())
+        val knowledgeManager = KnowledgeManager.createInMemory(context)
+        val lib = jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Library
 
         runBlocking {
           for (entry in patientImmunizationHistory.entry) {
             fhirEngine.create(entry.resource)
           }
+          knowledgeManager.install(
+            File(context.filesDir, lib.name).apply {
+              writeText(jsonParser.encodeResourceToString(lib))
+            }
+          )
         }
 
-        val lib = jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Bundle
-
-        FhirOperator(fhirContext, fhirEngine).also { it.loadLibs(lib) }
+        FhirOperatorBuilder(context)
+          .withFhirContext(fhirContext)
+          .withFhirEngine(fhirEngine)
+          .withIgManager(knowledgeManager)
+          .build()
       }
 
       val results =
@@ -74,4 +91,18 @@ class G_CqlEvaluatorBenchmark {
       assertThat(results.getParameterBool("CompletedImmunization")).isTrue()
     }
   }
+
+  companion object {
+
+    @JvmStatic
+    @BeforeClass
+    fun oneTimeSetup() {
+      FhirEngineProvider.init(FhirEngineConfiguration(testMode = true))
+    }
+    @JvmStatic
+    @AfterClass
+    fun oneTimeTearDown() {
+      FhirEngineProvider.cleanup()
+    }
+  }
 }