Upgrade FHIR SDK dependencies ⬆️ (#3423)

* Upgrade FHIR SDK dependencies ⬆️
* Replace JWT token parser library
* Update Kujaku library version
* Upgrade 3rd party dependencies
* Refactor Knowledge Manager Resources Persistance
* Refactor Cancel previous worflow to use native commands
* Upgrade CI API level to 34
* Clean up gradle dependencies configuration
* Move measure reporting evaluation to BG thread
* Remove unrecommended forced portrait format
* Clean up TOML catalog file
* Refactor usage of FHIR JSONParser to support concurrency
* Fix code coverage reporting
* Fix build 💚

.github/workflows/ci.yml

@@ -10,6 +10,10 @@ on:
   merge_group:
     branches: [ main ]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
  FHIRCORE_USERNAME: ${{ secrets.FHIRCORE_USERNAME }}
  FHIRCORE_ACCESS_TOKEN: ${{ secrets.FHIRCORE_ACCESS_TOKEN }}
@@ -21,13 +25,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        api-level: [30]
+        api-level: [34]
+
     steps:
-      - name: Cancel Previous workflow runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
-
       - name: Checkout 🛎️
         uses: actions/checkout@v4
 
@@ -106,21 +106,17 @@ jobs:
 
 
       - name: Upload Engine module test coverage report to Codecov
-        if: matrix.api-level == 30 # Only upload coverage on API level 30
+        if: matrix.api-level == 34 # Only upload coverage on API level 34
         working-directory: android
         run:  bash <(curl -s https://codecov.io/bash) -F engine -f "engine/build/reports/jacoco/fhircoreJacocoReport/fhircoreJacocoReport.xml"
 
   geowidget-tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        api-level: [30]
+        api-level: [34]
+
     steps:
-      - name: Cancel Previous workflow runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
-
       - name: Checkout 🛎️
         uses: actions/checkout@v4
 
@@ -198,20 +194,17 @@ jobs:
           path: android/geowidget/build/reports
 
       - name: Upload Geowidget module test coverage report to Codecov
-        if: matrix.api-level == 30 # Only upload coverage on API level 30
+        if: matrix.api-level == 34 # Only upload coverage on API level 34
         working-directory: android
         run:  bash <(curl -s https://codecov.io/bash) -F geowidget -f "geowidget/build/reports/jacoco/fhircoreJacocoReport/fhircoreJacocoReport.xml"
 
   quest-tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        api-level: [30]
-    steps:
-      - name: Cancel Previous workflow runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
+        api-level: [34]
+
+    steps: 
       - name: Checkout 🛎️
         uses: actions/checkout@v4
 
@@ -315,6 +308,6 @@ jobs:
           path: android/quest/build/reports
 
       - name: Upload Quest module test coverage report to Codecov
-        if: matrix.api-level == 30 # Only upload coverage on API level 30
+        if: matrix.api-level == 34 # Only upload coverage on API level 34
         working-directory: android
-        run:  bash <(curl -s https://codecov.io/bash) -F quest -f "quest/build/reports/jacoco/fhircoreJacocoReport/fhircoreJacocoReport.xml"
+        run:  bash <(curl -s https://codecov.io/bash) -F quest -f "quest/build/reports/jacoco/fhircoreJacocoReport/fhircoreJacocoReport.xml"

android/engine/build.gradle.kts

@@ -3,7 +3,7 @@ import org.gradle.api.tasks.testing.logging.TestLogEvent
 
 plugins {
   `jacoco-report`
-  `ktlint`
+  ktlint
   id("com.android.library")
   id("kotlin-android")
   id("kotlin-kapt")
@@ -162,7 +162,7 @@ dependencies {
   api(libs.glide)
   api(libs.knowledge) { exclude(group = "org.slf4j", module = "jcl-over-slf4j") }
   api(libs.p2p.lib)
-  api(libs.jjwt)
+  api(libs.java.jwt)
   api(libs.fhir.common.utils) { exclude(group = "org.slf4j", module = "jcl-over-slf4j") }
   api(libs.runtime.livedata)
   api(libs.foundation)
@@ -180,8 +180,8 @@ dependencies {
   api(libs.data.capture) {
     isTransitive = true
     exclude(group = "ca.uhn.hapi.fhir")
-    exclude(group = "com.google.android.fhir", module = "engine")
     exclude(group = "com.google.android.fhir", module = "common")
+    exclude(group = "org.smartregister", module = "common")
     exclude(group = "org.slf4j", module = "jcl-over-slf4j")
   }
   api(libs.cqf.fhir.cr) {
@@ -194,23 +194,19 @@ dependencies {
     exclude(group = "xerces")
     exclude(group = "com.github.java-json-tools")
     exclude(group = "org.codehaus.woodstox")
-    exclude(group = "com.google.android.fhir", module = "common")
     exclude(group = "com.google.android.fhir", module = "engine")
+    exclude(group = "org.smartregister", module = "engine")
     exclude(group = "com.github.ben-manes.caffeine")
   }
   api(libs.contrib.barcode) {
     isTransitive = true
     exclude(group = "org.smartregister", module = "data-capture")
     exclude(group = "ca.uhn.hapi.fhir")
-    exclude(group = "com.google.android.fhir", module = "common")
-    exclude(group = "com.google.android.fhir", module = "engine")
   }
   api(libs.contrib.locationwidget) {
     isTransitive = true
     exclude(group = "org.smartregister", module = "data-capture")
     exclude(group = "ca.uhn.hapi.fhir")
-    exclude(group = "com.google.android.fhir", module = "common")
-    exclude(group = "com.google.android.fhir", module = "engine")
   }
   api(libs.fhir.engine) {
     isTransitive = true

android/engine/src/androidTest/java/org/smartregister/fhircore/engine/util/extension/FhirEngineExtensionKtTest.kt

@@ -25,6 +25,7 @@ import com.google.android.fhir.FhirEngineProvider
 import com.google.android.fhir.search.search
 import kotlinx.coroutines.launch
 import kotlinx.coroutines.runBlocking
+import kotlinx.coroutines.test.runTest
 import org.hl7.fhir.r4.model.Patient
 import org.hl7.fhir.r4.model.Questionnaire
 import org.hl7.fhir.r4.model.Resource
@@ -57,19 +58,15 @@ class FhirEngineExtensionKtTest {
   }
 
   @Test
-  fun test_search_time_searches_sequentially_and_short_running_query_waits() {
+  fun test_search_time_searches_sequentially_and_short_running_query_waits() = runTest {
     val fetchedResources = mutableListOf<Resource>()
-    runBlocking {
-      launch {
-        val patients = fhirEngine.search<Patient> {}.map { it.resource }
-        fetchedResources += patients
-      }
 
-      launch {
-        val questionnaires = fhirEngine.search<Questionnaire> {}.map { it.resource }
-        fetchedResources += questionnaires
-      }
-    }
+    val patients = fhirEngine.search<Patient> {}.map { it.resource }
+    fetchedResources += patients
+
+    val questionnaires = fhirEngine.search<Questionnaire> {}.map { it.resource }
+    fetchedResources += questionnaires
+
     val indexOfResultOfShortQuery =
       fetchedResources.indexOfFirst { it.resourceType == ResourceType.Questionnaire }
     val indexOfResultOfLongQuery =

android/engine/src/main/java/org/smartregister/fhircore/engine/configuration/ConfigurationRegistry.kt

@@ -104,7 +104,6 @@ constructor(
   private var _isNonProxy = BuildConfig.IS_NON_PROXY_APK
   private val fhirContext = FhirContext.forR4Cached()
   private val authConfiguration = configService.provideAuthConfiguration()
-  private val jsonParser = fhirContext.newJsonParser()
 
   /**
    * Retrieve configuration for the provided [ConfigType]. The JSON retrieved from [configsJsonMap]
@@ -629,9 +628,14 @@ constructor(
         resource.idElement.idPart
       }
 
-    return File(context.filesDir, "$fileName.json").apply {
-      writeText(jsonParser.encodeResourceToString(resource))
-    }
+    return File(
+        context.filesDir,
+        "$KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER/${resource.resourceType}/$fileName.json",
+      )
+      .apply {
+        this.parentFile?.mkdirs()
+        writeText(fhirContext.newJsonParser().encodeResourceToString(resource))
+      }
   }
 
   /**
@@ -813,6 +817,7 @@ constructor(
     const val PAGINATION_NEXT = "next"
     const val RESOURCES_PATH = "resources/"
     const val SYNC_LOCATION_IDS = "_syncLocations"
+    const val KNOWLEDGE_MANAGER_ASSETS_SUBFOLDER = "km"
 
     /**
      * The list of resources whose types can be synced down as part of the Composition configs.

android/engine/src/main/java/org/smartregister/fhircore/engine/data/local/DefaultRepository.kt

@@ -114,18 +114,15 @@ constructor(
   @ApplicationContext open val context: Context,
 ) {
 
-  suspend inline fun <reified T : Resource> loadResource(resourceId: String): T? {
-    return withContext(dispatcherProvider.io()) { fhirEngine.loadResource(resourceId) }
-  }
+  suspend inline fun <reified T : Resource> loadResource(resourceId: String): T? =
+    fhirEngine.loadResource(resourceId)
 
   suspend fun loadResource(resourceId: String, resourceType: ResourceType): Resource =
-    withContext(dispatcherProvider.io()) { fhirEngine.get(resourceType, resourceId) }
+    fhirEngine.get(resourceType, resourceId)
 
   suspend fun loadResource(reference: Reference) =
-    withContext(dispatcherProvider.io()) {
-      IdType(reference.reference).let {
-        fhirEngine.get(ResourceType.fromCode(it.resourceType), it.idPart)
-      }
+    IdType(reference.reference).let {
+      fhirEngine.get(ResourceType.fromCode(it.resourceType), it.idPart)
     }
 
   suspend inline fun <reified T : Resource> searchResourceFor(
@@ -135,19 +132,17 @@ constructor(
     dataQueries: List<DataQuery> = listOf(),
     configComputedRuleValues: Map<String, Any>,
   ): List<T> =
-    withContext(dispatcherProvider.io()) {
-      fhirEngine
-        .batchedSearch<T> {
-          filterByResourceTypeId(token, subjectType, subjectId)
-          dataQueries.forEach {
-            filterBy(
-              dataQuery = it,
-              configComputedRuleValues = configComputedRuleValues,
-            )
-          }
+    fhirEngine
+      .batchedSearch<T> {
+        filterByResourceTypeId(token, subjectType, subjectId)
+        dataQueries.forEach {
+          filterBy(
+            dataQuery = it,
+            configComputedRuleValues = configComputedRuleValues,
+          )
         }
-        .map { it.resource }
-    }
+      }
+      .map { it.resource }
 
   suspend inline fun <reified R : Resource> search(search: Search) =
     fhirEngine.batchedSearch<R>(search).map { it.resource }
@@ -162,17 +157,13 @@ constructor(
    * param [addResourceTags]
    */
   suspend fun create(addResourceTags: Boolean = true, vararg resource: Resource): List<String> {
-    return withContext(dispatcherProvider.io()) {
-      preProcessResources(addResourceTags, *resource)
-      fhirEngine.create(*resource)
-    }
+    preProcessResources(addResourceTags, *resource)
+    return fhirEngine.create(*resource)
   }
 
   suspend fun createRemote(addResourceTags: Boolean = true, vararg resource: Resource) {
-    return withContext(dispatcherProvider.io()) {
-      preProcessResources(addResourceTags, *resource)
-      fhirEngine.create(*resource, isLocalOnly = true)
-    }
+    preProcessResources(addResourceTags, *resource)
+    fhirEngine.create(*resource, isLocalOnly = true)
   }
 
   private fun preProcessResources(addResourceTags: Boolean, vararg resource: Resource) {
@@ -198,23 +189,19 @@ constructor(
     resourceId: String,
     softDelete: Boolean = false,
   ) {
-    withContext(dispatcherProvider.io()) {
-      if (softDelete) {
-        val resource = fhirEngine.get(resourceType, resourceId)
-        softDelete(resource)
-      } else {
-        fhirEngine.delete(resourceType, resourceId)
-      }
+    if (softDelete) {
+      val resource = fhirEngine.get(resourceType, resourceId)
+      softDelete(resource)
+    } else {
+      fhirEngine.delete(resourceType, resourceId)
     }
   }
 
   suspend fun delete(resource: Resource, softDelete: Boolean = false) {
-    withContext(dispatcherProvider.io()) {
-      if (softDelete) {
-        softDelete(resource)
-      } else {
-        fhirEngine.delete(resource.resourceType, resource.logicalId)
-      }
+    if (softDelete) {
+      softDelete(resource)
+    } else {
+      fhirEngine.delete(resource.resourceType, resource.logicalId)
     }
   }
 
@@ -243,24 +230,20 @@ constructor(
    * param [addMandatoryTags]
    */
   suspend fun <R : Resource> addOrUpdate(addMandatoryTags: Boolean = true, resource: R) {
-    return withContext(dispatcherProvider.io()) {
-      resource.updateLastUpdated()
-      try {
-        fhirEngine.get(resource.resourceType, resource.logicalId).run {
-          val updateFrom = updateFrom(resource)
-          fhirEngine.update(updateFrom)
-        }
-      } catch (resourceNotFoundException: ResourceNotFoundException) {
-        create(addMandatoryTags, resource)
+    resource.updateLastUpdated()
+    try {
+      fhirEngine.get(resource.resourceType, resource.logicalId).run {
+        val updateFrom = updateFrom(resource)
+        fhirEngine.update(updateFrom)
       }
+    } catch (resourceNotFoundException: ResourceNotFoundException) {
+      create(addMandatoryTags, resource)
     }
   }
 
   suspend fun <R : Resource> update(resource: R) {
-    return withContext(dispatcherProvider.io()) {
-      resource.updateLastUpdated()
-      fhirEngine.update(resource)
-    }
+    resource.updateLastUpdated()
+    fhirEngine.update(resource)
   }
 
   suspend fun loadManagingEntity(group: Group) =
@@ -904,7 +887,7 @@ constructor(
     val updatedResource =
       parser.parseResource(resourceDefinition, updatedResourceDocument.jsonString())
     updatedResource.setId(updatedResource.idElement.idPart)
-    withContext(dispatcherProvider.io()) { fhirEngine.update(updatedResource as Resource) }
+    fhirEngine.update(updatedResource as Resource)
   }
 
   private fun getJsonContent(jsonElement: JsonElement): Any? {
@@ -935,9 +918,7 @@ constructor(
 
   suspend fun purge(resource: Resource, forcePurge: Boolean) {
     try {
-      withContext(dispatcherProvider.io()) {
-        fhirEngine.purge(resource.resourceType, resource.logicalId, forcePurge)
-      }
+      fhirEngine.purge(resource.resourceType, resource.logicalId, forcePurge)
     } catch (resourceNotFoundException: ResourceNotFoundException) {
       Timber.e(
         "Purge failed -> Resource with ID ${resource.logicalId} does not exist",