Validate extracted fhir resources while in debug

Author: LZRS

android/engine/build.gradle.kts

@@ -157,6 +157,8 @@ dependencies {
     exclude(group = "ca.uhn.hapi.fhir")
   }
 
+  implementation(libs.hapi.fhir.validation) { exclude(module = "commons-logging") }
+
   // Shared dependencies
   api(libs.glide)
   api(libs.knowledger)

android/engine/src/main/java/org/smartregister/fhircore/engine/di/FhirValidatorModule.kt

@@ -0,0 +1,39 @@
+/*
+ * Copyright 2021-2023 Ona Systems, Inc
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.smartregister.fhircore.engine.di
+
+import ca.uhn.fhir.context.FhirContext
+import ca.uhn.fhir.validation.FhirValidator
+import dagger.Module
+import dagger.Provides
+import dagger.hilt.InstallIn
+import dagger.hilt.components.SingletonComponent
+import javax.inject.Singleton
+import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator
+
+@Module
+@InstallIn(SingletonComponent::class)
+class FhirValidatorModule {
+
+  @Provides
+  @Singleton
+  fun provideFhirValidator(): FhirValidator {
+    val fhirContext = FhirContext.forR4()
+    val validatorModule = FhirInstanceValidator(fhirContext)
+    return fhirContext.newValidator().apply { registerValidatorModule(validatorModule) }
+  }
+}

android/engine/src/main/java/org/smartregister/fhircore/engine/task/FhirCarePlanGenerator.kt

@@ -19,12 +19,14 @@ package org.smartregister.fhircore.engine.task
 import androidx.annotation.VisibleForTesting
 import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.util.TerserUtil
+import ca.uhn.fhir.validation.FhirValidator
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.get
 import com.google.android.fhir.logicalId
 import com.google.android.fhir.search.search
 import java.util.Date
 import javax.inject.Inject
+import javax.inject.Provider
 import javax.inject.Singleton
 import org.hl7.fhir.r4.model.ActivityDefinition
 import org.hl7.fhir.r4.model.Base
@@ -56,7 +58,9 @@ import org.smartregister.fhircore.engine.configuration.event.EventType
 import org.smartregister.fhircore.engine.data.local.DefaultRepository
 import org.smartregister.fhircore.engine.util.extension.addResourceParameter
 import org.smartregister.fhircore.engine.util.extension.asReference
+import org.smartregister.fhircore.engine.util.extension.checkResourceValid
 import org.smartregister.fhircore.engine.util.extension.encodeResourceToString
+import org.smartregister.fhircore.engine.util.extension.errorMessages
 import org.smartregister.fhircore.engine.util.extension.extractFhirpathDuration
 import org.smartregister.fhircore.engine.util.extension.extractFhirpathPeriod
 import org.smartregister.fhircore.engine.util.extension.extractId
@@ -75,6 +79,7 @@ constructor(
   val transformSupportServices: TransformSupportServices,
   val defaultRepository: DefaultRepository,
   val fhirResourceUtil: FhirResourceUtil,
+  val fhirValidatorProvider: Provider<FhirValidator>,
   val workflowCarePlanGenerator: WorkflowCarePlanGenerator,
 ) {
   private val structureMapUtilities by lazy {
@@ -186,7 +191,22 @@ constructor(
 
     val carePlanTasks = output.contained.filterIsInstance<Task>()
 
-    if (carePlanModified) saveCarePlan(output)
+    if (carePlanModified) {
+      fhirValidatorProvider
+        .get()
+        .checkResourceValid(output)
+        .filterNot { it.isSuccessful }
+        .takeIf { it.isNotEmpty() }
+        ?.let {
+          val errors = buildString {
+            it.forEach { validationResult -> appendLine(validationResult.errorMessages) }
+          }
+
+          throw IllegalStateException(errors)
+        }
+
+      saveCarePlan(output)
+    }
 
     if (carePlanTasks.isNotEmpty()) {
       fhirResourceUtil.updateUpcomingTasksToDue(
@@ -208,7 +228,9 @@ constructor(
         carePlan.contained.clear()
 
         // Save CarePlan only if it has activity, otherwise just save contained/dependent resources
-        if (output.hasActivity()) defaultRepository.create(true, carePlan)
+        if (output.hasActivity()) {
+          defaultRepository.create(true, carePlan)
+        }
 
         dependents.forEach { defaultRepository.create(true, it) }
 

android/engine/src/main/java/org/smartregister/fhircore/engine/util/extension/FhirValidatorExtensions.kt

@@ -0,0 +1,40 @@
+/*
+ * Copyright 2021-2023 Ona Systems, Inc
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.smartregister.fhircore.engine.util.extension
+
+import ca.uhn.fhir.validation.FhirValidator
+import ca.uhn.fhir.validation.ResultSeverityEnum
+import ca.uhn.fhir.validation.ValidationResult
+import kotlin.coroutines.coroutineContext
+import kotlinx.coroutines.withContext
+import org.hl7.fhir.r4.model.Resource
+import org.smartregister.fhircore.engine.BuildConfig
+
+suspend fun FhirValidator.checkResourceValid(vararg resource: Resource): List<ValidationResult> {
+  if (!BuildConfig.BUILD_TYPE.contains("debug", ignoreCase = true)) return emptyList()
+
+  return withContext(coroutineContext) {
+    resource.map { this@checkResourceValid.validateWithResult(it) }
+  }
+}
+
+val ValidationResult.errorMessages
+  get() = buildString {
+    for (validationMsg in messages.filter { it.severity == ResultSeverityEnum.ERROR }) {
+      appendLine("${validationMsg.message} - ${validationMsg.locationString}")
+    }
+  }

android/engine/src/test/java/org/smartregister/fhircore/engine/task/FhirCarePlanGeneratorTest.kt

@@ -21,6 +21,7 @@ import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
 import ca.uhn.fhir.parser.IParser
 import ca.uhn.fhir.rest.gclient.ReferenceClientParam
+import ca.uhn.fhir.validation.FhirValidator
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.SearchResult
 import com.google.android.fhir.get
@@ -45,6 +46,7 @@ import java.util.Calendar
 import java.util.Date
 import java.util.UUID
 import javax.inject.Inject
+import javax.inject.Provider
 import kotlin.time.Duration.Companion.seconds
 import kotlinx.coroutines.Dispatchers
 import kotlinx.coroutines.ExperimentalCoroutinesApi
@@ -128,6 +130,8 @@ class FhirCarePlanGeneratorTest : RobolectricTest() {
 
   @Inject lateinit var workflowCarePlanGenerator: WorkflowCarePlanGenerator
 
+  @Inject lateinit var fhirValidatorProvider: Provider<FhirValidator>
+
   @Inject lateinit var fhirPathEngine: FHIRPathEngine
 
   @Inject lateinit var fhirEngine: FhirEngine
@@ -166,6 +170,7 @@ class FhirCarePlanGeneratorTest : RobolectricTest() {
         fhirPathEngine = fhirPathEngine,
         defaultRepository = defaultRepository,
         fhirResourceUtil = fhirResourceUtil,
+        fhirValidatorProvider = fhirValidatorProvider,
         workflowCarePlanGenerator = workflowCarePlanGenerator,
       )
 

android/gradle/libs.versions.toml

@@ -98,6 +98,7 @@ work-runtime-ktx = "2.8.1"
 work-testing = "2.8.1"
 workflow = "0.1.0-alpha02-preview9.1-SNAPSHOT"
 xercesImpl = "2.12.2"
+hapi-fhir = "6.0.1"
 
 [libraries]
 accompanist-flowlayout = { group = "com.google.accompanist", name = "accompanist-flowlayout", version.ref = "accompanist-flowlayout" }
@@ -205,5 +206,6 @@ work-runtime-ktx = { group = "androidx.work", name = "work-runtime-ktx", version
 work-testing = { group = "androidx.work", name = "work-testing", version.ref = "work-testing" }
 workflow = { group = "org.smartregister", name = "workflow", version.ref = "workflow" }
 xercesImpl = { group = "xerces", name = "xercesImpl", version.ref = "xercesImpl" }
+hapi-fhir-validation = {group = "ca.uhn.hapi.fhir", name="hapi-fhir-validation", version.ref = "hapi-fhir"}
 
 [plugins]

android/quest/src/main/java/org/smartregister/fhircore/quest/ui/questionnaire/QuestionnaireViewModel.kt

@@ -22,6 +22,7 @@ import androidx.lifecycle.LiveData
 import androidx.lifecycle.MutableLiveData
 import androidx.lifecycle.ViewModel
 import androidx.lifecycle.viewModelScope
+import ca.uhn.fhir.validation.FhirValidator
 import com.google.android.fhir.datacapture.mapping.ResourceMapper
 import com.google.android.fhir.datacapture.mapping.StructureMapExtractionContext
 import com.google.android.fhir.datacapture.validation.NotValidated
@@ -35,6 +36,7 @@ import dagger.hilt.android.lifecycle.HiltViewModel
 import java.util.Date
 import java.util.UUID
 import javax.inject.Inject
+import javax.inject.Provider
 import kotlinx.coroutines.SupervisorJob
 import kotlinx.coroutines.launch
 import kotlinx.coroutines.withContext
@@ -45,7 +47,6 @@ import org.hl7.fhir.r4.model.Group
 import org.hl7.fhir.r4.model.IdType
 import org.hl7.fhir.r4.model.ListResource
 import org.hl7.fhir.r4.model.ListResource.ListEntryComponent
-import org.hl7.fhir.r4.model.Patient
 import org.hl7.fhir.r4.model.Questionnaire
 import org.hl7.fhir.r4.model.QuestionnaireResponse
 import org.hl7.fhir.r4.model.RelatedPerson
@@ -66,7 +67,9 @@ import org.smartregister.fhircore.engine.util.extension.DEFAULT_PLACEHOLDER_PREF
 import org.smartregister.fhircore.engine.util.extension.appendOrganizationInfo
 import org.smartregister.fhircore.engine.util.extension.appendPractitionerInfo
 import org.smartregister.fhircore.engine.util.extension.asReference
+import org.smartregister.fhircore.engine.util.extension.checkResourceValid
 import org.smartregister.fhircore.engine.util.extension.cqfLibraryUrls
+import org.smartregister.fhircore.engine.util.extension.errorMessages
 import org.smartregister.fhircore.engine.util.extension.extractByStructureMap
 import org.smartregister.fhircore.engine.util.extension.extractId
 import org.smartregister.fhircore.engine.util.extension.extractLogicalIdUuid
@@ -93,6 +96,7 @@ constructor(
   val transformSupportServices: TransformSupportServices,
   val sharedPreferencesHelper: SharedPreferencesHelper,
   val fhirOperator: FhirOperator,
+  val fhirValidatorProvider: Provider<FhirValidator>,
   val fhirPathDataExtractor: FhirPathDataExtractor,
 ) : ViewModel() {
 
@@ -206,6 +210,18 @@ constructor(
           context = context,
         )
 
+      val validationResults =
+        bundle.entry
+          .map { it.resource }
+          .flatMap { fhirValidatorProvider.get().checkResourceValid(it) }
+      val validationFailures = validationResults.filterNot { it.isSuccessful }
+      if (validationFailures.isNotEmpty()) {
+        val errorMessages = buildString {
+          validationFailures.map { it.errorMessages }.forEach(this::appendLine)
+        }
+        throw IllegalStateException(errorMessages)
+      }
+
       saveExtractedResources(
         bundle = bundle,
         questionnaire = questionnaire,

android/quest/src/test/java/org/smartregister/fhircore/quest/ui/questionnaire/QuestionnaireViewModelTest.kt

@@ -18,6 +18,7 @@ package org.smartregister.fhircore.quest.ui.questionnaire
 
 import android.app.Application
 import androidx.test.core.app.ApplicationProvider
+import ca.uhn.fhir.validation.FhirValidator
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.datacapture.mapping.ResourceMapper
 import com.google.android.fhir.db.ResourceNotFoundException
@@ -40,6 +41,7 @@ import io.mockk.verify
 import java.util.Date
 import java.util.UUID
 import javax.inject.Inject
+import javax.inject.Provider
 import kotlin.time.Duration.Companion.seconds
 import kotlinx.coroutines.ExperimentalCoroutinesApi
 import kotlinx.coroutines.runBlocking
@@ -108,6 +110,8 @@ class QuestionnaireViewModelTest : RobolectricTest() {
 
   @Inject lateinit var sharedPreferencesHelper: SharedPreferencesHelper
 
+  @Inject lateinit var fhirValidatorProvider: Provider<FhirValidator>
+
   @Inject lateinit var configService: ConfigService
 
   @Inject lateinit var resourceDataRulesExecutor: ResourceDataRulesExecutor
@@ -180,6 +184,7 @@ class QuestionnaireViewModelTest : RobolectricTest() {
           fhirCarePlanGenerator = fhirCarePlanGenerator,
           resourceDataRulesExecutor = resourceDataRulesExecutor,
           fhirPathDataExtractor = fhirPathDataExtractor,
+          fhirValidatorProvider = fhirValidatorProvider,
           fhirOperator = fhirOperator,
         ),
       )