work in progress

android/build.gradle

@@ -35,6 +35,14 @@ allprojects {
             url = uri("/Users/ndegwamartin/.m2.dev/fhirsdk")
         }
     }
+
+    configurations {
+        configureEach {
+            resolutionStrategy {
+                force "ca.uhn.hapi.fhir:hapi-fhir-validation:6.0.1"
+            }
+        }
+    }
 }
 
 subprojects {

android/engine/build.gradle

@@ -112,12 +112,6 @@ android {
             }
         }
     }
-
-    configurations.all {
-        resolutionStrategy {
-            force "ca.uhn.hapi.fhir:org.hl7.fhir.utilities:5.5.7"
-        }
-    }
 }
 
 dependencies {
@@ -147,6 +141,9 @@ dependencies {
     implementation(group: "com.github.java-json-tools", name: "msg-simple", version: "1.2");
     implementation 'org.codehaus.woodstox:woodstox-core-asl:4.4.1'
     implementation "ca.uhn.hapi.fhir:hapi-fhir-android:5.4.0"
+    implementation ("ca.uhn.hapi.fhir:hapi-fhir-validation:6.0.1"){
+        exclude module: "commons-logging"
+    }
     implementation 'org.opencds.cqf.cql:engine:1.5.4'
     implementation 'org.opencds.cqf.cql:engine.fhir:1.5.4'
     implementation 'org.opencds.cqf.cql:evaluator:1.4.2'

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

@@ -0,0 +1,55 @@
+/*
+ * Copyright 2021 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 ca.uhn.fhir.validation.ResultSeverityEnum
+import ca.uhn.fhir.validation.ValidationResult
+import dagger.Module
+import dagger.Provides
+import dagger.hilt.InstallIn
+import dagger.hilt.components.SingletonComponent
+import javax.inject.Singleton
+import kotlin.coroutines.coroutineContext
+import kotlinx.coroutines.withContext
+import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator
+import org.hl7.fhir.r4.model.Resource
+
+@InstallIn(SingletonComponent::class)
+@Module
+class FhirValidatorModule {
+
+  @Singleton
+  @Provides
+  fun provideFhirValidator(): FhirValidator {
+    val fhirContext = FhirContext.forR4()
+    val validatorModule = FhirInstanceValidator(fhirContext)
+    return fhirContext.newValidator().apply { registerValidatorModule(validatorModule) }
+  }
+}
+
+val ValidationResult.errorMessages
+  get() = buildString {
+    for (validationMsg in messages.filter { it.severity == ResultSeverityEnum.ERROR }) {
+      appendLine("${validationMsg.message} - ${validationMsg.locationString}")
+    }
+  }
+
+suspend fun FhirValidator.checkResourceValid(resource: Resource): ValidationResult {
+  return withContext(coroutineContext) { this@checkResourceValid.validateWithResult(resource) }
+}

android/engine/src/main/java/org/smartregister/fhircore/engine/sync/AppSyncWorker.kt

@@ -58,5 +58,6 @@ constructor(
           }
         }
     )
+
   override fun getFhirEngine(): FhirEngine = engine
 }

android/engine/src/main/java/org/smartregister/fhircore/engine/ui/questionnaire/ExtractionProgress.kt

@@ -20,5 +20,5 @@ import org.hl7.fhir.r4.model.Resource
 
 sealed class ExtractionProgress {
   class Success(val extras: List<Resource>? = null) : ExtractionProgress()
-  object Failed : ExtractionProgress()
+  class Failed(val errorMessages: String? = null) : ExtractionProgress()
 }

android/engine/src/main/java/org/smartregister/fhircore/engine/ui/questionnaire/QuestionnaireActivity.kt

@@ -356,6 +356,13 @@ open class QuestionnaireActivity : BaseMultiLanguageActivity(), View.OnClickList
       if (result is ExtractionProgress.Success) {
         onPostSave(true, questionnaireResponse, result.extras)
       } else {
+        result as ExtractionProgress.Failed
+        AlertDialogue.showErrorAlert(
+          this,
+          result.errorMessages ?: "",
+          getString(R.string.questionnaire_alert_extraction_fail)
+        )
+
         onPostSave(false, questionnaireResponse)
       }
     }

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

@@ -18,13 +18,16 @@ package org.smartregister.fhircore.engine.ui.questionnaire
 
 import android.content.Context
 import android.content.Intent
+import androidx.annotation.VisibleForTesting
+import androidx.lifecycle.LiveData
 import androidx.lifecycle.MutableLiveData
 import androidx.lifecycle.ViewModel
 import androidx.lifecycle.viewModelScope
 import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
 import ca.uhn.fhir.rest.gclient.TokenClientParam
 import ca.uhn.fhir.rest.param.ParamPrefixEnum
+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.datacapture.mapping.StructureMapExtractionContext
@@ -71,6 +74,8 @@ import org.smartregister.fhircore.engine.configuration.view.FormConfiguration
 import org.smartregister.fhircore.engine.cql.LibraryEvaluator
 import org.smartregister.fhircore.engine.data.local.DefaultRepository
 import org.smartregister.fhircore.engine.data.remote.model.response.UserInfo
+import org.smartregister.fhircore.engine.di.checkResourceValid
+import org.smartregister.fhircore.engine.di.errorMessages
 import org.smartregister.fhircore.engine.task.FhirCarePlanGenerator
 import org.smartregister.fhircore.engine.trace.PerformanceReporter
 import org.smartregister.fhircore.engine.util.AssetUtil
@@ -110,14 +115,20 @@ constructor(
   val dispatcherProvider: DispatcherProvider,
   val sharedPreferencesHelper: SharedPreferencesHelper,
   val libraryEvaluatorProvider: Provider<LibraryEvaluator>,
+  val fhirValidatorProvider: Provider<FhirValidator>,
   var tracer: PerformanceReporter
 ) : ViewModel() {
   @Inject lateinit var fhirCarePlanGenerator: FhirCarePlanGenerator
 
-  val extractionProgress = MutableLiveData<ExtractionProgress>()
+  private val _extractionProgress = MutableLiveData<ExtractionProgress>()
+  val extractionProgress: LiveData<ExtractionProgress> = _extractionProgress
+
   val questionnaireResponseLiveData = MutableLiveData<QuestionnaireResponse?>(null)
 
-  val extractionProgressMessage = MutableLiveData<String>()
+  @Suppress("PropertyName")
+  @VisibleForTesting(otherwise = VisibleForTesting.PRIVATE)
+  val _extractionProgressMessage = MutableLiveData<String>()
+  val extractionProgressMessage: LiveData<String> = _extractionProgressMessage
 
   var editQuestionnaireResponse: QuestionnaireResponse? = null
 
@@ -334,7 +345,23 @@ constructor(
           Timber.w(
             "${questionnaire.name}(${questionnaire.logicalId}) is experimental and not save any data"
           )
-        } else saveBundleResources(bundle)
+        } else {
+          val unsuccessfulValidationResults =
+            bundle.entry
+              .map { fhirValidatorProvider.get().checkResourceValid(it.resource) }
+              .filter { !it.isSuccessful }
+
+
+          if (unsuccessfulValidationResults.isNotEmpty()) {
+            val mergedErrorMessages = buildString {
+              unsuccessfulValidationResults.forEach { appendLine(it.errorMessages) }
+            }
+            _extractionProgress.postValue(ExtractionProgress.Failed(mergedErrorMessages))
+            return@launch
+          }
+
+          saveBundleResources(bundle)
+        }
 
         if (questionnaireType.isEditMode() && editQuestionnaireResponse != null) {
           questionnaireResponse.retainMetadata(editQuestionnaireResponse!!)
@@ -357,7 +384,7 @@ constructor(
       }
       tracer.stopTrace(QUESTIONNAIRE_TRACE)
       viewModelScope.launch(Dispatchers.Main) {
-        extractionProgress.postValue(ExtractionProgress.Success(extras))
+        _extractionProgress.postValue(ExtractionProgress.Success(extras))
       }
     }
   }
@@ -398,7 +425,7 @@ constructor(
         .runCatching { fhirCarePlanGenerator.generateCarePlan(planId, subject, data) }
         .onFailure {
           Timber.e(it)
-          extractionProgressMessage.postValue("Error extracting care plan. ${it.message}")
+          _extractionProgressMessage.postValue("Error extracting care plan. ${it.message}")
         }
     }
   }
@@ -420,7 +447,7 @@ constructor(
           libraryEvaluatorProvider.get().runCqlLibrary(it, patient, data, defaultRepository)
         }
         .forEach { output ->
-          if (output.isNotEmpty()) extractionProgressMessage.postValue(output.joinToString("\n"))
+          if (output.isNotEmpty()) _extractionProgressMessage.postValue(output.joinToString("\n"))
         }
     }
   }
@@ -466,7 +493,6 @@ constructor(
     questionnaire.useContext.filter { it.hasValueCodeableConcept() }.forEach {
       it.valueCodeableConcept.coding.forEach { questionnaireResponse.meta.addTag(it) }
     }
-
     defaultRepository.addOrUpdate(true, questionnaireResponse)
   }
 
@@ -615,10 +641,6 @@ constructor(
     return tasks.filter { it.status in arrayOf(TaskStatus.READY, TaskStatus.INPROGRESS) }
   }
 
-  fun saveResource(resource: Resource) {
-    viewModelScope.launch { defaultRepository.save(resource = resource) }
-  }
-
   fun extractRelevantObservation(
     resource: Bundle,
     questionnaireLogicalId: String,

android/engine/src/main/res/values/strings.xml

@@ -71,6 +71,7 @@
     <string name="questionnaire_alert_confirm_button_title">Yes</string>
     <string name="questionnaire_alert_invalid_message">Given details have validation errors. Resolve errors and submit again</string>
     <string name="questionnaire_alert_invalid_title">Validation Failed</string>
+    <string name="questionnaire_alert_extraction_fail">Extraction did not succeed</string>
     <string name="questionnaire_alert_ack_button_title">Ok</string>
     <string name="username">Username</string>
     <string name="password">Password</string>

android/engine/src/test/java/org/smartregister/fhircore/engine/ui/questionnaire/QuestionnaireActivityTest.kt

@@ -31,24 +31,31 @@ import androidx.fragment.app.commitNow
 import androidx.test.core.app.ApplicationProvider
 import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
+import ca.uhn.fhir.validation.FhirValidator
 import com.google.android.fhir.datacapture.QuestionnaireFragment
 import com.google.android.fhir.datacapture.validation.QuestionnaireResponseValidator.checkQuestionnaireResponse
 import dagger.hilt.android.testing.BindValue
 import dagger.hilt.android.testing.HiltAndroidRule
 import dagger.hilt.android.testing.HiltAndroidTest
 import dagger.hilt.android.testing.UninstallModules
 import io.mockk.coEvery
+import io.mockk.coVerify
 import io.mockk.every
 import io.mockk.just
 import io.mockk.mockk
 import io.mockk.runs
 import io.mockk.spyk
 import io.mockk.unmockkObject
 import io.mockk.verify
+import javax.inject.Inject
+import javax.inject.Provider
 import kotlin.test.assertFailsWith
 import kotlinx.coroutines.ExperimentalCoroutinesApi
+import kotlinx.coroutines.test.advanceUntilIdle
 import kotlinx.coroutines.test.runBlockingTest
 import kotlinx.coroutines.test.runTest
+import org.hl7.fhir.r4.model.CanonicalType
+import org.hl7.fhir.r4.model.CarePlan
 import org.hl7.fhir.r4.model.CodeableConcept
 import org.hl7.fhir.r4.model.Coding
 import org.hl7.fhir.r4.model.Encounter
@@ -110,25 +117,29 @@ class QuestionnaireActivityTest : ActivityRobolectricTest() {
 
   @BindValue val syncBroadcaster = mockk<SyncBroadcaster>()
 
-  @BindValue
-  val questionnaireViewModel: QuestionnaireViewModel =
-    spyk(
-      QuestionnaireViewModel(
-        fhirEngine = mockk(),
-        defaultRepository = mockk { coEvery { addOrUpdate(true, any()) } just runs },
-        configurationRegistry = mockk(),
-        transformSupportServices = mockk(),
-        dispatcherProvider = dispatcherProvider,
-        sharedPreferencesHelper = mockk(),
-        libraryEvaluatorProvider = { mockk<LibraryEvaluator>() },
-        tracer = FakePerformanceReporter()
-      )
-    )
+  @Inject lateinit var fhirValidatorProvider: Provider<FhirValidator>
+
+  @BindValue lateinit var questionnaireViewModel: QuestionnaireViewModel
 
   @Before
   fun setUp() {
     // TODO Proper set up
     hiltRule.inject()
+    questionnaireViewModel =
+      spyk(
+        QuestionnaireViewModel(
+          fhirEngine = mockk(),
+          defaultRepository = mockk { coEvery { addOrUpdate(true, any()) } just runs },
+          configurationRegistry = mockk(),
+          transformSupportServices = mockk(),
+          dispatcherProvider = dispatcherProvider,
+          sharedPreferencesHelper = mockk(),
+          libraryEvaluatorProvider = { mockk<LibraryEvaluator>() },
+          fhirValidatorProvider = fhirValidatorProvider,
+          tracer = FakePerformanceReporter()
+        )
+      )
+
     ApplicationProvider.getApplicationContext<Context>().apply { setTheme(R.style.AppTheme) }
     intent =
       Intent().apply {
@@ -508,6 +519,46 @@ class QuestionnaireActivityTest : ActivityRobolectricTest() {
     }
   }
 
+  @Test
+  fun testHandleQuestionnaireSubmitWithExtractionProgressFailureShowsErrorDialog() = runTest {
+    val sampleExtractedCarePlan = CarePlan()
+    coEvery { questionnaireViewModel.performExtraction(any(), any(), any()) } returns
+      org.hl7.fhir.r4.model.Bundle().apply {
+        addEntry().apply { resource = sampleExtractedCarePlan }
+      }
+    val questionnaire =
+      Questionnaire().apply {
+        addExtension(
+          "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-targetStructureMap",
+          CanonicalType("1234")
+        )
+      }
+
+    ReflectionHelpers.setField(
+      questionnaireViewModel,
+      "questionnaireConfig",
+      QuestionnaireConfig("form", "title", "form-id", setPractitionerDetails = false)
+    )
+    ReflectionHelpers.setField(questionnaireActivity, "questionnaire", questionnaire)
+    questionnaireActivity.handleQuestionnaireSubmit()
+    advanceUntilIdle()
+
+    val dialog = shadowOf(ShadowAlertDialog.getLatestDialog())
+    val alertDialog = ReflectionHelpers.getField<AlertDialog>(dialog, "realDialog")
+
+    Assert.assertNotNull(questionnaireViewModel.extractionProgress.value)
+    Assert.assertTrue(questionnaireViewModel.extractionProgress.value is ExtractionProgress.Failed)
+
+    Assert.assertEquals(
+      "CarePlan.status: minimum required = 1, but only found 0 (from http://hl7.org/fhir/StructureDefinition/CarePlan) - CarePlan\n" +
+        "CarePlan.intent: minimum required = 1, but only found 0 (from http://hl7.org/fhir/StructureDefinition/CarePlan) - CarePlan\n" +
+        "CarePlan.subject: minimum required = 1, but only found 0 (from http://hl7.org/fhir/StructureDefinition/CarePlan) - CarePlan\n",
+      alertDialog.findViewById<TextView>(R.id.tv_alert_message)!!.text
+    )
+
+    coVerify(exactly = 0) { questionnaireViewModel.defaultRepository.addOrUpdate(resource = any()) }
+  }
+
   @Test
   fun testOnClickSaveButtonShouldShowSubmitConfirmationAlert() {
     ReflectionHelpers.setField(
@@ -599,7 +650,7 @@ class QuestionnaireActivityTest : ActivityRobolectricTest() {
 
   @Test
   fun testPostSaveSuccessfulWithExtractionMessageShouldShowAlert() = runTest {
-    questionnaireActivity.questionnaireViewModel.extractionProgressMessage.postValue("ABC")
+    questionnaireActivity.questionnaireViewModel._extractionProgressMessage.postValue("ABC")
     questionnaireActivity.postSaveSuccessful(QuestionnaireResponse())
 
     val dialog = shadowOf(ShadowAlertDialog.getLatestDialog())