[MWCore] Validate extracted fhir resources

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 +1,59 @@
+/*
+ * 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.context.support.DefaultProfileValidationSupport
+import ca.uhn.fhir.context.support.IValidationSupport
+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.support.CommonCodeSystemsTerminologyService
+import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport
+import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport
+import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain
+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 validationSupportChain =
+      ValidationSupportChain(
+        DefaultProfileValidationSupport(fhirContext),
+        InMemoryTerminologyServerValidationSupport(fhirContext),
+        CommonCodeSystemsTerminologyService(fhirContext),
+        UnknownCodeSystemWarningValidationSupport(fhirContext).apply {
+          setNonExistentCodeSystemSeverity(IValidationSupport.IssueSeverity.WARNING)
+        },
+      )
+    val instanceValidator = FhirInstanceValidator(validationSupportChain)
+    instanceValidator.isAssumeValidRestReferences = true
+    //    instanceValidator.validatorResourceFetcher
+    //    instanceValidator.setCustomExtensionDomains()
+    instanceValidator.invalidateCaches()
+    return fhirContext.newValidator().apply { registerValidatorModule(instanceValidator) }
+  }
+}

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 @@
 
 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
@@ -82,8 +85,10 @@
 import org.smartregister.fhircore.engine.util.extension.addTags
 import org.smartregister.fhircore.engine.util.extension.asReference
 import org.smartregister.fhircore.engine.util.extension.assertSubject
+import org.smartregister.fhircore.engine.util.extension.checkResourceValid
 import org.smartregister.fhircore.engine.util.extension.cqfLibraryIds
 import org.smartregister.fhircore.engine.util.extension.deleteRelatedResources
+import org.smartregister.fhircore.engine.util.extension.errorMessages
 import org.smartregister.fhircore.engine.util.extension.extractId
 import org.smartregister.fhircore.engine.util.extension.extractLogicalIdUuid
 import org.smartregister.fhircore.engine.util.extension.filterByResourceTypeId
@@ -110,14 +115,20 @@
   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 @@
           Timber.w(
             "${questionnaire.name}(${questionnaire.logicalId}) is experimental and not save any data"
           )
-        } else saveBundleResources(bundle)
+        } else {
+          val unsuccessfulValidationResults =
+            bundle.entry
+              .flatMap { fhirValidatorProvider.get().checkResourceValid(it.resource) }
+              .filter { it.errorMessages.isNotBlank() }
+
+          if (unsuccessfulValidationResults.isNotEmpty()) {
+            val mergedErrorMessages = buildString {
+              unsuccessfulValidationResults.forEach { appendLine(it.errorMessages) }
+            }
+            Timber.e(mergedErrorMessages)
+            _extractionProgress.postValue(ExtractionProgress.Failed(mergedErrorMessages))
+            return@launch
+          }
+
+          saveBundleResources(bundle)
+        }
 
         if (questionnaireType.isEditMode() && editQuestionnaireResponse != null) {
           questionnaireResponse.retainMetadata(editQuestionnaireResponse!!)
@@ -357,7 +384,7 @@
       }
       tracer.stopTrace(QUESTIONNAIRE_TRACE)
       viewModelScope.launch(Dispatchers.Main) {
-        extractionProgress.postValue(ExtractionProgress.Success(extras))
+        _extractionProgress.postValue(ExtractionProgress.Success(extras))
       }
     }
   }
@@ -398,7 +425,7 @@
         .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 @@
           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 @@
     questionnaire.useContext.filter { it.hasValueCodeableConcept() }.forEach {
       it.valueCodeableConcept.coding.forEach { questionnaireResponse.meta.addTag(it) }
     }
-
     defaultRepository.addOrUpdate(true, questionnaireResponse)
   }
 
@@ -615,10 +641,6 @@
     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/java/org/smartregister/fhircore/engine/util/extension/FhirValidatorExtension.kt

@@ -0,0 +1,40 @@
+/*
+ * 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.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
+
+suspend fun FhirValidator.checkResourceValid(
+  vararg resource: Resource,
+): List<ValidationResult> {
+  return withContext(coroutineContext) {
+    resource.map { [email protected](it) }
+  }
+}
+
+val ValidationResult.errorMessages
+  get() = buildString {
+    for (validationMsg in
+      messages.filter { it.severity.ordinal >= ResultSeverityEnum.WARNING.ordinal }) {
+      appendLine("${validationMsg.message} - ${validationMsg.locationString}")
+    }
+  }

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>