Quirks patches [DNM]

buildSrc/src/main/kotlin/Dependencies.kt

@@ -141,7 +141,7 @@ object Dependencies {
   object Versions {
 
     object Cql {
-      const val clinicalReasoning = "3.0.0-PRE9-SNAPSHOT"
+      const val clinicalReasoning = "3.0.0-PRE9"
     }
 
     const val androidFhirCommon = "0.1.0-alpha05"

engine/src/main/java/com/google/android/fhir/FhirEngine.kt

@@ -174,6 +174,8 @@ interface FhirEngine {
    */
   suspend fun getLocalChanges(type: ResourceType, id: String): List<LocalChange>
 
+  suspend fun getUnsyncedLocalChanges(): List<LocalChange>
+
   /**
    * Purges a resource from the database without deleting data from the server.
    *

engine/src/main/java/com/google/android/fhir/impl/FhirEngineImpl.kt

@@ -80,6 +80,9 @@ internal class FhirEngineImpl(private val database: Database, private val contex
     return database.getLocalChanges(type, id)
   }
 
+  // FhirEngineImpl.kt
+  override suspend fun getUnsyncedLocalChanges(): List<LocalChange> = database.getAllLocalChanges()
+
   override suspend fun purge(type: ResourceType, id: String, forcePurge: Boolean) {
     database.purge(type, setOf(id), forcePurge)
   }

engine/src/main/java/com/google/android/fhir/sync/FhirSyncWorker.kt

@@ -21,6 +21,7 @@ import androidx.work.CoroutineWorker
 import androidx.work.Data
 import androidx.work.WorkerParameters
 import androidx.work.workDataOf
+import ca.uhn.fhir.context.FhirContext
 import com.google.android.fhir.FhirEngine
 import com.google.android.fhir.FhirEngineProvider
 import com.google.android.fhir.OffsetDateTimeTypeAdapter
@@ -32,11 +33,15 @@ import com.google.android.fhir.sync.upload.request.UploadRequestGeneratorFactory
 import com.google.gson.ExclusionStrategy
 import com.google.gson.FieldAttributes
 import com.google.gson.GsonBuilder
+import java.nio.charset.StandardCharsets
 import java.time.OffsetDateTime
 import kotlinx.coroutines.CoroutineScope
 import kotlinx.coroutines.Dispatchers
 import kotlinx.coroutines.cancel
 import kotlinx.coroutines.launch
+import org.apache.commons.io.IOUtils
+import org.hl7.fhir.r4.model.OperationOutcome
+import retrofit2.HttpException
 import timber.log.Timber
 
 /**
@@ -135,6 +140,8 @@ abstract class FhirSyncWorker(appContext: Context, workerParams: WorkerParameter
       }
 
     val result = synchronizer.synchronize()
+    if (result is SyncJobStatus.Failed) onFailedSyncJobResult(result)
+
     val output = buildWorkData(result)
 
     // await/join is needed to collect states completely
@@ -155,6 +162,33 @@ abstract class FhirSyncWorker(appContext: Context, workerParams: WorkerParameter
     }
   }
 
+  open fun onFailedSyncJobResult(failedSyncJobStatus: SyncJobStatus.Failed) {
+    try {
+      CoroutineScope(Dispatchers.IO).launch {
+        val jsonParser = FhirContext.forR4().newJsonParser()
+
+        (failedSyncJobStatus).exceptions.filterIsInstance<HttpException>().forEach {
+          resourceSyncHTTPException ->
+          val operationOutcome =
+            jsonParser.parseResource(
+              IOUtils.toString(
+                resourceSyncHTTPException.response()?.errorBody()?.byteStream(),
+                StandardCharsets.UTF_8,
+              ),
+            ) as OperationOutcome
+
+          operationOutcome.issue.forEach { operationOutcome ->
+            Timber.e(
+              "SERVER ${operationOutcome.severity} - HTTP ${resourceSyncHTTPException.code()} | Code - ${operationOutcome.code} | Diagnostics - ${operationOutcome.diagnostics}",
+            )
+          }
+        }
+      }
+    } catch (e: Exception) {
+      Timber.e(e)
+    }
+  }
+
   private fun buildWorkData(state: SyncJobStatus): Data {
     return workDataOf(
       // send serialized state and type so that consumer can convert it back

engine/src/main/java/com/google/android/fhir/sync/upload/request/UploadRequestGenerator.kt

@@ -62,6 +62,7 @@ internal object UploadRequestGeneratorFactory {
           mode.httpVerbToUseForCreate,
           mode.httpVerbToUseForUpdate,
           mode.bundleSize,
+          useETagForUpload = false
         )
     }
 }

engine/src/main/java/com/google/android/fhir/testing/Utilities.kt

@@ -199,6 +199,10 @@ internal object TestFhirEngineImpl : FhirEngine {
     )
   }
 
+  override suspend fun getUnsyncedLocalChanges(): List<LocalChange> {
+    TODO("Not yet implemented")
+  }
+
   override suspend fun purge(type: ResourceType, id: String, forcePurge: Boolean) {}
 
   override suspend fun purge(type: ResourceType, ids: Set<String>, forcePurge: Boolean) {}

workflow/src/main/java/com/google/android/fhir/workflow/FhirEngineR4MeasureProcessor.java

@@ -0,0 +1,62 @@
+package com.google.android.fhir.workflow;
+
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.r4.model.Measure;
+import org.hl7.fhir.r4.model.MeasureReport;
+import org.opencds.cqf.fhir.api.Repository;
+import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
+import org.opencds.cqf.fhir.cr.measure.common.MeasureEvalType;
+import org.opencds.cqf.fhir.cr.measure.common.SubjectProvider;
+import org.opencds.cqf.fhir.cr.measure.r4.R4MeasureProcessor;
+import org.opencds.cqf.fhir.cr.measure.r4.R4RepositorySubjectProvider;
+import org.opencds.cqf.fhir.utility.repository.FederatedRepository;
+import org.opencds.cqf.fhir.utility.repository.InMemoryFhirRepository;
+
+import java.lang.reflect.Field;
+import java.util.List;
+import java.util.stream.Collectors;
+
+public class FhirEngineR4MeasureProcessor extends R4MeasureProcessor {
+    private static String FIELD_SUBJECT_PROVIDER="subjectProvider";
+    private Repository repository;
+
+    public FhirEngineR4MeasureProcessor(Repository repository, MeasureEvaluationOptions measureEvaluationOptions) {
+        super(repository, measureEvaluationOptions);
+        this.repository = repository;
+    }
+
+    public FhirEngineR4MeasureProcessor(Repository repository, MeasureEvaluationOptions measureEvaluationOptions, SubjectProvider subjectProvider) {
+        super(repository, measureEvaluationOptions, subjectProvider);
+        this.repository = repository;
+    }
+
+    @Override
+    public MeasureReport evaluateMeasure(Measure measure, String periodStart, String periodEnd, String reportType, List<String> subjectIds, IBaseBundle additionalData, MeasureEvalType evalType) {
+        var actualRepo = this.repository;
+        if (additionalData != null) {
+            actualRepo = new FederatedRepository(
+                    this.repository, new InMemoryFhirRepository(this.repository.fhirContext(), additionalData));
+        }
+
+        SubjectProvider subjectProvider = getSubjectProvider();
+        var subjects = subjectProvider.getSubjects(actualRepo, evalType, subjectIds).collect(Collectors.toList());
+        return super.evaluateMeasure( measure,  periodStart,  periodEnd,  reportType, subjects,  additionalData,  evalType) ;
+    }
+
+
+    /***
+     * We have two constructors that could result in different subject providers. So for this field we will use reflection
+     * @return [SubjectProvider] the SubjectProvider
+     */
+    public SubjectProvider getSubjectProvider(){
+        SubjectProvider subjectProvider;
+        try {
+            Field field = this.getClass().getSuperclass().getDeclaredField(FIELD_SUBJECT_PROVIDER);
+            field.setAccessible(true);
+            subjectProvider = (SubjectProvider) field.get(this);
+        }catch (Exception e){
+            subjectProvider = null;
+        }
+        return subjectProvider;
+    }
+}

workflow/src/main/java/com/google/android/fhir/workflow/FhirOperator.kt

@@ -31,15 +31,16 @@ import org.hl7.fhir.instance.model.api.IBaseParameters
 import org.hl7.fhir.instance.model.api.IBaseResource
 import org.hl7.fhir.r4.model.CanonicalType
 import org.hl7.fhir.r4.model.IdType
+import org.hl7.fhir.r4.model.Measure
 import org.hl7.fhir.r4.model.MeasureReport
 import org.hl7.fhir.r4.model.Parameters
 import org.hl7.fhir.r4.model.PlanDefinition
 import org.hl7.fhir.r4.model.Reference
 import org.opencds.cqf.fhir.cql.EvaluationSettings
 import org.opencds.cqf.fhir.cql.LibraryEngine
 import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions
+import org.opencds.cqf.fhir.cr.measure.common.MeasureEvalType
 import org.opencds.cqf.fhir.cr.measure.common.MeasureReportType
-import org.opencds.cqf.fhir.cr.measure.r4.R4MeasureProcessor
 import org.opencds.cqf.fhir.cr.plandefinition.r4.PlanDefinitionProcessor
 import org.opencds.cqf.fhir.utility.monad.Eithers
 import org.opencds.cqf.fhir.utility.repository.ProxyRepository
@@ -68,7 +69,8 @@ internal constructor(
 
   private val libraryProcessor = LibraryEngine(repository, evaluationSettings)
 
-  private val measureProcessor = R4MeasureProcessor(repository, measureEvaluationOptions)
+  private val measureProcessor: FhirEngineR4MeasureProcessor =
+    FhirEngineR4MeasureProcessor(repository, measureEvaluationOptions)
   private val planDefinitionProcessor = PlanDefinitionProcessor(repository, evaluationSettings)
 
   /**
@@ -148,6 +150,55 @@ internal constructor(
     return report
   }
 
+  /**
+   * Generates a [MeasureReport] based on the provided inputs.
+   *
+   * NOTE: The API may internally result in a blocking IO operation. The user should call the API
+   * from a worker thread or it may throw [BlockingMainThreadException] exception.
+   */
+  @WorkerThread
+  fun evaluateMeasure(
+    measure: Measure,
+    start: String,
+    end: String,
+    reportType: String,
+    subjectId: String? = null,
+    practitioner: String? = null,
+    additionalData: IBaseBundle? = null,
+  ): MeasureReport {
+    val subject =
+      if (!practitioner.isNullOrBlank()) {
+        checkAndAddType(practitioner, "Practitioner")
+      } else if (!subjectId.isNullOrBlank()) {
+        checkAndAddType(subjectId, "Patient")
+      } else {
+        // List of null is required to run population-level measures
+        null
+      }
+    val evalType =
+      MeasureEvalType.fromCode(reportType)
+        .orElse(
+          if (!subjectId.isNullOrEmpty()) MeasureEvalType.SUBJECT else MeasureEvalType.POPULATION,
+        ) as MeasureEvalType
+
+    val report =
+      measureProcessor.evaluateMeasure(
+        /* measure = */ measure,
+        /* periodStart = */ start,
+        /* periodEnd = */ end,
+        /* reportType = */ reportType,
+        /* subjectIds = */ if (subject.isNullOrEmpty()) listOf() else listOf(subject),
+        /* additionalData = */ additionalData,
+        /* evalType = */ evalType,
+      )
+
+    // add subject reference for non-individual reportTypes
+    if (report.type.name == MeasureReportType.SUMMARY.name && !subject.isNullOrBlank()) {
+      report.setSubject(Reference(subject))
+    }
+    return report
+  }
+
   /**
    * Generates a [CarePlan] based on the provided inputs.
    *