Merge branch 'main' of https://github.com/microsoft/fhir-server into …

…114284_githubaction_ci1

.github/workflows/validate-prs.yml

@@ -1,7 +1,7 @@
 name: Validate Pull Request
 
 on:
-  pull_request:
+  pull_request_target:
     branches:
       - main
     types:
@@ -11,8 +11,6 @@ on:
       - reopened
       - synchronize
       - edited
-      - milestoned
-      - demilestoned
 
 env:
   LABELS: ${{ join( github.event.pull_request.labels.*.name, ' ' ) }}

build/jobs/run-tests.yml

@@ -6,7 +6,8 @@ parameters:
 - name: appServiceName
   type: string
 jobs:
-- job: "integrationTests"
+
+- job: "CosmosIntegrationTests"
   pool:
     name: '$(SharedLinuxPool)'
     vmImage: '$(LinuxVmImage)'
@@ -34,22 +35,53 @@ jobs:
       azureSubscription: $(ConnectedServiceName)
       KeyVaultName: '${{ parameters.keyVaultName }}'
 
+  - task: DotNetCoreCLI@2
+    displayName: 'Run Cosmos Integration Tests'
+    inputs:
+      command: test
+      arguments: '"$(Agent.TempDirectory)/IntegrationTests/**/*${{ parameters.version }}.Tests.Integration*.dll" --filter DisplayName!~SqlServer -v normal'
+      workingDirectory: "$(System.ArtifactsDirectory)"
+      testRunTitle: '${{ parameters.version }} Integration'
+    env:
+      'CosmosDb:Host': $(CosmosDb--Host)
+      'CosmosDb:Key': $(CosmosDb--Key)
+
+- job: "SqlIntegrationTests"
+  pool:
+    name: '$(SharedLinuxPool)'
+    vmImage: '$(LinuxVmImage)'
+  steps:
+  - task: DownloadBuildArtifacts@0
+    inputs:
+      buildType: 'current'
+      downloadType: 'single'
+      downloadPath: '$(System.ArtifactsDirectory)'
+      artifactName: 'IntegrationTests'
+
+  - task: ExtractFiles@1
+    displayName: 'Extract Integration Test Binaries'
+    inputs:
+      archiveFilePatterns: '$(System.ArtifactsDirectory)/IntegrationTests/Microsoft.Health.Fhir.${{ parameters.version }}.Tests.Integration.zip'
+      destinationFolder: '$(Agent.TempDirectory)/IntegrationTests/'
+
+  - task: UseDotNet@2
+    inputs:
+      useGlobalJson: true
+
   - task: AzureKeyVault@1
     displayName: 'Azure Key Vault: ${{ parameters.keyVaultName }}-sql'
     inputs:
       azureSubscription: $(ConnectedServiceName)
       KeyVaultName: '${{ parameters.keyVaultName }}-sql'
 
   - task: DotNetCoreCLI@2
-    displayName: 'Run Integration Tests'
+    displayName: 'Run Sql Integration Tests'
     inputs:
       command: test
-      arguments: '"$(Agent.TempDirectory)/IntegrationTests/**/*${{ parameters.version }}.Tests.Integration*.dll" --blame-hang-timeout 15m'
+      arguments: '"$(Agent.TempDirectory)/IntegrationTests/**/*${{ parameters.version }}.Tests.Integration*.dll" --filter DisplayName!~Cosmos -v normal'
       workingDirectory: "$(System.ArtifactsDirectory)"
       testRunTitle: '${{ parameters.version }} Integration'
     env:
-      'CosmosDb:Host': $(CosmosDb--Host)
-      'CosmosDb:Key': $(CosmosDb--Key)
       'SqlServer:ConnectionString': $(SqlServer--ConnectionString)
 
 - job: 'cosmosE2eTests'

src/Microsoft.Health.Fhir.Core/Features/Persistence/Orchestration/BundleOrchestratorOperation.cs

@@ -112,6 +112,7 @@ public async Task<UpsertOutcome> AppendResourceAsync(ResourceWrapperOperation re
             {
                 if (!_resources.Any())
                 {
+                    cancellationToken.ThrowIfCancellationRequested();
                     SetStatusSafe(BundleOrchestratorOperationStatus.WaitingForResources);
                 }
 
@@ -197,6 +198,7 @@ public async Task ReleaseResourceAsync(string reason, CancellationToken cancella
             {
                 if (!_resources.Any())
                 {
+                    cancellationToken.ThrowIfCancellationRequested();
                     SetStatusSafe(BundleOrchestratorOperationStatus.WaitingForResources);
                 }
 

src/Microsoft.Health.Fhir.Shared.Api/Features/Resources/Bundle/BundleHandler.cs

@@ -300,12 +300,15 @@ private async Task ProcessAllResourcesInABundleAsRequestsAsync(Hl7.Fhir.Model.Bu
                     EntryComponent throttledEntryComponent = null;
                     foreach (HTTPVerb verb in _verbExecutionOrder)
                     {
-                        throttledEntryComponent = await ExecuteRequestsWithSingleHttpVerbInSequenceAsync(
-                            responseBundle: responseBundle,
-                            httpVerb: verb,
-                            throttledEntryComponent: throttledEntryComponent,
-                            statistics: statistics,
-                            cancellationToken: cancellationToken);
+                        if (_requests[verb].Any())
+                        {
+                            throttledEntryComponent = await ExecuteRequestsWithSingleHttpVerbInSequenceAsync(
+                                responseBundle: responseBundle,
+                                httpVerb: verb,
+                                throttledEntryComponent: throttledEntryComponent,
+                                statistics: statistics,
+                                cancellationToken: cancellationToken);
+                        }
                     }
                 }
                 else if (processingLogic == BundleProcessingLogic.Parallel && _bundleType == BundleType.Batch)
@@ -607,6 +610,8 @@ private async Task<EntryComponent> ExecuteRequestsWithSingleHttpVerbInSequenceAs
                     {
                         HttpContext httpContext = resourceContext.Context.HttpContext;
 
+                        // Ensure to pass original callers cancellation token to honor client request cancellations and httprequest timeouts
+                        httpContext.RequestAborted = cancellationToken;
                         SetupContexts(resourceContext, httpContext);
 
                         Func<string> originalResourceIdProvider = _resourceIdProvider.Create;

src/Microsoft.Health.Fhir.Shared.Api/Features/Resources/Bundle/BundleHandlerParallelOperations.cs

@@ -117,6 +117,11 @@ private async Task<EntryComponent> ExecuteRequestsInParallelAsync(
                         watch.Stop();
                         _logger.LogInformation("BundleHandler - '{HttpVerb}' Request #{RequestNumber} completed with status code '{StatusCode}' in {TotalElapsedMilliseconds}ms.", resourceExecutionContext.HttpVerb, resourceExecutionContext.Index, entry.Response.Status, watch.ElapsedMilliseconds);
                     }
+                    catch (OperationCanceledException ex)
+                    {
+                        // If the exception raised is a OperationCanceledException, then either client cancelled the request or httprequest timed out
+                        _logger.LogInformation(ex, "Bundle request timedout. Error: {ErrorMessage}", ex.Message);
+                    }
                     catch (FhirTransactionFailedException ex)
                     {
                         _logger.LogError(ex, "BundleHandler - Failed transaction. Canceling Bundle Orchestrator Operation: {ErrorMessage}", ex.Message);
@@ -262,6 +267,9 @@ private static async Task<EntryComponent> HandleRequestAsync(
                 else
                 {
                     HttpContext httpContext = request.HttpContext;
+
+                    // Ensure to pass original callers cancellation token to honor client request cancellations and httprequest timeouts
+                    httpContext.RequestAborted = cancellationToken;
                     Func<string> originalResourceIdProvider = resourceIdProvider.Create;
                     if (!string.IsNullOrWhiteSpace(persistedId))
                     {

src/Microsoft.Health.Fhir.SqlServer/Features/Operations/Import/ImportProcessingJob.cs

@@ -12,6 +12,7 @@
 using Azure;
 using EnsureThat;
 using MediatR;
+using Microsoft.Data.SqlClient;
 using Microsoft.Extensions.Logging;
 using Microsoft.Extensions.Primitives;
 using Microsoft.Health.Core.Features.Audit;
@@ -22,6 +23,7 @@
 using Microsoft.Health.Fhir.Core.Features.Operations;
 using Microsoft.Health.Fhir.Core.Features.Operations.Import;
 using Microsoft.Health.JobManagement;
+using Microsoft.Health.SqlServer.Features.Storage;
 using Newtonsoft.Json;
 
 namespace Microsoft.Health.Fhir.SqlServer.Features.Operations.Import
@@ -31,6 +33,7 @@ public class ImportProcessingJob : IJob
     {
         private const string CancelledErrorMessage = "Import processing job is canceled.";
         internal const string DefaultCallerAgent = "Microsoft.Health.Fhir.Server";
+        internal const string SurrogateIdsErrorMessage = "Unable to generate internal IDs. If the lastUpdated meta element is provided as input, reduce the number of resources with the same up to millisecond lastUpdated below 10,000.";
 
         private readonly IMediator _mediator;
         private readonly IQueueClient _queueClient;
@@ -152,6 +155,12 @@ public async Task<string> ExecuteAsync(JobInfo jobInfo, CancellationToken cancel
                 var error = new ImportJobErrorResult() { ErrorMessage = CancelledErrorMessage };
                 throw new JobExecutionException(canceledEx.Message, error, canceledEx);
             }
+            catch (SqlException ex) when (ex.Number == SqlErrorCodes.Conflict)
+            {
+                _logger.LogJobInformation(ex, jobInfo, "Exceeded retries on conflicts. Most likely reason - too many input resources with the same last updated.");
+                var error = new ImportJobErrorResult() { ErrorMessage = SurrogateIdsErrorMessage, HttpStatusCode = HttpStatusCode.BadRequest, ErrorDetails = ex.ToString() };
+                throw new JobExecutionException(ex.Message, error, ex);
+            }
             catch (Exception ex)
             {
                 _logger.LogJobError(ex, jobInfo, "Critical error in import processing job.");

src/Microsoft.Health.Fhir.SqlServer/Features/Schema/Migrations/77.diff.sql

@@ -1,3 +1,7 @@
+IF object_id('dbo.ReindexResource') IS NOT NULL DROP PROCEDURE dbo.ReindexResource -- Ths still exists on old accounts and prevents TVP drop
+GO
+IF object_id('dbo.BulkReindexResources') IS NOT NULL DROP PROCEDURE dbo.BulkReindexResources -- Ths still exists on old accounts and prevents TVP drop
+GO
 DECLARE @Names TABLE (Name varchar(100) PRIMARY KEY)
 INSERT INTO @Names SELECT name FROM sys.objects WHERE type = 'p' AND name LIKE '%[0-9]' AND name NOT LIKE '%ResourceChanges%'
 DECLARE @Name varchar(100)

src/Microsoft.Health.Fhir.SqlServer/Features/Schema/Migrations/80.diff.sql

@@ -0,0 +1 @@
+Execute dbo.DeleteHistory 0,0,0