Fix $bulk-delete bugs with custom search parameter

src/Microsoft.Health.Fhir.Core.UnitTests/Features/Operations/BulkDelete/BulkDeleteProcessingJobTests.cs

@@ -9,14 +9,15 @@
 using System.Threading;
 using System.Threading.Tasks;
 using MediatR;
+using Microsoft.Extensions.Logging;
 using Microsoft.Health.Core.Features.Context;
-using Microsoft.Health.Extensions.DependencyInjection;
 using Microsoft.Health.Fhir.Core.Features.Context;
 using Microsoft.Health.Fhir.Core.Features.Operations;
 using Microsoft.Health.Fhir.Core.Features.Operations.BulkDelete;
 using Microsoft.Health.Fhir.Core.Features.Persistence;
 using Microsoft.Health.Fhir.Core.Features.Search;
 using Microsoft.Health.Fhir.Core.Messages.Delete;
+using Microsoft.Health.Fhir.Core.Models;
 using Microsoft.Health.Fhir.Core.UnitTests.Extensions;
 using Microsoft.Health.Fhir.Tests.Common;
 using Microsoft.Health.JobManagement;
@@ -43,7 +44,14 @@ public BulkDeleteProcessingJobTests()
                 .Returns(Task.FromResult(new SearchResult(5, new List<Tuple<string, string>>())));
             _queueClient = Substitute.For<IQueueClient>();
             _deleter = Substitute.For<IDeletionService>();
-            _processingJob = new BulkDeleteProcessingJob(_deleter.CreateMockScopeFactory(), Substitute.For<RequestContextAccessor<IFhirRequestContext>>(), Substitute.For<IMediator>(), _searchService.CreateMockScopeFactory(), _queueClient);
+            _processingJob = new BulkDeleteProcessingJob(
+                _deleter.CreateMockScopeFactory(),
+                Substitute.For<RequestContextAccessor<IFhirRequestContext>>(),
+                Substitute.For<IMediator>(),
+                _searchService.CreateMockScopeFactory(),
+                _queueClient,
+                Substitute.For<IModelInfoProvider>(),
+                Substitute.For<ILogger<BulkDeleteProcessingJob>>());
         }
 
         [Fact]
@@ -61,14 +69,14 @@ public async Task GivenProcessingJob_WhenJobIsRun_ThenResourcesAreDeleted()
             var substituteResults = new Dictionary<string, long>();
             substituteResults.Add("Patient", 3);
 
-            _deleter.DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>())
+            _deleter.DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>(), Arg.Any<IList<ResourceWrapper>>())
                 .Returns(args => substituteResults);
 
             var result = JsonConvert.DeserializeObject<BulkDeleteResult>(await _processingJob.ExecuteAsync(jobInfo, CancellationToken.None));
             Assert.Single(result.ResourcesDeleted);
             Assert.Equal(3, result.ResourcesDeleted["Patient"]);
 
-            await _deleter.ReceivedWithAnyArgs(1).DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>());
+            await _deleter.ReceivedWithAnyArgs(1).DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>(), Arg.Any<IList<ResourceWrapper>>());
         }
 
         [Fact]
@@ -86,14 +94,14 @@ public async Task GivenProcessingJob_WhenJobIsRunWithMultipleResourceTypes_ThenF
             var substituteResults = new Dictionary<string, long>();
             substituteResults.Add("Patient", 3);
 
-            _deleter.DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>())
+            _deleter.DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>(), Arg.Any<IList<ResourceWrapper>>())
                 .Returns(args => substituteResults);
 
             var result = JsonConvert.DeserializeObject<BulkDeleteResult>(await _processingJob.ExecuteAsync(jobInfo, CancellationToken.None));
             Assert.Single(result.ResourcesDeleted);
             Assert.Equal(3, result.ResourcesDeleted["Patient"]);
 
-            await _deleter.ReceivedWithAnyArgs(1).DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>());
+            await _deleter.ReceivedWithAnyArgs(1).DeleteMultipleAsync(Arg.Any<ConditionalDeleteResourceRequest>(), Arg.Any<CancellationToken>(), Arg.Any<IList<string>>(), Arg.Any<IList<ResourceWrapper>>());
 
             // Checks that one processing job was queued
             var calls = _queueClient.ReceivedCalls();

src/Microsoft.Health.Fhir.Core/Features/Definition/SearchParameterDefinitionManager.cs

@@ -19,7 +19,6 @@
 using Microsoft.Health.Fhir.Core.Exceptions;
 using Microsoft.Health.Fhir.Core.Extensions;
 using Microsoft.Health.Fhir.Core.Features.Definition.BundleWrappers;
-using Microsoft.Health.Fhir.Core.Features.Health;
 using Microsoft.Health.Fhir.Core.Features.Operations;
 using Microsoft.Health.Fhir.Core.Features.Search;
 using Microsoft.Health.Fhir.Core.Features.Search.Expressions;
@@ -269,14 +268,13 @@
 
             // find all derived resources from the list of base resources
             var allResourceTypes = GetDerivedResourceTypes(searchParameterInfo.BaseResourceTypes);
             foreach (var resourceType in allResourceTypes)
             {
-                TypeLookup[resourceType].TryRemove(searchParameterInfo.Code, out var removedParam);
-                if (removedParam.Url != searchParameterInfo.Url)
+                if (TypeLookup[resourceType].TryRemove(searchParameterInfo.Code, out var removedParam) && removedParam?.Url != searchParameterInfo.Url)
                 {
-                    _logger.LogError("Error, Search Param {RemovedParam} removed from Search Param Definition manager.  It does not match deleted Search Param {Url}", removedParam.Url, url);
+                    _logger.LogError("Error, Search Param {RemovedParam} removed from Search Param Definition manager.  It does not match deleted Search Param {Url}", removedParam?.Url, url);
                 }
             }
 
             if (calculateHash)
             {

src/Microsoft.Health.Fhir.Core/Features/Operations/BulkDelete/BulkDeleteProcessingJob.cs

@@ -11,15 +11,18 @@
 using System.Threading.Tasks;
 using EnsureThat;
 using MediatR;
+using Microsoft.Extensions.Logging;
 using Microsoft.Extensions.Primitives;
 using Microsoft.Health.Core.Features.Context;
 using Microsoft.Health.Extensions.DependencyInjection;
 using Microsoft.Health.Fhir.Core.Exceptions;
+using Microsoft.Health.Fhir.Core.Extensions;
 using Microsoft.Health.Fhir.Core.Features.Context;
 using Microsoft.Health.Fhir.Core.Features.Operations.BulkDelete.Messages;
 using Microsoft.Health.Fhir.Core.Features.Persistence;
 using Microsoft.Health.Fhir.Core.Features.Search;
 using Microsoft.Health.Fhir.Core.Messages.Delete;
+using Microsoft.Health.Fhir.Core.Models;
 using Microsoft.Health.JobManagement;
 using Newtonsoft.Json;
 
@@ -33,19 +36,25 @@
         private readonly IMediator _mediator;
         private readonly Func<IScoped<ISearchService>> _searchService;
         private readonly IQueueClient _queueClient;
+        private readonly IModelInfoProvider _modelInfoProvider;
+        private readonly ILogger<BulkDeleteProcessingJob> _logger;
 
         public BulkDeleteProcessingJob(
             Func<IScoped<IDeletionService>> deleterFactory,
             RequestContextAccessor<IFhirRequestContext> contextAccessor,
             IMediator mediator,
             Func<IScoped<ISearchService>> searchService,
-            IQueueClient queueClient)
+            IQueueClient queueClient,
+            IModelInfoProvider modelInfoProvider,
+            ILogger<BulkDeleteProcessingJob> logger)
         {
             _deleterFactory = EnsureArg.IsNotNull(deleterFactory, nameof(deleterFactory));
             _contextAccessor = EnsureArg.IsNotNull(contextAccessor, nameof(contextAccessor));
             _mediator = EnsureArg.IsNotNull(mediator, nameof(mediator));
             _searchService = EnsureArg.IsNotNull(searchService, nameof(searchService));
             _queueClient = EnsureArg.IsNotNull(queueClient, nameof(queueClient));
+            _modelInfoProvider = EnsureArg.IsNotNull(modelInfoProvider, nameof(modelInfoProvider));
+            _logger = EnsureArg.IsNotNull(logger, nameof(logger));
         }
 
         public async Task<string> ExecuteAsync(JobInfo jobInfo, CancellationToken cancellationToken)
@@ -75,6 +84,7 @@
                 using IScoped<IDeletionService> deleter = _deleterFactory.Invoke();
                 Exception exception = null;
                 List<string> types = definition.Type.SplitByOrSeparator().ToList();
+                List<ResourceWrapper> deletedSearchParameters = new List<ResourceWrapper>();
 
                 try
                 {
@@ -88,14 +98,21 @@
                             versionType: definition.VersionType,
                             allowPartialSuccess: false), // Explicitly setting to call out that this can be changed in the future if we want to. Bulk delete offers the possibility of automatically rerunning the operation until it succeeds, fully automating the process.
                         cancellationToken,
-                        definition.ExcludedResourceTypes);
+                        definition.ExcludedResourceTypes,
+                        deletedSearchParameters);
                 }
                 catch (IncompleteOperationException<IDictionary<string, long>> ex)
                 {
+                    _logger.LogError(ex, "Deleting resources failed.");
                     resourcesDeleted = ex.PartialResults;
                     result.Issues.Add(ex.Message);
                     exception = ex;
                 }
+                catch (Exception ex)
+                {
+                    _logger.LogError(ex, "Deleting resources failed.");
+                    throw;
+                }
 
                 foreach (var (key, value) in resourcesDeleted)
                 {
@@ -105,7 +122,20 @@
                     }
                 }
 
-                await _mediator.Publish(new BulkDeleteMetricsNotification(jobInfo.Id, resourcesDeleted.Sum(resource => resource.Value)), cancellationToken);
+                try
+                {
+                    var notification = new BulkDeleteMetricsNotification(jobInfo.Id, resourcesDeleted.Count)
+                    {
+                        Content = CreateNotificationContent(deletedSearchParameters),
+                    };
+
+                    await _mediator.Publish(notification, cancellationToken);
+                }
+                catch (Exception ex)
+                {
+                    _logger.LogError(ex, "Failed to create and publish the notification.");
+                    throw;
+                }
 
                 if (exception != null)
                 {
@@ -131,5 +161,40 @@
                 _contextAccessor.RequestContext = existingFhirRequestContext;
             }
         }
+
+        private string CreateNotificationContent(List<ResourceWrapper> resources)
+        {
+            try
+            {
+                var searchParameterUrls = resources
+                    .Where(x => string.Equals(x.ResourceTypeName, KnownResourceTypes.SearchParameter, StringComparison.OrdinalIgnoreCase) && x.RawResource != null)
+                    .Select(x =>
+                    {
+                        try
+                        {
+                            return _modelInfoProvider.ToTypedElement(x.RawResource).GetStringScalar("url");
+                        }
+                        catch (Exception ex)
+                        {
+                            _logger.LogError(ex, $"Failed to extract the url from the resource, '{x.ResourceId}'.");
+                            return null;
+                        }
+                    })
+                    .Where(x => x != null)
+                    .ToList();
+                _logger.LogInformation($"Creating the notification content with {searchParameterUrls.Count} search parameters.");
+                if (searchParameterUrls.Any())
+                {
+                    return JsonConvert.SerializeObject(searchParameterUrls);
+                }
+
+                return null;
+            }
+            catch (Exception ex)
+            {
+                _logger.LogError(ex, $"Failed to create the notification content for {resources.Count} search parameters.");
+                throw;
+            }
+        }
     }
 }

src/Microsoft.Health.Fhir.Core/Features/Operations/BulkDelete/Messages/BulkDeleteMetricsNotification.cs

@@ -29,5 +29,11 @@ public BulkDeleteMetricsNotification(long id, long resourcesDeleted)
         public long JobId { get; }
 
         public OperationStatus Status { get; }
+
+        /// <summary>
+        /// Gets or sets a content associated with this notification. (e.g. A list of deleted search parameter urls.)
+        /// TODO: this should probably be Stream but MediatR doesn't look like cloning a notification before it sends to handlers.
+        /// </summary>
+        public object Content { get; set; }
     }
 }

src/Microsoft.Health.Fhir.Core/Features/Persistence/IDeletionService.cs

@@ -14,6 +14,6 @@ public interface IDeletionService
     {
         public Task<ResourceKey> DeleteAsync(DeleteResourceRequest request, CancellationToken cancellationToken);
 
-        public Task<IDictionary<string, long>> DeleteMultipleAsync(ConditionalDeleteResourceRequest request, CancellationToken cancellationToken, IList<string> excludedResourceTypes = null);
+        public Task<IDictionary<string, long>> DeleteMultipleAsync(ConditionalDeleteResourceRequest request, CancellationToken cancellationToken, IList<string> excludedResourceTypes = null, IList<ResourceWrapper> deletedSearchParameters = null);
     }
 }

src/Microsoft.Health.Fhir.Core/Features/Search/Parameters/SearchParameterOperations.cs

@@ -6,24 +6,30 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using System.Text.Json;
 using System.Threading;
 using System.Threading.Tasks;
 using EnsureThat;
 using Hl7.Fhir.ElementModel;
+using Hl7.Fhir.Rest;
+using MediatR;
 using Microsoft.Extensions.Logging;
 using Microsoft.Health.Extensions.DependencyInjection;
 using Microsoft.Health.Fhir.Core.Exceptions;
 using Microsoft.Health.Fhir.Core.Extensions;
 using Microsoft.Health.Fhir.Core.Features.Definition;
 using Microsoft.Health.Fhir.Core.Features.Definition.BundleWrappers;
+using Microsoft.Health.Fhir.Core.Features.Operations.BulkDelete.Messages;
 using Microsoft.Health.Fhir.Core.Features.Persistence;
 using Microsoft.Health.Fhir.Core.Features.Search.Registry;
 using Microsoft.Health.Fhir.Core.Models;
 
 namespace Microsoft.Health.Fhir.Core.Features.Search.Parameters
 {
-    public class SearchParameterOperations : ISearchParameterOperations
+    public class SearchParameterOperations : ISearchParameterOperations, INotificationHandler<BulkDeleteMetricsNotification>
     {
+        private const int DefaultDeleteTasksPerPage = 5;
+
         private readonly ISearchParameterDefinitionManager _searchParameterDefinitionManager;
         private readonly SearchParameterStatusManager _searchParameterStatusManager;
         private readonly IModelInfoProvider _modelInfoProvider;
@@ -283,6 +289,35 @@
                 cancellationToken);
         }
 
+        public async Task Handle(BulkDeleteMetricsNotification notification, CancellationToken cancellationToken)
+        {
+            var content = notification?.Content?.ToString();
+            if (!string.IsNullOrWhiteSpace(content))
+            {
+                try
+                {
+                    var urls = JsonSerializer.Deserialize<List<string>>(content);
+                    if (urls.Any(x => !string.IsNullOrWhiteSpace(x)))
+                    {
+                        await DeleteSearchParametersAsync(urls, DefaultDeleteTasksPerPage, cancellationToken);
+                    }
+                    else
+                    {
+                        _logger.LogInformation("Ignoring the notification as its content doesn't have any search parameter Uri.");
+                    }
+                }
+                catch (JsonException ex)
+                {
+                    _logger.LogError(ex, "Failed to deserialize the notification content.");
+                    throw;
+                }
+            }
+            else
+            {
+                _logger.LogInformation("Ignoring the notification as its content is empty.");
+            }
+        }
+
         private void DeleteSearchParameter(string url)
         {
             try
@@ -316,5 +351,51 @@
 
             return null;
         }
+
+        private async Task DeleteSearchParametersAsync(List<string> urls, int pageSize, CancellationToken cancellationToken)
+        {
+            if (urls?.Any() ?? false)
+            {
+                var urlMap = urls.ToHashSet(StringComparer.OrdinalIgnoreCase);
+                var allSearchParameterStatuses = await _searchParameterStatusManager.GetAllSearchParameterStatus(cancellationToken);
+                var searchParameterStatusesToUpdate = allSearchParameterStatuses
+                    .Where(x => urlMap.TryGetValue(x.Uri.OriginalString, out _) && (x.Status != SearchParameterStatus.PendingDelete && x.Status != SearchParameterStatus.Deleted))
+                    .ToList();
+                _logger.LogInformation($"Updating the status of {searchParameterStatusesToUpdate.Count} search parameters (out of {urls.Count} urls) to PendingDelete...");
+                var count = 0;
+                while (count < searchParameterStatusesToUpdate.Count)
+                {
+                    var statusesInPage = searchParameterStatusesToUpdate.Skip(count).Take(pageSize).ToList();
+                    count += statusesInPage.Count;
+
+                    var urlsString = string.Join(Environment.NewLine, statusesInPage.Select(x => x.Uri.OriginalString));
+                    try
+                    {
+                        statusesInPage.ForEach(
+                            x =>
+                            {
+                                x.Status = SearchParameterStatus.PendingDelete;
+                                x.LastUpdated = Clock.UtcNow;
+                            });
+
+                        _logger.LogInformation($"Updating the status of search parameters:{Environment.NewLine}{urlsString}");
+                        await _searchParameterStatusManager.UpdateSearchParameterStatusAsync(statusesInPage, cancellationToken);
+
+                        statusesInPage.ForEach(
+                            x =>
+                            {
+                                _searchParameterDefinitionManager.UpdateSearchParameterStatus(
+                                    x.Uri.OriginalString,
+                                    SearchParameterStatus.PendingDelete);
+                            });
+                    }
+                    catch (Exception ex)
+                    {
+                        // Note: ignore the exception and continue updating the rest.
+                        _logger.LogError(ex, $"Failed to update the status of search parameters:{Environment.NewLine}{urlsString}");
+                    }
+                }
+            }
+        }
     }
 }