Merge pull request #1012 from Project-MONAI/nds-addAccessionId

neildsouth · web-flow · commit 150e36da76a8 · 2024-07-05T14:38:55.000+01:00
adding accession Id filtering for counts
diff --git a/src/WorkflowManager/Common/Interfaces/IPaginatedApi.cs b/src/WorkflowManager/Common/Interfaces/IPaginatedApi.cs
@@ -14,11 +14,13 @@
  * limitations under the License.
  */
 
+using MongoDB.Driver;
+
 namespace Monai.Deploy.WorkflowManager.Common.Miscellaneous.Interfaces
 {
     public interface IPaginatedApi<T>
     {
-        Task<long> CountAsync();
+        Task<long> CountAsync(FilterDefinition<T>? filter = null);
 
         Task<IList<T>> GetAllAsync(int? skip = null, int? limit = null);
     }
diff --git a/src/WorkflowManager/Common/Interfaces/IPayloadService.cs b/src/WorkflowManager/Common/Interfaces/IPayloadService.cs
@@ -16,6 +16,7 @@
 
 using Monai.Deploy.Messaging.Events;
 using Monai.Deploy.WorkflowManager.Common.Contracts.Models;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.Miscellaneous.Interfaces
 {
@@ -38,8 +39,9 @@ public interface IPayloadService : IPaginatedApi<PayloadDto>
         /// </summary>
         Task<IList<PayloadDto>> GetAllAsync(int? skip = null,
                                          int? limit = null,
-                                         string? patientId = "",
-                                         string? patientName = "");
+                                         string? patientId = null,
+                                         string? patientName = null,
+                                         string? accessionId = null);
         new Task<IList<PayloadDto>> GetAllAsync(int? skip = null, int? limit = null);
 
         /// <summary>
@@ -63,5 +65,7 @@ Task<IList<PayloadDto>> GetAllAsync(int? skip = null,
         /// <param name="payload">updated payload.</param>
         /// <returns>true if the update is successful, false otherwise.</returns>
         Task<bool> UpdateAsyncWorkflowIds(Payload payload);
+
+        Task<long> CountAsync(FilterDefinition<Payload> filter);
     }
 }
diff --git a/src/WorkflowManager/Common/Services/PayloadService.cs b/src/WorkflowManager/Common/Services/PayloadService.cs
@@ -26,6 +26,7 @@
 using Monai.Deploy.WorkflowManager.Common.Storage.Services;
 using Microsoft.Extensions.Options;
 using Monai.Deploy.WorkflowManager.Common.Configuration;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.Miscellaneous.Services
 {
@@ -149,10 +150,11 @@ public async Task<Payload> GetByIdAsync(string payloadId)
 
         public async Task<IList<PayloadDto>> GetAllAsync(int? skip = null,
                                                       int? limit = null,
-                                                      string? patientId = "",
-                                                      string? patientName = "")
+                                                      string? patientId = null,
+                                                      string? patientName = null,
+                                                      string? accessionId = null)
             => await CreatePayloadsDto(
-                await _payloadRepository.GetAllAsync(skip, limit, patientId ?? string.Empty, patientName ?? string.Empty)
+                await _payloadRepository.GetAllAsync(skip, limit, patientId, patientName, accessionId)
             );
 
         public async Task<IList<PayloadDto>> GetAllAsync(int? skip = null, int? limit = null)
@@ -193,7 +195,13 @@ private async Task<IList<PayloadDto>> CreatePayloadsDto(IList<Payload> payloads)
             return dtos;
         }
 
-        public async Task<long> CountAsync() => await _payloadRepository.CountAsync();
+        public async Task<long> CountAsync(FilterDefinition<Payload> filter)
+            => await _payloadRepository.CountAsync(filter);
+
+
+        // this has to be here because of the base, but dont use it !
+        public Task<long> CountAsync(FilterDefinition<PayloadDto>? filter)
+            => throw new NotImplementedException();
 
         public async Task<bool> DeletePayloadFromStorageAsync(string payloadId)
         {
diff --git a/src/WorkflowManager/Common/Services/WorkflowInstanceService.cs b/src/WorkflowManager/Common/Services/WorkflowInstanceService.cs
@@ -14,14 +14,14 @@
  * limitations under the License.
  */
 
-using Ardalis.GuardClauses;
 using Microsoft.Extensions.Logging;
 using Monai.Deploy.Messaging.Events;
 using Monai.Deploy.WorkflowManager.Common.Miscellaneous.Exceptions;
 using Monai.Deploy.WorkflowManager.Common.Miscellaneous.Interfaces;
 using Monai.Deploy.WorkflowManager.Common.Contracts.Models;
 using Monai.Deploy.WorkflowManager.Common.Database.Interfaces;
 using Monai.Deploy.WorkflowManager.Common.Logging;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.Miscellaneous.Services
 {
@@ -87,7 +87,11 @@ public async Task UpdateExportCompleteMetadataAsync(string workflowInstanceId, s
             await _workflowInstanceRepository.UpdateExportCompleteMetadataAsync(workflowInstanceId, executionId, resultMetadata);
         }
 
-        public async Task<long> CountAsync() => await _workflowInstanceRepository.CountAsync();
+        public async Task<long> CountAsync(FilterDefinition<WorkflowInstance>? filter)
+        {
+            filter = filter ?? Builders<WorkflowInstance>.Filter.Empty;
+            return await _workflowInstanceRepository.CountAsync(filter);
+        }
 
         public async Task<IList<WorkflowInstance>> GetAllAsync(int? skip = null, int? limit = null, Status? status = null, string? payloadId = null)
             => await _workflowInstanceRepository.GetAllAsync(skip, limit, status, payloadId);
diff --git a/src/WorkflowManager/Common/Services/WorkflowService.cs b/src/WorkflowManager/Common/Services/WorkflowService.cs
@@ -19,6 +19,7 @@
 using Monai.Deploy.WorkflowManager.Common.Contracts.Models;
 using Monai.Deploy.WorkflowManager.Common.Database.Interfaces;
 using Monai.Deploy.WorkflowManager.Common.Logging;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.Miscellaneous.Services
 {
@@ -83,7 +84,8 @@ public Task<DateTime> DeleteWorkflowAsync(WorkflowRevision workflow)
             return result;
         }
 
-        public async Task<long> CountAsync() => await _workflowRepository.CountAsync();
+        public async Task<long> CountAsync(FilterDefinition<WorkflowRevision>? filter)
+            => await _workflowRepository.CountAsync(filter ?? Builders<WorkflowRevision>.Filter.Empty);
 
         public async Task<IList<WorkflowRevision>> GetAllAsync(int? skip = null, int? limit = null)
             => await _workflowRepository.GetAllAsync(skip, limit);
diff --git a/src/WorkflowManager/Database/Interfaces/IPayloadRepository.cs b/src/WorkflowManager/Database/Interfaces/IPayloadRepository.cs
@@ -18,6 +18,7 @@
 using System.Collections.Generic;
 using System.Threading.Tasks;
 using Monai.Deploy.WorkflowManager.Common.Contracts.Models;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.Database.Interfaces
 {
@@ -32,7 +33,7 @@ public interface IPayloadRepository
         /// <summary>
         /// Retrieves a list of payloads in the database.
         /// </summary>
-        Task<IList<Payload>> GetAllAsync(int? skip = null, int? limit = null, string patientId = "", string patientName = "");
+        Task<IList<Payload>> GetAllAsync(int? skip = null, int? limit = null, string? patientId = null, string? patientName = null, string? accessionId = null);
 
         /// <summary>
         /// Retrieves a payload by id in the database.
@@ -44,7 +45,7 @@ public interface IPayloadRepository
         /// Gets count of objects
         /// </summary>
         /// <returns>Count of objects.</returns>
-        Task<long> CountAsync();
+        Task<long> CountAsync(FilterDefinition<Payload> filter);
 
         /// <summary>
         /// Updates a payload in the database.
diff --git a/src/WorkflowManager/Database/Interfaces/IWorkflowInstanceRepository.cs b/src/WorkflowManager/Database/Interfaces/IWorkflowInstanceRepository.cs
@@ -18,6 +18,7 @@
 using System.Threading.Tasks;
 using Monai.Deploy.Messaging.Events;
 using Monai.Deploy.WorkflowManager.Common.Contracts.Models;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.Database.Interfaces
 {
@@ -44,7 +45,7 @@ public interface IWorkflowInstanceRepository
         /// Gets count of Workflow Instances.
         /// </summary>
         /// <returns></returns>
-        Task<long> CountAsync();
+        Task<long> CountAsync(FilterDefinition<WorkflowInstance> filter);
 
         /// <summary>
         /// Gets the count of workflow instances with a filter.
diff --git a/src/WorkflowManager/Database/Interfaces/IWorkflowRepository.cs b/src/WorkflowManager/Database/Interfaces/IWorkflowRepository.cs
@@ -18,6 +18,7 @@
 using System.Collections.Generic;
 using System.Threading.Tasks;
 using Monai.Deploy.WorkflowManager.Common.Contracts.Models;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.Database.Interfaces
 {
@@ -97,7 +98,7 @@ public interface IWorkflowRepository
         /// <returns></returns>
         Task<DateTime> SoftDeleteWorkflow(WorkflowRevision workflow);
 
-        Task<long> CountAsync();
+        Task<long> CountAsync(FilterDefinition<WorkflowRevision> filter);
 
         Task<IList<WorkflowRevision>> GetAllAsync(int? skip, int? limit);
 
diff --git a/src/WorkflowManager/Database/Repositories/PayloadRepository.cs b/src/WorkflowManager/Database/Repositories/PayloadRepository.cs
@@ -71,7 +71,10 @@ private async Task EnsureIndex()
             }
         }
 
-        public Task<long> CountAsync() => CountAsync(_payloadCollection, null);
+        public Task<long> CountAsync(FilterDefinition<Payload> filter)
+        {
+            return CountAsync(_payloadCollection, filter);
+        }
 
         public async Task<bool> CreateAsync(Payload payload)
         {
@@ -91,18 +94,19 @@ public async Task<bool> CreateAsync(Payload payload)
             }
         }
 
-        public async Task<IList<Payload>> GetAllAsync(int? skip = null, int? limit = null, string? patientId = "", string? patientName = "")
+        public async Task<IList<Payload>> GetAllAsync(int? skip = null, int? limit = null, string? patientId = null, string? patientName = null, string? accessionId = null)
         {
             var builder = Builders<Payload>.Filter;
             var filter = builder.Empty;
-            if (!string.IsNullOrEmpty(patientId))
-            {
-                filter &= builder.Regex(p => p.PatientDetails.PatientId, new BsonRegularExpression($"/{patientId}/i"));
-            }
-            if (!string.IsNullOrEmpty(patientName))
-            {
-                filter &= builder.Regex(p => p.PatientDetails.PatientName, new BsonRegularExpression($"/{patientName}/i"));
-            }
+            if (!string.IsNullOrEmpty(patientId)) filter
+                    &= builder.Regex(p => p.PatientDetails.PatientId, new BsonRegularExpression($"/{patientId}/i"));
+
+            if (!string.IsNullOrEmpty(patientName)) filter
+                    &= builder.Regex(p => p.PatientDetails.PatientName, new BsonRegularExpression($"/{patientName}/i"));
+
+            if (!string.IsNullOrWhiteSpace(accessionId)) filter
+                    &= builder.Regex(p => p.AccessionId, new BsonRegularExpression($"/{accessionId}/i"));
+
 
             return await GetAllAsync(_payloadCollection,
                                       filter,
diff --git a/src/WorkflowManager/Database/Repositories/WorkflowInstanceRepository.cs b/src/WorkflowManager/Database/Repositories/WorkflowInstanceRepository.cs
@@ -313,7 +313,10 @@ public async Task<WorkflowInstance> GetByWorkflowInstanceIdAsync(string workflow
             return workflow;
         }
 
-        public async Task<long> CountAsync() => await CountAsync(_workflowInstanceCollection, null);
+        public async Task<long> CountAsync(FilterDefinition<WorkflowInstance> filter)
+        {
+            return await CountAsync(_workflowInstanceCollection, filter);
+        }
 
         public async Task<long> FilteredCountAsync(Status? status = null, string? payloadId = null)
         {
diff --git a/src/WorkflowManager/Database/Repositories/WorkflowRepository.cs b/src/WorkflowManager/Database/Repositories/WorkflowRepository.cs
@@ -272,7 +272,12 @@ await _workflowCollection.UpdateManyAsync(
             return deletedTimeStamp;
         }
 
-        public async Task<long> CountAsync() => await _workflowCollection.CountDocumentsAsync(x => x.Deleted == null);
+        public async Task<long> CountAsync(FilterDefinition<WorkflowRevision> filter)
+        {
+            var builder = Builders<WorkflowRevision>.Filter;
+            filter &= builder.Eq(p => p.Deleted, null);
+            return await _workflowCollection.CountDocumentsAsync(filter);
+        }
 
         public async Task<IList<WorkflowRevision>> GetAllAsync(int? skip = null, int? limit = null)
             => await GetAllAsync(_workflowCollection,
diff --git a/src/WorkflowManager/WorkflowManager/Controllers/PayloadsController.cs b/src/WorkflowManager/WorkflowManager/Controllers/PayloadsController.cs
@@ -30,6 +30,8 @@
 using Monai.Deploy.WorkflowManager.Common.Miscellaneous.Interfaces;
 using Monai.Deploy.WorkflowManager.Common.Miscellaneous.Services;
 using Monai.Deploy.WorkflowManager.Common.Miscellaneous.Wrappers;
+using MongoDB.Bson;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManager.Common.ControllersShared
 {
@@ -72,11 +74,16 @@ public PayloadsController(
         /// <param name="filter">Filters.</param>
         /// <param name="patientId">Optional patient Id.</param>
         /// <param name="patientName">Optional patient name.</param>
+        /// <param name="accessionId">Optional accession Id.</param>
         /// <returns>paged response of subset of all workflows.</returns>
         [HttpGet]
         [ProducesResponseType(typeof(PagedResponse<List<Payload>>), StatusCodes.Status200OK)]
         [ProducesResponseType(typeof(ProblemDetails), StatusCodes.Status500InternalServerError)]
-        public async Task<IActionResult> GetAllAsync([FromQuery] PaginationFilter filter, [FromQuery] string patientId = "", [FromQuery] string patientName = "")
+        public async Task<IActionResult> GetAllAsync(
+            [FromQuery] PaginationFilter filter,
+            [FromQuery] string patientId = null,
+            [FromQuery] string patientName = null,
+            [FromQuery] string accessionId = null)
         {
             try
             {
@@ -88,9 +95,28 @@ public async Task<IActionResult> GetAllAsync([FromQuery] PaginationFilter filter
                     (validFilter.PageNumber - 1) * validFilter.PageSize,
                     validFilter.PageSize,
                     patientId,
-                    patientName);
+                    patientName,
+                    accessionId);
 
-                var dataTotal = await _payloadService.CountAsync();
+                var builder = Builders<Payload>.Filter;
+                var dbFilter = builder.Empty;
+
+                if (!string.IsNullOrEmpty(patientId))
+                {
+                    dbFilter &= builder.Regex(p => p.PatientDetails.PatientId, new BsonRegularExpression($"/{patientId}/i"));
+                }
+
+                if (!string.IsNullOrEmpty(patientName))
+                {
+                    dbFilter &= builder.Regex(p => p.PatientDetails.PatientName, new BsonRegularExpression($"/{patientName}/i"));
+                }
+
+                if (!string.IsNullOrWhiteSpace(accessionId))
+                {
+                    dbFilter &= builder.Regex(p => p.AccessionId, new BsonRegularExpression($"/{accessionId}/i"));
+                }
+
+                var dataTotal = await _payloadService.CountAsync(dbFilter);
                 var pagedReponse = CreatePagedResponse(pagedData.ToList(), validFilter, dataTotal, _uriService, route);
 
                 return Ok(pagedReponse);
diff --git a/src/WorkflowManager/WorkflowManager/Controllers/TaskStatsController.cs b/src/WorkflowManager/WorkflowManager/Controllers/TaskStatsController.cs
@@ -140,12 +140,11 @@ public async Task<IActionResult> GetDailyStatsAsync([FromQuery] TimeFilter filte
                         TotalApprovals = g.Count(i => string.Compare(i.Status, "Succeeded", true) == 0 && i.Reason == FailureReason.None),
                         TotalRejections = g.Count(i => string.Compare(i.Status, "Failed", true) == 0 && i.Reason == FailureReason.Rejected),
                         TotalCancelled = g.Count(i => string.Compare(i.Status, "Failed", true) == 0 && i.Reason == FailureReason.TimedOut),
-                        //TotalAwaitingReview = g.Count(i => string.Compare(i.Status, ApplicationReviewStatus.AwaitingReview.ToString(), true) == 0),
+
+                        // TotalAwaitingReview = g.Count(i => string.Compare(i.Status, ApplicationReviewStatus.AwaitingReview.ToString(), true) == 0),
                         TotalAwaitingReview = g.Count(i => string.Compare(i.Status, TaskExecutionStatus.Accepted.ToString(), true) == 0),
                     });
 
-
-
                 var pagedStats = statsDto.Skip((filter.PageNumber - 1) * pageSize).Take(pageSize);
 
                 var res = CreateStatsPagedResponse(pagedStats, validFilter, statsDto.Count(), _uriService, route);
diff --git a/tests/UnitTests/Common.Tests/Services/PayloadServiceTests.cs b/tests/UnitTests/Common.Tests/Services/PayloadServiceTests.cs
@@ -234,7 +234,7 @@ public async Task GetAll_ReturnsCompletedPayloads()
 
             _payloadRepository.Setup(p =>
                 p.GetAllAsync(
-                    It.IsAny<int?>(), It.IsAny<int?>(), It.IsAny<string>(), It.IsAny<string>())
+                    It.IsAny<int?>(), It.IsAny<int?>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<string>())
                 ).ReturnsAsync(() => input);
             var param = new List<string>() { input.First().Id };
             _workflowInstanceRepository.Setup(r =>
@@ -301,7 +301,7 @@ public async Task GetAll_ReturnsPayloads()
 
             _payloadRepository.Setup(p =>
                 p.GetAllAsync(
-                    It.IsAny<int?>(), It.IsAny<int?>(), It.IsAny<string>(), It.IsAny<string>())
+                    It.IsAny<int?>(), It.IsAny<int?>(), It.IsAny<string>(), It.IsAny<string>(), It.IsAny<string>())
                 ).ReturnsAsync(() => input);
             var param = input.Select(i => i.PayloadId).ToList();
             _workflowInstanceRepository.Setup(r =>
diff --git a/tests/UnitTests/Common.Tests/Services/WorkflowServiceTests.cs b/tests/UnitTests/Common.Tests/Services/WorkflowServiceTests.cs
@@ -21,6 +21,7 @@
 using Monai.Deploy.WorkflowManager.Common.Database.Interfaces;
 using Moq;
 using Xunit;
+using MongoDB.Driver;
 
 namespace Monai.Deploy.WorkflowManger.Common.Tests.Services
 {
@@ -137,7 +138,7 @@ public async Task WorkflowService_DeleteWorkflow_Calls_SoftDelete()
         public async Task WorkflowService_Count_Calls_Count()
         {
             var result = await WorkflowService.CountAsync();
-            _workflowRepository.Verify(r => r.CountAsync(), Times.Once());
+            _workflowRepository.Verify(r => r.CountAsync(Builders<WorkflowRevision>.Filter.Empty), Times.Once());
         }
 
         [Fact]
diff --git a/tests/UnitTests/WorkflowManager.Tests/Controllers/PayloadControllerTests.cs b/tests/UnitTests/WorkflowManager.Tests/Controllers/PayloadControllerTests.cs
diff --git a/tests/UnitTests/WorkflowManager.Tests/Controllers/WorkflowInstanceControllerTests.cs b/tests/UnitTests/WorkflowManager.Tests/Controllers/WorkflowInstanceControllerTests.cs
diff --git a/tests/UnitTests/WorkflowManager.Tests/Controllers/WorkflowsControllerTests.cs b/tests/UnitTests/WorkflowManager.Tests/Controllers/WorkflowsControllerTests.cs

Original file line number	Diff line number	Diff line change
`@@ -14,11 +14,13 @@`
`14`	`14`	`* limitations under the License.`
`15`	`15`	`*/`
`16`	`16`
	`17`	`+using MongoDB.Driver;`
	`18`	`+`
`17`	`19`	`namespace Monai.Deploy.WorkflowManager.Common.Miscellaneous.Interfaces`
`18`	`20`	`{`
`19`	`21`	`public interface IPaginatedApi<T>`
`20`	`22`	`{`
`21`		`- Task<long> CountAsync();`
	`23`	`+ Task<long> CountAsync(FilterDefinition<T>? filter = null);`
`22`	`24`
`23`	`25`	`Task<IList<T>> GetAllAsync(int? skip = null, int? limit = null);`
`24`	`26`	`}`
Original file line number	Diff line number	Diff line change
`@@ -19,6 +19,7 @@`
`19`	`19`	`using Monai.Deploy.WorkflowManager.Common.Contracts.Models;`
`20`	`20`	`using Monai.Deploy.WorkflowManager.Common.Database.Interfaces;`
`21`	`21`	`using Monai.Deploy.WorkflowManager.Common.Logging;`
	`22`	`+using MongoDB.Driver;`
`22`	`23`
`23`	`24`	`namespace Monai.Deploy.WorkflowManager.Common.Miscellaneous.Services`
`24`	`25`	`{`
`@@ -83,7 +84,8 @@ public Task<DateTime> DeleteWorkflowAsync(WorkflowRevision workflow)`
`83`	`84`	`return result;`
`84`	`85`	`}`
`85`	`86`
`86`		`- public async Task<long> CountAsync() => await _workflowRepository.CountAsync();`
	`87`	`+ public async Task<long> CountAsync(FilterDefinition<WorkflowRevision>? filter)`
	`88`	`+ => await _workflowRepository.CountAsync(filter ?? Builders<WorkflowRevision>.Filter.Empty);`
`87`	`89`
`88`	`90`	`public async Task<IList<WorkflowRevision>> GetAllAsync(int? skip = null, int? limit = null)`
`89`	`91`	`=> await _workflowRepository.GetAllAsync(skip, limit);`
Original file line number	Diff line number	Diff line change
`@@ -313,7 +313,10 @@ public async Task<WorkflowInstance> GetByWorkflowInstanceIdAsync(string workflow`
`313`	`313`	`return workflow;`
`314`	`314`	`}`
`315`	`315`
`316`		`- public async Task<long> CountAsync() => await CountAsync(_workflowInstanceCollection, null);`
	`316`	`+ public async Task<long> CountAsync(FilterDefinition<WorkflowInstance> filter)`
	`317`	`+ {`
	`318`	`+ return await CountAsync(_workflowInstanceCollection, filter);`
	`319`	`+ }`
`317`	`320`
`318`	`321`	`public async Task<long> FilteredCountAsync(Status? status = null, string? payloadId = null)`
`319`	`322`	`{`