Merge pull request #1006 from Project-MONAI/nds-addAccessionId

Nds add accession

Author: neildsouth

src/WorkflowManager/Common/Interfaces/IPayloadService.cs

@@ -97,7 +97,8 @@ public PayloadService(
                     PatientDetails = patientDetails,
                     PayloadDeleted = PayloadDeleted.No,
                     Expires = await GetExpiry(DateTime.UtcNow, eventPayload.WorkflowInstanceId),
-                    SeriesInstanceUid = _dicomService.GetSeriesInstanceUID(dict)
+                    SeriesInstanceUid = _dicomService.GetSeriesInstanceUID(dict),
+                    AccessionId = _dicomService.GetAccessionID(dict) ?? string.Empty
                 };
 
                 if (await _payloadRepository.CreateAsync(payload))

src/WorkflowManager/Common/Services/PayloadService.cs

@@ -21,7 +21,7 @@ namespace Monai.Deploy.WorkflowManager.Common.Contracts.Migrations
 {
     public class M002_WorkflowRevision_addVerion : DocumentMigration<WorkflowRevision>
     {
-        public M002_WorkflowRevision_addVerion() : base("1.0.0") { }
+        public M002_WorkflowRevision_addVerion() : base("1.0.2") { }
 
         public override void Up(BsonDocument document)
         {

src/WorkflowManager/Contracts/Migrations/M001_Payload_addVerion.cs

@@ -22,7 +22,7 @@ namespace Monai.Deploy.WorkflowManager.Common.Contracts.Migrations
 {
     public class M003_WorkflowRevision_addDataRetension : DocumentMigration<WorkflowRevision>
     {
-        public M003_WorkflowRevision_addDataRetension() : base("1.0.1") { }
+        public M003_WorkflowRevision_addDataRetension() : base("1.0.3") { }
 
         public override void Up(BsonDocument document)
         {

src/WorkflowManager/Contracts/Migrations/M002_Payload_addPayloadDeleted.cs

@@ -22,7 +22,7 @@ namespace Monai.Deploy.WorkflowManager.Common.Contracts.Migrations
 {
     public class M004_WorkflowRevision_addConditions : DocumentMigration<WorkflowRevision>
     {
-        public M004_WorkflowRevision_addConditions() : base("1.0.2") { }
+        public M004_WorkflowRevision_addConditions() : base("1.0.4") { }
 
         public override void Up(BsonDocument document)
         {

src/WorkflowManager/Contracts/Migrations/M002_WorkflowRevision_addVerion.cs

@@ -19,19 +19,20 @@
 
 namespace Monai.Deploy.WorkflowManager.Common.Contracts.Migrations
 {
-    public class M001_WorkflowRevision_addVerion : DocumentMigration<WorkflowRevision>
+    public class M007_Payload_addAccessionId : DocumentMigration<Payload>
     {
-        public M001_WorkflowRevision_addVerion() : base("1.0.0") { }
+        public M007_Payload_addAccessionId() : base("1.0.7") { }
 
         public override void Up(BsonDocument document)
         {
-            // empty, but this will make all objects re-saved with a version
+            document.Add("AccessionId", new BsonString(""), true);
         }
+
         public override void Down(BsonDocument document)
         {
             try
             {
-                document.Remove("Version");
+                document.Remove("AccessionId");
             }
             catch
             {  // can ignore we dont want failures stopping startup !

src/WorkflowManager/Contracts/Migrations/M003_Payload_addDataTrigger.cs

@@ -27,18 +27,21 @@
 
 namespace Monai.Deploy.WorkflowManager.Common.Contracts.Models
 {
-    [CollectionLocation("Payloads"), RuntimeVersion("1.0.6")]
+    [CollectionLocation("Payloads"), RuntimeVersion("1.0.7")]
     public class Payload : IDocument
     {
         [JsonConverter(typeof(DocumentVersionConvert)), BsonSerializer(typeof(DocumentVersionConverBson))]
-        public DocumentVersion Version { get; set; } = new DocumentVersion(1, 0, 5);
+        public DocumentVersion Version { get; set; } = new DocumentVersion(1, 0, 7);
 
         [JsonProperty(PropertyName = "id")]
         public string Id { get; set; } = string.Empty;
 
         [JsonProperty(PropertyName = "payload_id")]
         public string PayloadId { get; set; } = string.Empty;
 
+        [JsonProperty(PropertyName = "accession_id")]
+        public string AccessionId { get; set; } = string.Empty;
+
         [JsonProperty(PropertyName = "workflows")]
         public IEnumerable<string> Workflows { get; set; } = [];
 

src/WorkflowManager/Contracts/Migrations/M003_WorkflowRevision_addDataRetension.cs

@@ -23,7 +23,7 @@
 
 namespace Monai.Deploy.WorkflowManager.Common.Contracts.Models
 {
-    [CollectionLocation("Workflows"), RuntimeVersion("1.0.2")]
+    [CollectionLocation("Workflows"), RuntimeVersion("1.0.4")]
     public class WorkflowRevision : ISoftDeleteable, IDocument
     {
         [BsonId]

src/WorkflowManager/Contracts/Migrations/M004_Payload_expires.cs

@@ -31,5 +31,7 @@ public static class DicomTagConstants
         public const string PatientHospitalIdTag = "00100021";
 
         public const string SeriesInstanceUIDTag = "0020000E";
+
+        public const string AccessionNumberTag = "00080050";
     }
 }

src/WorkflowManager/Contracts/Migrations/M004_WorkflowRevision_addConditions.cs

@@ -65,8 +65,8 @@ public DicomService(IStorageService storageService, ILogger<DicomService> logger
 
         public async Task<PatientDetails> GetPayloadPatientDetailsAsync(string payloadId, string bucketName)
         {
-            ArgumentNullException.ThrowIfNullOrWhiteSpace(bucketName, nameof(bucketName));
-            ArgumentNullException.ThrowIfNullOrWhiteSpace(payloadId, nameof(payloadId));
+            ArgumentNullException.ThrowIfNullOrWhiteSpace(bucketName);
+            ArgumentNullException.ThrowIfNullOrWhiteSpace(payloadId);
 
             var dict = await GetMetaData(payloadId, bucketName);
 
@@ -91,7 +91,7 @@ public async Task<PatientDetails> GetPayloadPatientDetailsAsync(string payloadId
 
         private string? GetFirstValueAsync(Dictionary<string, DicomValue>? dict, string keyId)
         {
-            ArgumentNullException.ThrowIfNullOrWhiteSpace(keyId, nameof(keyId));
+            ArgumentNullException.ThrowIfNullOrWhiteSpace(keyId);
             if (dict is null)
             {
                 return null;
@@ -117,8 +117,8 @@ public async Task<PatientDetails> GetPayloadPatientDetailsAsync(string payloadId
 
         public async Task<Dictionary<string, DicomValue>?> GetMetaData(string payloadId, string bucketId)
         {
-            ArgumentNullException.ThrowIfNullOrWhiteSpace(bucketId, nameof(bucketId));
-            ArgumentNullException.ThrowIfNullOrWhiteSpace(payloadId, nameof(payloadId));
+            ArgumentNullException.ThrowIfNullOrWhiteSpace(bucketId);
+            ArgumentNullException.ThrowIfNullOrWhiteSpace(payloadId);
             var items = await _storageService.ListObjectsAsync(bucketId, $"{payloadId}/dcm", true);
             var dict = new Dictionary<string, DicomValue>(StringComparer.OrdinalIgnoreCase);
             try
@@ -296,6 +296,20 @@ public string GetValue(Dictionary<string, DicomValue> dict, string keyId)
             return null;
         }
 
+        public string? GetAccessionID(Dictionary<string, DicomValue>? dict)
+        {
+            if (dict is null)
+            {
+                return null;
+            }
+
+            if (dict.TryGetValue(DicomTagConstants.AccessionNumberTag, out var value))
+            {
+                return JsonConvert.SerializeObject(value.Value);
+            }
+            return null;
+        }
+
         private string TryGetValueAndLogSupported(string vrFullString, DicomValue value, string jsonString)
         {
             var result = TryGetValue(value);

src/WorkflowManager/Contracts/Migrations/M005_Payload_seriesUid.cs

@@ -76,7 +76,14 @@ public interface IDicomService
         /// Get the seriers instance UID from the metadata.
         /// </summary>
         /// <param name="dict"></param>
-        /// <returns>a string containing the seriers instanceUid</returns>
+        /// <returns>a string containing the series instanceUid</returns>
         string? GetSeriesInstanceUID(Dictionary<string, DicomValue>? dict);
+
+        /// <summary>
+        /// Gets the Accession number from the metadata.
+        /// </summary>
+        /// <param name="dict">the metadata from the file</param>
+        /// <returns>a string containing the accession number</returns>
+        string? GetAccessionID(Dictionary<string, DicomValue>? dict);
     }
 }