Merge pull request #43 from Project-MONAI/vchang/message-structure

Extract and store DICOM JSON.

Author: GreySeaWolf

docs/setup/setup.md

@@ -136,7 +136,34 @@ Locate the storage section of the configuration in `appsettings.json`:
  }
 }
 ```
+### DICOM JSON Model
 
+By default, Informatics Gateway stores all received and retrieved DICOM instances into JSON in additional to storing
+the original in DICOM part-10 format. The JSON stored is as specified by the [DICOM JSON model](https://dicom.nema.org/dicom/2013/output/chtml/part18/sect_F.2.html)
+without the following VR types:
+
+- OB
+- OD
+- OF
+- OL
+- OV
+- OW
+- UN
+
+This behavior may be changed in the configuration file:
+```json
+{
+
+ "InformaticsGateway": {
+ "dicom": {
+ "writeDicomJson": "None|IgnoreOthers|Complete"
+ }, 
+ ...
+ }
+}
+```
+
+Refer to the [DicomJsonOptions](xref:Monai.Deploy.InformaticsGateway.Configuration.DicomJsonOptions) for complete description.
 
 ## Summary
 

src/Api/MessageBroker/Message.cs

@@ -61,20 +61,6 @@ public sealed class Message : MessageBase
  /// </summary>
  public byte[] Body { get; init; }
 
- public Message(byte[] body,
- string bodyDescription,
- string contentType,
- string correlationId)
- : this(body,
- bodyDescription,
- Guid.NewGuid().ToString(),
- Message.InformaticsGatewayApplicationId,
- contentType,
- correlationId,
- DateTime.UtcNow)
- {
- }
-
  public Message(byte[] body,
  string bodyDescription,
  string messageId,

src/Api/MessageBroker/WorkflowRequestMessage.cs

@@ -1,33 +1,57 @@
-using System;
+// Copyright 2022 MONAI Consortium
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+// http://www.apache.org/licenses/LICENSE-2.0
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+using Monai.Deploy.InformaticsGateway.Api.Storage;
+using Newtonsoft.Json;
+using System;
 using System.Collections.Generic;
 
 namespace Monai.Deploy.InformaticsGateway.Api.MessageBroker
 {
  public class WorkflowRequestMessage
  {
- /// <summary>
- /// Gets or sets the name of bucket where the payload is stored.
- /// </summary>
- public string Bucket { get; set; }
-
  /// <summary>
  /// Gets or sets the ID of the payload which is also used as the root path of the payload.
  /// </summary>
+ [JsonProperty(PropertyName = "payload_id")]
  public Guid PayloadId { get; set; }
 
  /// <summary>
  /// Gets or sets the associated workflows to be launched.
  /// </summary>
+ [JsonProperty(PropertyName = "workflows")]
  public IEnumerable<string> Workflows { get; set; }
 
  /// <summary>
  /// Gets or sets number of files in the payload.
  /// </summary>
+ [JsonProperty(PropertyName = "file_count")]
  public int FileCount { get; set; }
 
  /// <summary>
  /// For DIMSE, the correlation ID is the UUID associated with the first DICOM association received. For an ACR inference request, the correlation ID is the Transaction ID in the original request.
  /// </summary>
+ [JsonProperty(PropertyName = "correlation_id")]
  public string CorrelationId { get; set; }
+
+ /// <summary>
+ /// Gets or sets the time the data was received.
+ /// </summary>
+ [JsonProperty(PropertyName = "timestamp")]
+ public DateTime Timestamp { get; set; }
+
+ /// <summary>
+ /// Gets or sets a list of files and metadata files in this request.
+ /// </summary>
+ [JsonProperty(PropertyName = "payload")]
+ public List<BlockStorageInfo> Payload { get; } = new List<BlockStorageInfo>();
  }
 }

src/Api/Storage/BlockStorageInfo.cs

@@ -0,0 +1,36 @@
+// Copyright 2022 MONAI Consortium
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+// http://www.apache.org/licenses/LICENSE-2.0
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+using Newtonsoft.Json;
+
+namespace Monai.Deploy.InformaticsGateway.Api.Storage
+{
+ public class BlockStorageInfo
+ {
+ /// <summary>
+ /// Gets or sets the name of bucket where the file is stored.
+ /// </summary>
+ [JsonProperty(PropertyName = "bucket")]
+ public string Bucket { get; set; }
+
+ /// <summary>
+ /// Gets or sets the root path to the file.
+ /// </summary>
+ [JsonProperty(PropertyName = "path")]
+ public string Path { get; set; }
+
+ /// <summary>
+ /// Gets or sets the root path to the metadata file.
+ /// </summary>
+ [JsonProperty(PropertyName = "metadata")]
+ public string Metadata { get; set; }
+ }
+}

src/Api/Storage/DicomFileStorageInfo.cs

@@ -10,6 +10,7 @@
 // limitations under the License.
 
 using Ardalis.GuardClauses;
+using System.Collections.Generic;
 using System.IO.Abstractions;
 
 namespace Monai.Deploy.InformaticsGateway.Api.Storage
@@ -19,31 +20,66 @@ namespace Monai.Deploy.InformaticsGateway.Api.Storage
  /// </summary>
  public sealed record DicomFileStorageInfo : FileStorageInfo
  {
- public static readonly string FILE_EXTENSION = ".dcm";
- public static readonly string CONTENT_TYPE = "application/dicom";
+ public static readonly string FilExtension = ".dcm";
+ public static readonly string DicomJsonFileExtension = ".json";
+ public static readonly string DicomContentType = "application/dicom";
+ public static readonly string DicomJsonContentType = "application/json";
+
  public string StudyInstanceUid { get; set; }
  public string SeriesInstanceUid { get; set; }
  public string SopInstanceUid { get; set; }
+ public string DicomJsonFilePath { get; set; }
+
+ /// <summary>
+ /// Gets the file path to be stored on the shared storage.
+ /// </summary>
+ public string DicomJsonUploadPath
+ {
+ get
+ {
+ if (string.IsNullOrWhiteSpace(FilePath))
+ {
+ _ = FilePath;
+ };
+
+ var path = DicomJsonFilePath[StorageRootPath.Length..];
+ if (FileSystem.Path.IsPathRooted(path))
+ {
+ return path[1..];
+ }
+ return path;
+ }
+ }
+
+ public override IEnumerable<string> FilePaths
+ {
+ get
+ {
+ yield return FilePath;
+ yield return DicomJsonFilePath;
+ }
+ }
+ 
 
  public DicomFileStorageInfo() { }
 
  public DicomFileStorageInfo(string correlationId,
  string storageRootPath,
  string messageId,
  string source)
- : base(correlationId, storageRootPath, messageId, FILE_EXTENSION, source, new FileSystem())
+ : base(correlationId, storageRootPath, messageId, FilExtension, source, new FileSystem())
  {
- this.ContentType = CONTENT_TYPE;
+ ContentType = DicomContentType;
  }
 
  public DicomFileStorageInfo(string correlationId,
  string storageRootPath,
  string messageId,
  string source,
  IFileSystem fileSystem)
- : base(correlationId, storageRootPath, messageId, FILE_EXTENSION, source, fileSystem)
+ : base(correlationId, storageRootPath, messageId, FilExtension, source, fileSystem)
  {
- this.ContentType = CONTENT_TYPE;
+ ContentType = DicomContentType;
  }
 
  protected override string GenerateStoragePath()
@@ -61,7 +97,15 @@ protected override string GenerateStoragePath()
  filePath = filePath.ToLowerInvariant();
  }
 
+ DicomJsonFilePath = $"{filePath}{DicomJsonFileExtension}";
  return filePath;
  }
+
+ public override BlockStorageInfo ToBlockStorageInfo(string bucket)
+ {
+ var blockStorage = base.ToBlockStorageInfo(bucket);
+ blockStorage.Metadata = DicomJsonUploadPath;
+ return blockStorage;
+ }
  }
 }

src/Api/Storage/FhirFileStorageInfo.cs

@@ -20,7 +20,9 @@ namespace Monai.Deploy.InformaticsGateway.Api.Storage
  /// </summary>
  public sealed record FhirFileStorageInfo : FileStorageInfo
  {
- const string DirectoryPath = "ehr";
+ public static readonly string JsonFilExtension = ".json";
+ public static readonly string XmlFilExtension = ".xml";
+ private static readonly string DirectoryPath = "ehr";
 
  public string ResourceType { get; set; }
 
@@ -31,15 +33,15 @@ public FhirFileStorageInfo(string correlationId,
  string messageId,
  FhirStorageFormat fhirFileFormat,
  string source)
- : base(correlationId, storageRootPath, messageId, fhirFileFormat == FhirStorageFormat.Json ? ".json" : ".xml", source, new FileSystem()) { }
+ : base(correlationId, storageRootPath, messageId, fhirFileFormat == FhirStorageFormat.Json ? JsonFilExtension : XmlFilExtension, source, new FileSystem()) { }
 
  public FhirFileStorageInfo(string correlationId,
  string storageRootPath,
  string messageId,
  FhirStorageFormat fhirFileFormat,
  string source,
  IFileSystem fileSystem)
- : base(correlationId, storageRootPath, messageId, fhirFileFormat == FhirStorageFormat.Json ? ".json" : ".xml", source, fileSystem)
+ : base(correlationId, storageRootPath, messageId, fhirFileFormat == FhirStorageFormat.Json ? JsonFilExtension : XmlFilExtension, source, fileSystem)
  {
  }
 

src/Api/Storage/FileStorageInfo.cs

@@ -11,6 +11,7 @@
 
 using Ardalis.GuardClauses;
 using System;
+using System.Collections.Generic;
 using System.IO.Abstractions;
 
 namespace Monai.Deploy.InformaticsGateway.Api.Storage
@@ -71,10 +72,10 @@ public string UploadPath
  {
  get
  {
- var path = FilePath.Substring(StorageRootPath.Length);
+ var path = FilePath[StorageRootPath.Length..];
  if (FileSystem.Path.IsPathRooted(path))
  {
- return path.Substring(1);
+ return path[1..];
  }
  return path;
  }
@@ -118,6 +119,17 @@ public string UploadFilename
  /// </summary>
  public string ContentType { get; set; }
 
+ /// <summary>
+ /// Gets the file and any associated meta files.
+ /// </summary>
+ public virtual IEnumerable<string> FilePaths
+ {
+ get
+ {
+ yield return _filePath;
+ }
+ }
+
  public FileStorageInfo() { }
 
  public FileStorageInfo(string correlationId,
@@ -185,5 +197,14 @@ protected virtual string GenerateStoragePath()
 
  return filePath;
  }
+
+ public virtual BlockStorageInfo ToBlockStorageInfo(string bucket)
+ {
+ return new BlockStorageInfo
+ {
+ Bucket = bucket,
+ Path = UploadPath,
+ };
+ }
  }
 }

src/Api/Storage/Payload.cs

@@ -48,6 +48,8 @@ public enum PayloadState
 
  public string Key { get; init; }
 
+ public DateTime DateTimeCreated { get; private set; }
+
  public int RetryCount { get; set; }
 
  public bool HasTimedOut { get => ElapsedTime().TotalSeconds >= Timeout; }
@@ -67,6 +69,7 @@ public IEnumerable<string> Workflows
  }
 
  public string CorrelationId { get; init; }
+ public IList<BlockStorageInfo> UploadedFiles { get; set; }
 
  public Payload(string key, string correlationId, uint timeout)
  {
@@ -80,6 +83,7 @@ public Payload(string key, string correlationId, uint timeout)
  RetryCount = 0;
  State = PayloadState.Created;
  Files = new List<FileStorageInfo>();
+ UploadedFiles = new List<BlockStorageInfo>();
  }
 
  public void Add(FileStorageInfo value)
@@ -89,6 +93,11 @@ public void Add(FileStorageInfo value)
  Files.Add(value);
  _lastReceived.Reset();
  _lastReceived.Start();
+
+ if(Files.Count == 1)
+ {
+ DateTimeCreated = value.Received;
+ }
  }
 
  public TimeSpan ElapsedTime()

src/Configuration/DicomConfiguration.cs

@@ -46,5 +46,11 @@ public class DicomConfiguration
  /// </summary>
  [JsonProperty(PropertyName = "scu")]
  public ScuConfiguration Scu { get; set; } = new ScuConfiguration();
+
+ /// <summary>
+ /// Gets or sets whether to write DICOM JSON file for each instance received.
+ /// </summary>
+ [JsonProperty(PropertyName = "writeDicomJson")]
+ public DicomJsonOptions WriteDicomJson { get; set; } = DicomJsonOptions.IgnoreOthers;
  }
 }