adding HL7 plugin

Signed-off-by: Neil South <[email protected]>

Author: neildsouth

.github/workflows/ci.yml

@@ -183,11 +183,11 @@ jobs:
         ports:
         - 27017:27017
     steps:
-      - name: Set up JDK 11
+      - name: Set up JDK 17
         uses: actions/setup-java@v3
         with:
           distribution: zulu
-          java-version: '11'
+          java-version: '17'
 
       - uses: actions/setup-dotnet@v3
         with:

.gitignore

@@ -560,3 +560,4 @@ FodyWeavers.xsd
 # Additional files built by Visual Studio
 
 # End of https://www.toptal.com/developers/gitignore/api/aspnetcore,dotnetcore,visualstudio,visualstudiocode
+/src/InformaticsGateway/Properties/launchSettings.json

doc/dependency_decisions.yml

@@ -314,62 +314,77 @@
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
-    :when: 2022-08-16 23:05:49.698463427 Z
+    - 6.0.25
+    - :when: 2022-08-16 23:05:49.698463427 Z
 - - :approve
   - Microsoft.EntityFrameworkCore
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
+    - 6.0.25
     :when: 2022-08-16 23:05:50.137694970 Z
 - - :approve
   - Microsoft.EntityFrameworkCore.Abstractions
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
-    :when: 2022-08-16 23:05:51.008105271 Z
+    - 6.0.25
+    - :when: 2022-08-16 23:05:51.008105271 Z
 - - :approve
   - Microsoft.EntityFrameworkCore.Analyzers
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
-    :when: 2022-08-16 23:05:51.445711308 Z
+    - 6.0.25
+    - :when: 2022-08-16 23:05:51.445711308 Z
 - - :approve
   - Microsoft.EntityFrameworkCore.Design
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
-    :when: 2022-08-16 23:05:51.922790944 Z
+    - 6.0.25
+    - :when: 2022-08-16 23:05:51.922790944 Z
 - - :approve
   - Microsoft.EntityFrameworkCore.InMemory
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
-    :when: 2022-08-16 23:05:52.375150938 Z
+    - 6.0.25
+    - :when: 2022-08-16 23:05:52.375150938 Z
 - - :approve
   - Microsoft.EntityFrameworkCore.Relational
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
-    :when: 2022-08-16 23:05:52.828879230 Z
+    - 6.0.25
+    - :when: 2022-08-16 23:05:52.828879230 Z
+- - :approve
+  - Microsoft.EntityFrameworkCore.Tools
+  - :who: ndsouth
+    :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
+    :versions:
+    - 6.0.25
+    - :when: 2022-08-16 23:05:52.828879230 Z
 - - :approve
   - Microsoft.EntityFrameworkCore.Sqlite
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
-    - 6.0.22
+    - 6.0.25
     :when: 2022-08-16 23:05:53.270526921 Z
 - - :approve
   - Microsoft.EntityFrameworkCore.Sqlite.Core
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/dotnet/efcore/release/6.0/LICENSE.txt)
     :versions:
     - 6.0.22
+    - 6.0.25
     :when: 2022-08-16 23:05:53.706997823 Z
 - - :approve
   - Microsoft.Extensions.ApiDescription.Server
@@ -512,22 +527,25 @@
     :versions:
     - 6.0.21
     - 6.0.22
-    :when: 2022-08-29 18:11:22.090772006 Z
+    - 6.0.25
+    - :when: 2022-08-29 18:11:22.090772006 Z
 - - :approve
   - Microsoft.Extensions.Diagnostics.HealthChecks.Abstractions
   - :who: mocsharp
     :why: MIT (https://github.com/dotnet/aspnetcore/raw/main/LICENSE.txt)
     :versions:
     - 6.0.21
     - 6.0.22
-    :when: 2022-08-29 18:11:22.090772006 Z
+    - 6.0.25
+    - :when: 2022-08-29 18:11:22.090772006 Z
 - - :approve
   - Microsoft.Extensions.Diagnostics.HealthChecks.EntityFrameworkCore
   - :who: mocsharp
     :why: MIT (https://github.com/dotnet/aspnetcore/raw/main/LICENSE.txt)
     :versions:
     - 6.0.22
-    :when: 2022-08-29 18:11:22.090772006 Z
+    - 6.0.25
+    - :when: 2022-08-29 18:11:22.090772006 Z
 - - :approve
   - Microsoft.Extensions.FileProviders.Abstractions
   - :who: mocsharp
@@ -774,16 +792,16 @@
   - :who: neilsouth
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 1.0.3
-    - 1.0.4
+    - 1.0.5-rc0006
+    - 1.0.5
     :when: 2023-10-13 18:06:21.511789690 Z
 - - :approve
   - Monai.Deploy.Messaging.RabbitMQ
   - :who: neilsouth
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 1.0.3
-    - 1.0.4
+    - 1.0.5-rc0006
+    - 1.0.5
     :when: 2023-10-13 18:06:21.511789690 Z
 - - :approve
   - Monai.Deploy.Storage

src/Api/HL7DestinationEntity.cs

@@ -0,0 +1,40 @@
+/*
+ * Copyright 2021-2022 MONAI Consortium
+ * Copyright 2019-2020 NVIDIA Corporation
+ *
+ * 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.
+ */
+
+namespace Monai.Deploy.InformaticsGateway.Api.Models
+{
+    /// <summary>
+    /// HL7 Destination Entity
+    /// </summary>
+    /// <example>
+    /// <code>
+    /// {
+    ///     "name": "MYPACS",
+    ///     "hostIp": "10.20.100.200",
+    ///     "aeTitle": "MONAIPACS",
+    ///     "port": 1104
+    /// }
+    /// </code>
+    /// </example>
+    public class HL7DestinationEntity : BaseApplicationEntity
+    {
+        /// <summary>
+        /// Gets or sets the port to connect to.
+        /// </summary>
+        public int Port { get; set; }
+    }
+}

src/Api/Hl7ApplicationConfigEntity.cs

@@ -0,0 +1,170 @@
+/*
+ * 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 System;
+using System.Collections.Generic;
+using System.ComponentModel.DataAnnotations;
+using System.ComponentModel.DataAnnotations.Schema;
+using System.Linq;
+using FellowOakDicom;
+using Monai.Deploy.InformaticsGateway.Api.Storage;
+using Monai.Deploy.InformaticsGateway.Common;
+using Newtonsoft.Json;
+
+namespace Monai.Deploy.InformaticsGateway.Api
+{
+    public class Hl7ApplicationConfigEntity : MongoDBEntityBase
+    {
+        /// <summary>
+        /// Gets or sets the name of a Hl7 application entity.
+        /// This value must be unique.
+        /// </summary>
+        [Key, Column(Order = 0)]
+        public string Name { get; set; } = default!;
+
+        /// <summary>
+        /// Gets or sets the sending identifier.
+        /// </summary>
+        [JsonProperty("sending_identifier")]
+        public StringKeyValuePair SendingId { get; set; } = new();
+
+        /// <summary>
+        /// Gets or sets the data link.
+        /// Value is either PatientId or StudyInstanceUid
+        /// </summary>
+        [JsonProperty("data_link")]
+        public DataKeyValuePair DataLink { get; set; } = new();
+
+        /// <summary>
+        /// Gets or sets the data mapping.
+        /// Value is a DICOM Tag
+        /// </summary>
+        [JsonProperty("data_mapping")]
+        public List<StringKeyValuePair> DataMapping { get; set; } = new();
+
+        /// <summary>
+        /// Optional list of data input plug-in type names to be executed by the <see cref="IInputHL7DataPlugInEngine"/>.
+        /// </summary>
+        public List<string> PlugInAssemblies { get; set; } = default!;
+
+        public DateTime LastModified { get; set; } = DateTime.UtcNow;
+
+        public IEnumerable<string> Validate()
+        {
+            var errors = new List<string>();
+            if (string.IsNullOrWhiteSpace(SendingId.Key))
+                errors.Add($"{nameof(SendingId.Key)} is missing.");
+            if (string.IsNullOrWhiteSpace(SendingId.Value))
+                errors.Add($"{nameof(SendingId.Value)} is missing.");
+
+            if (string.IsNullOrWhiteSpace(DataLink.Key))
+                errors.Add($"{nameof(DataLink.Key)} is missing.");
+
+            if (DataMapping.IsNullOrEmpty())
+                errors.Add($"{nameof(DataMapping)} is missing values.");
+
+            ValidateDataMapping(errors);
+
+            return errors;
+        }
+
+        private void ValidateDataMapping(List<string> errors)
+        {
+            for (var idx = 0; idx < DataMapping.Count; idx++)
+            {
+                var dataMapKvp = DataMapping[idx];
+
+                if (string.IsNullOrWhiteSpace(dataMapKvp.Key) || dataMapKvp.Value.Length < 8)
+                {
+                    if (string.IsNullOrWhiteSpace(dataMapKvp.Key))
+                        errors.Add($"{nameof(DataMapping)} is missing a name at index {idx}.");
+
+                    if (string.IsNullOrWhiteSpace(dataMapKvp.Value) || dataMapKvp.Value.Length < 8)
+                        errors.Add($"{nameof(DataMapping)} ({dataMapKvp.Key}) @ index {idx} is not a valid DICOM Tag.");
+
+                    continue;
+                }
+
+                try
+                {
+                    DicomTag.Parse(dataMapKvp.Value);
+                }
+                catch (Exception e)
+                {
+                    errors.Add($"DataMapping.Value is not a valid DICOM Tag. {e.Message}");
+                }
+            }
+        }
+
+        public override string ToString()
+        {
+            return JsonConvert.SerializeObject(this);
+        }
+    }
+
+    //string key, string value
+    public class StringKeyValuePair : IKeyValuePair<string, string>
+    {
+        [Key]
+        public string Key { get; set; } = string.Empty;
+        public string Value { get; set; } = string.Empty;
+
+        public static implicit operator StringKeyValuePair(KeyValuePair<string, string> kvp)
+        {
+            return new StringKeyValuePair { Key = kvp.Key, Value = kvp.Value };
+        }
+
+        public static List<StringKeyValuePair> FromDictionary(Dictionary<string, string> dictionary) =>
+            dictionary.Select(kvp => new StringKeyValuePair { Key = kvp.Key, Value = kvp.Value }).ToList();
+
+        public override bool Equals(object? obj) => Equals(obj as StringKeyValuePair);
+
+        public bool Equals(StringKeyValuePair? other) => other != null && Key == other.Key && Value == other.Value;
+
+        public override int GetHashCode() => HashCode.Combine(Key, Value);
+
+    }
+
+    public class DataKeyValuePair : IKeyValuePair<string, DataLinkType>
+    {
+        [Key]
+        public string Key { get; set; } = string.Empty;
+        public DataLinkType Value { get; set; }
+
+        public static implicit operator DataKeyValuePair(KeyValuePair<string, DataLinkType> kvp)
+        {
+            return new DataKeyValuePair { Key = kvp.Key, Value = kvp.Value };
+        }
+
+        public override bool Equals(object? obj) => Equals(obj as DataKeyValuePair);
+
+        public bool Equals(DataKeyValuePair? other) => other != null && Key == other.Key && Value == other.Value;
+
+        public override int GetHashCode() => HashCode.Combine(Key, Value);
+    }
+
+    public interface IKeyValuePair<TKey, TValue>
+    {
+        public TKey Key { get; set; }
+        public TValue Value { get; set; }
+    }
+
+    public enum DataLinkType
+    {
+        PatientId,
+        StudyInstanceUid
+    }
+}

src/InformaticsGateway/Services/HealthLevel7/IMllpClient.cs renamed to src/Api/Mllp/IMllpClient.cs

@@ -18,14 +18,14 @@
 using System.Threading;
 using System.Threading.Tasks;
 
-namespace Monai.Deploy.InformaticsGateway.Services.HealthLevel7
+namespace Monai.Deploy.InformaticsGateway.Api.Mllp
 {
-    internal interface IMllpClient : IDisposable
+    public interface IMllpClient : IDisposable
     {
         Guid ClientId { get; }
 
         string ClientIp { get; }
 
         Task Start(Func<IMllpClient, MllpClientResult, Task> onDisconnect, CancellationToken cancellationToken);
     }
-}
+}