Merge main back into develop

.github/dependabot.yml

@@ -3,13 +3,14 @@ updates:
 - package-ecosystem: "github-actions"
   directory: "/"
   schedule:
-    interval: daily
+    interval: weekly
+  reviewers:
+    - SMI/reviewers
 - package-ecosystem: nuget
   directory: "/"
   schedule:
-    interval: daily
-  open-pull-requests-limit: 10
+    interval: weekly
+  open-pull-requests-limit: 99
   target-branch: develop
   reviewers:
-  - tznind
-  - jas88
+    - SMI/reviewers

.github/workflows/codeql.yml

@@ -0,0 +1,41 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    branches: [ "develop" ]
+  schedule:
+    - cron: "22 19 * * 4"
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ csharp ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          queries: +security-and-quality
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2
+        with:
+          category: "/language:${{ matrix.language }}"

.github/workflows/testpack.yml

@@ -8,16 +8,18 @@ jobs:
     steps:
       - name: Disable disk flush
         run: sudo apt-get install -y libeatmydata1
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-dotnet@v3
         with:
-          dotnet-version: '6.0.x'
+          dotnet-version: |
+            6.0.x
+            7.0.x
       - name: Start MySQL for testing
         run: sudo systemctl start mysql.service
       - name: Test
         run: |
-          dotnet test "./BadMedicine.Dicom.Tests/BadMedicine.Dicom.Tests.csproj" -nologo -c Release
-          curl https://raw.githubusercontent.com/HicServices/DicomTypeTranslation/master/Templates/CT.it > ./CT.it
+          dotnet test "./BadMedicine.Dicom.Tests/BadMedicine.Dicom.Tests.csproj" --nologo -c Release
+          curl -sL https://raw.githubusercontent.com/SMI/DicomTypeTranslation/master/Templates/CT.it > ./CT.it
           cp BadDicom/BadDicom.template.yaml BadDicom.yaml
           dotnet run --project BadDicom/BadDicom.csproj -- ./ 50000 10 CT
           sed -i "s/Batches: 1/Batches: 5/g" ./BadDicom.yaml
@@ -27,18 +29,22 @@ jobs:
         run: |
           mkdir -p dist
           dotnet pack ./BadMedicine.Dicom/BadMedicine.Dicom.csproj -c Release -p:IncludeSymbols=true -p:Version=$(grep AssemblyInformationalVersion SharedAssemblyInfo.cs | cut -d'"' -f2) -nologo
-          for platform in linux win
+          for platform in linux-x64 win-x64 osx-{arm64,x64}
           do
-            dotnet publish BadDicom/BadDicom.csproj -c Release -r $platform-x64 -o $platform-x64 --self-contained true -nologo -v q -p:PublishSingleFile=true -p:DebugType=embedded -p:GenerateDocumentationFile=false
+            dotnet publish BadDicom/BadDicom.csproj -c Release -r $platform -o $platform --self-contained true -nologo -v q -p:PublishSingleFile=true -p:DebugType=embedded -p:GenerateDocumentationFile=false
           done
           zip -9r dist/baddicom-win-x64-v$(grep AssemblyInformationalVersion SharedAssemblyInfo.cs | cut -d'"' -f2).zip ./win-x64
-          tar czf dist/baddicom-linux-x64-v$(grep AssemblyInformationalVersion SharedAssemblyInfo.cs | cut -d'"' -f2).tar.gz ./linux-x64
+          for platform in linux-x64 win-x64 osx-{arm64,x64}
+          do
+            tar cJf dist/baddicom-${platform}-v$(grep AssemblyInformationalVersion SharedAssemblyInfo.cs | cut -d'"' -f2).tar.xz ./$platform
+          done
+          ls -lh dist
       - name: Nuget push
         if: contains(github.ref,'refs/tags/')
         run: |
           dotnet nuget push ./BadMedicine.Dicom/bin/Release/HIC.BadMedicine.Dicom.*.nupkg -k ${{ secrets.NUGET_KEY }} --skip-duplicate -s https://api.nuget.org/v3/index.json
       - name: Upload release binaries
-        uses: svenstaro/upload-release-action@2.3.0
+        uses: svenstaro/upload-release-action@2.7.0
         if: contains(github.ref, 'refs/tags/v')
         with:
           repo_token: ${{ secrets.GITHUB_TOKEN }}

BadDicom/BadDicom.csproj

@@ -1,34 +1,24 @@
-<Project Sdk="Microsoft.NET.Sdk">
+<Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net7.0</TargetFramework>
     <AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
-    <StartupObject></StartupObject>
     <ApplicationIcon />
     <OutputType>Exe</OutputType>
     <SatelliteResourceLanguages>en</SatelliteResourceLanguages>
     <StartupObject>BadDicom.Program</StartupObject>
     <GenerateAssemblyInfo>false</GenerateAssemblyInfo>
-    <GenerateDocumentationFile>true</GenerateDocumentationFile>
+    <GenerateDocumentationFile>false</GenerateDocumentationFile>
     <PublishRepositoryUrl>true</PublishRepositoryUrl>
     <IncludeSymbols>true</IncludeSymbols>
+    <DebugType>embedded</DebugType>
     <SymbolPackageFormat>snupkg</SymbolPackageFormat>
+    <PublishSingleFile>true</PublishSingleFile>
+    <Nullable>enable</Nullable>
   </PropertyGroup>
 
   <ItemGroup>
     <PackageReference Include="Microsoft.SourceLink.GitHub" Version="1.1.1" PrivateAssets="All" />
-    <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
   </ItemGroup>
-
-  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
-  </PropertyGroup>
-  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
-  </PropertyGroup>
-  <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Test|AnyCPU'">
-    <DebugSymbols>true</DebugSymbols>
-    <DefineConstants>DEBUG;TRACE</DefineConstants>
-    <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
-  </PropertyGroup>
   <ItemGroup>
     <None Remove="BadDicom.template.yaml" />
   </ItemGroup>
@@ -42,8 +32,9 @@
   </ItemGroup>
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.9.1" />
-    <PackageReference Include="HIC.DicomTypeTranslation" Version="4.0.1" />
-    <PackageReference Include="YamlDotNet" Version="12.0.2" />
+    <PackageReference Include="HIC.DicomTypeTranslation" Version="4.0.3" />
+    <PackageReference Include="Vecc.YamlDotNet.Analyzers.StaticGenerator" Version="13.4.0" />
+    <PackageReference Include="YamlDotNet" Version="13.4.0" />
   </ItemGroup>
   <ItemGroup>
     <Folder Include="Properties\" />

BadDicom/Configuration/Config.cs

@@ -1,8 +1,10 @@
-namespace BadDicom.Configuration
+using YamlDotNet.Serialization;
+
+namespace BadDicom.Configuration;
+
+[YamlSerializable]
+internal class Config
 {
-    class Config
-    {
-        public TargetDatabase Database { get;set; }
-        public ExplicitUIDs UIDs { get; set; }
-    }
+    public TargetDatabase? Database { get;set; }
+    public ExplicitUIDs? UIDs { get; set; }
 }

BadDicom/Configuration/ConfigContext.cs

@@ -0,0 +1,8 @@
+using YamlDotNet.Serialization;
+
+namespace BadDicom.Configuration;
+
+[YamlStaticContext]
+public partial class ConfigContext : StaticContext
+{
+}

BadDicom/Configuration/ExplicitUIDs.cs

@@ -2,55 +2,56 @@
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
+using YamlDotNet.Serialization;
 
-namespace BadDicom.Configuration
+namespace BadDicom.Configuration;
+
+/// <summary>
+/// Config section for loading explicit UIDs from disk and using those in file creation
+/// </summary>
+[YamlSerializable]
+public class ExplicitUIDs
 {
     /// <summary>
-    /// Config section for loading explicit UIDs from disk and using those in file creation
+    /// Path to a file containing a list of study instance UIDs to use
+    /// </summary>
+    public string? StudyInstanceUIDs { get; set; }
+
+    /// <summary>
+    /// Path to a file containing a list of series instance UIDs to use
+    /// </summary>
+    public string? SeriesInstanceUIDs { get; set; }
+
+    /// <summary>
+    /// Path to a file containing a list of SOP instance UIDs to use
+    /// </summary>
+    public string? SOPInstanceUIDs { get; set; }
+
+    /// <summary>
+    /// Loads the UID files referenced (if they exist) in the configuration
+    /// and populates <see cref="UIDAllocator"/> with the values.
     /// </summary>
-    public class ExplicitUIDs
+    public void Load()
+    {
+        // unlikely but if someone else has pre queued some stuff, this replaces that
+        UIDAllocator.StudyUIDs.Clear();
+        UIDAllocator.SeriesUIDs.Clear();
+        UIDAllocator.SOPUIDs.Clear();
+
+        foreach (var u in GetUIDsFrom(StudyInstanceUIDs))
+            UIDAllocator.StudyUIDs.Enqueue(u);
+
+        foreach (var u in GetUIDsFrom(SeriesInstanceUIDs))
+            UIDAllocator.SeriesUIDs.Enqueue(u);
+
+        foreach (var u in GetUIDsFrom(SOPInstanceUIDs))
+            UIDAllocator.SOPUIDs.Enqueue(u);
+    }
+
+    private static IEnumerable<string> GetUIDsFrom(string? path)
     {
-        /// <summary>
-        /// Path to a file containing a list of study instance UIDs to use
-        /// </summary>
-        public string StudyInstanceUIDs { get; set; }
-
-        /// <summary>
-        /// Path to a file containing a list of series instance UIDs to use
-        /// </summary>
-        public string SeriesInstanceUIDs { get; set; }
-
-        /// <summary>
-        /// Path to a file containing a list of SOP instance UIDs to use
-        /// </summary>
-        public string SOPInstanceUIDs { get; set; }
-
-        /// <summary>
-        /// Loads the UID files referenced (if they exist) in the configuration
-        /// and populates <see cref="UIDAllocator"/> with the values.
-        /// </summary>
-        public void Load()
-        {
-            // unlikely but if someone else has pre queued some stuff, this replaces that
-            UIDAllocator.StudyUIDs.Clear();
-            UIDAllocator.SeriesUIDs.Clear();
-            UIDAllocator.SOPUIDs.Clear();
-
-            foreach (var u in GetUIDsFrom(StudyInstanceUIDs))
-                UIDAllocator.StudyUIDs.Enqueue(u);
-
-            foreach (var u in GetUIDsFrom(SeriesInstanceUIDs))
-                UIDAllocator.SeriesUIDs.Enqueue(u);
-
-            foreach (var u in GetUIDsFrom(SOPInstanceUIDs))
-                UIDAllocator.SOPUIDs.Enqueue(u);
-        }
-
-        private IEnumerable<string> GetUIDsFrom(string path)
-        {
-            if (string.IsNullOrWhiteSpace(path) || !File.Exists(path)) return Enumerable.Empty<string>();
+        if (string.IsNullOrWhiteSpace(path) || !File.Exists(path)) return Enumerable.Empty<string>();
 
-            return File.ReadLines(StudyInstanceUIDs).Where(l => !string.IsNullOrWhiteSpace(l));
-        }
+        return File.ReadLines(path).Where(l => !string.IsNullOrWhiteSpace(l));
     }
 }

BadDicom/Configuration/TargetDatabase.cs

@@ -1,46 +1,47 @@
 using FAnsi;
+using YamlDotNet.Serialization;
 
-namespace BadDicom.Configuration
+namespace BadDicom.Configuration;
+
+/// <summary>
+/// Identify the target database and configuration for generated data
+/// </summary>
+[YamlSerializable]
+public class TargetDatabase
 {
     /// <summary>
-    /// Identify the target database and configuration for generated data
+    /// Which RDBMS the database is (MySQL, Microsoft SQL Server, etc)
+    /// </summary>
+    public DatabaseType DatabaseType { get; set; }
+    /// <summary>
+    /// The ConnectionString containing the server name, credentials and other parameters for the connection
     /// </summary>
-    public class TargetDatabase
-    {
-        /// <summary>
-        /// Which RDBMS the database is (MySQL, Microsoft SQL Server, etc)
-        /// </summary>
-        public DatabaseType DatabaseType { get; set; }
-        /// <summary>
-        /// The ConnectionString containing the server name, credentials and other parameters for the connection
-        /// </summary>
-        public string ConnectionString { get; set; }
+    public string? ConnectionString { get; set; }
 
-        /// <summary>
-        /// The name of database
-        /// </summary>
-        public string DatabaseName { get; set; }
+    /// <summary>
+    /// The name of database
+    /// </summary>
+    public string? DatabaseName { get; set; }
 
-        /// <summary>
-        /// The filename of a YAML template file to be used for this database
-        /// </summary>
-        public string Template { get; set; }
+    /// <summary>
+    /// The filename of a YAML template file to be used for this database
+    /// </summary>
+    public string? Template { get; set; }
 
-        /// <summary>
-        /// Pass true to create tables from template that do not have primary key.  Do bulk insert
-        /// then deduplicate final tables and recreate primary key
-        /// </summary>
-        public bool MakeDistinct { get; set; }
+    /// <summary>
+    /// Pass true to create tables from template that do not have primary key.  Do bulk insert
+    /// then deduplicate final tables and recreate primary key
+    /// </summary>
+    public bool MakeDistinct { get; set; }
 
-        /// <summary>
-        /// Set to true to drop and recreate tables described in the Template
-        /// </summary>
-        public bool DropTables { get; set; }
+    /// <summary>
+    /// Set to true to drop and recreate tables described in the Template
+    /// </summary>
+    public bool DropTables { get; set; }
 
-        /// <summary>
-        /// The number of parallel batches to execute (each batch gets the full count of studies
-        /// then they are merged at the end).
-        /// </summary>
-        public int Batches { get; set; } = 1;
-    }
-}
+    /// <summary>
+    /// The number of parallel batches to execute (each batch gets the full count of studies
+    /// then they are merged at the end).
+    /// </summary>
+    public int Batches { get; set; } = 1;
+}