Merge pull request #2194 from BEXIS2/rc

Rc -> dev -> 4.1.0

Author: DavidBlaa

.github/workflows/codeql.yml

@@ -0,0 +1,104 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL Advanced"
+
+on:
+  push:
+    branches: 
+      - rc
+  pull_request:
+    branches: 
+      - rc
+  schedule:
+    - cron: '38 14 * * 4'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: actions
+          build-mode: none
+        - language: csharp
+          build-mode: none
+        - language: javascript-typescript
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Add any setup steps before running the `github/codeql-action/init` action.
+    # This includes steps like installing compilers or runtimes (`actions/setup-node`
+    # or others). This is typically only required for manual builds.
+    # - name: Setup runtime (example)
+    #   uses: actions/setup-example@v1
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/main.yml

@@ -11,7 +11,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install .NET SDK
         uses: actions/setup-dotnet@v3

BExIS++.sln

@@ -1582,8 +1582,8 @@ Global
 		{9BFFFD11-03C6-47DF-9CC9-F458A9A49377} = {F3354AC7-CDA1-44E2-8E85-8DB532ED8C75}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
-		EnterpriseLibraryConfigurationToolBinariesPath = packages\Unity.2.1.505.0\lib\NET35;packages\Unity.2.1.505.2\lib\NET35
 		SolutionGuid = {9B6E4921-8EBA-487D-A098-3E473A0EAC64}
+		EnterpriseLibraryConfigurationToolBinariesPath = packages\Unity.2.1.505.0\lib\NET35;packages\Unity.2.1.505.2\lib\NET35
 	EndGlobalSection
 	GlobalSection(SubversionScc) = preSolution
 		Svn-Managed = True

CITATION.cff

@@ -0,0 +1,30 @@
+cff-version: 1.2.0
+message: "If you use BEXIS2 in your research, please cite it using the following metadata."
+title: "BEXIS2"
+version: 4.1.0
+date-released: 15.08.2025
+authors:
+- family-names: "Zander"
+  given-names: "Franziska"
+  orcid: "https://orcid.org/0000-0001-6892-7046"
+- family-names: "Schöne"
+  given-names: "David"
+  orcid: "https://orcid.org/0009-0009-4663-8716"
+- family-names: "Thiel"
+  given-names: "Sven"
+  orcid: "https://orcid.org/0000-0003-3093-5635"
+- family-names: "Hohmuth"
+  given-names: "Martin"
+  orcid: "https://orcid.org/0000-0001-7492-3631"
+- family-names: "König-Ries"
+  given-names: "Birgitta"
+  orcid: "https://orcid.org/0000-0002-2382-9722"
+doi: ..
+url: "https://github.com/BEXIS2/Core"
+license: "LGPL-3.0 license"
+type: software
+keywords:
+  - research data management
+  - data repository
+  - data infrastructure
+  - open source

Components/AAA/BExIS.Security.Services/Authentication/LdapAuthenticationManager.cs

@@ -10,7 +10,7 @@
 
 namespace BExIS.Security.Services.Authentication
 {
-    public class LdapAuthenticationManager
+    public class LdapAuthenticationManager : IDisposable
     {
         private readonly IUnitOfWork _guow;
         private bool _isDisposed;

Components/AAA/BExIS.Security.Services/Authentication/SignInManager.cs

@@ -8,8 +8,8 @@ namespace BExIS.Security.Services.Authentication
     public sealed class SignInManager : SignInManager<User, long>
     {
         [System.Diagnostics.CodeAnalysis.SuppressMessage("Reliability", "CA2000:Objekte verwerfen, bevor Bereich verloren geht", Justification = "<Ausstehend>")]
-        public SignInManager(IAuthenticationManager authenticationManager)
-             : base(new IdentityUserService(), authenticationManager)
+        public SignInManager(IAuthenticationManager authenticationManager, UserManager userManager)
+             : base(new IdentityUserService(userManager), authenticationManager)
         {
         }
     }

Components/AAA/BExIS.Security.Services/Subjects/GroupManager.cs

@@ -1,4 +1,5 @@
-using BExIS.Security.Entities.Subjects;
+using BExIS.Security.Entities.Authorization;
+using BExIS.Security.Entities.Subjects;
 using BExIS.Utils.NH.Querying;
 using Microsoft.AspNet.Identity;
 using System;
@@ -116,6 +117,45 @@ public Task DeleteAsync(Group role)
             return Task.CompletedTask;
         }
 
+        public Task<bool> DeleteByIdAsync(long roleId)
+        {
+            var groupRepository = _guow.GetRepository<Group>();
+            var group = groupRepository.Get(roleId);
+
+            if (group == null)
+                //return Task.FromException(new Exception());
+                return Task.FromResult(false);
+
+
+            // Users
+            var userRepository = _guow.GetRepository<User>();
+            foreach (var user in group.Users)
+            {
+                user.Groups.Remove(group);
+                userRepository.Put(user);
+            }
+
+            // EntityPermissions
+            var entityPermissionRepository = _guow.GetRepository<EntityPermission>();
+            foreach (var entityPermission in entityPermissionRepository.Get(e => e.Subject.Id == roleId))
+            {
+                entityPermissionRepository.Delete(entityPermission);
+            }
+
+            // FeaturePermissions
+            var featurePermissionRepository = _guow.GetRepository<FeaturePermission>();
+            foreach (var featurePermission in featurePermissionRepository.Get(e => e.Subject.Id == roleId))
+            {
+                featurePermissionRepository.Delete(featurePermission);
+            }
+
+            var result = groupRepository.Delete(group);
+
+            _guow.Commit();
+
+            return Task.FromResult(result);
+        }
+
         public void Dispose()
         {
             this.Dispose(true);

Components/AAA/BExIS.Security.Services/Subjects/IdentityGroupService.cs

@@ -1,22 +1,49 @@
 using BExIS.Security.Entities.Subjects;
+using BExIS.Utils.NH.Querying;
 using Microsoft.AspNet.Identity;
+using System;
+using System.Collections.Generic;
+using System.Threading.Tasks;
 
 namespace BExIS.Security.Services.Subjects
 {
     public class IdentityGroupService : RoleManager<Group, long>
     {
-        [System.Diagnostics.CodeAnalysis.SuppressMessage("Reliability", "CA2000:Objekte verwerfen, bevor Bereich verloren geht", Justification = "<Ausstehend>")]
-        public IdentityGroupService() : base(new GroupManager())
+        private readonly GroupManager _groupManager;
+        private bool _disposed;
+
+        //[System.Diagnostics.CodeAnalysis.SuppressMessage("Reliability", "CA2000:Objekte verwerfen, bevor Bereich verloren geht", Justification = "<Ausstehend>")]
+        public IdentityGroupService(GroupManager groupManager) : base(groupManager)
         {
+            _groupManager = groupManager ?? throw new ArgumentNullException(nameof(groupManager));
+
             RoleValidator = new RoleValidator<Group, long>(this)
             {
             };
         }
 
+        public Task<bool> DeleteByIdAsync(long roleId)
+        {
+            return _groupManager.DeleteByIdAsync(roleId);
+        }
+
+        public List<Group> GetGroups(FilterExpression filter, OrderByExpression orderBy, int pageNumber, int pageSize, out int count)
+        {
+            return _groupManager.GetGroups(filter, orderBy, pageNumber, pageSize, out count);
+        }
         protected override void Dispose(bool disposing)
         {
+            if (!_disposed)
+            {
+                if (disposing)
+                {
+                    _groupManager?.Dispose();
+                }
+
+                _disposed = true;
+            }
+
             base.Dispose(disposing);
-            Store.Dispose();
         }
     }
 }

Components/AAA/BExIS.Security.Services/Subjects/IdentityUserService.cs

@@ -9,9 +9,14 @@ namespace BExIS.Security.Services.Subjects
 {
     public class IdentityUserService : UserManager<User, long>
     {
-        [System.Diagnostics.CodeAnalysis.SuppressMessage("Reliability", "CA2000:Objekte verwerfen, bevor Bereich verloren geht", Justification = "<Ausstehend>")]
-        public IdentityUserService() : base(new UserManager())
+        private readonly UserManager _userManager;
+        private bool _disposed;
+
+        //[System.Diagnostics.CodeAnalysis.SuppressMessage("Reliability", "CA2000:Objekte verwerfen, bevor Bereich verloren geht", Justification = "<Ausstehend>")]
+        public IdentityUserService(UserManager userManager) : base(userManager)
         {
+            _userManager = userManager;
+
             // Configure validation logic for usernames
             UserValidator = new UserValidator<User, long>(this)
             {
@@ -54,8 +59,17 @@ public IdentityUserService() : base(new UserManager())
 
         protected override void Dispose(bool disposing)
         {
+            if (!_disposed)
+            {
+                if (disposing)
+                {
+                    _userManager?.Dispose();
+                }
+
+                _disposed = true;
+            }
+
             base.Dispose(disposing);
-            Store.Dispose();
         }
     }
 }

Components/AAA/BExIS.Security.Services/Subjects/UserManager.cs

@@ -1,4 +1,5 @@
 using BExIS.Security.Entities.Authentication;
+using BExIS.Security.Entities.Authorization;
 using BExIS.Security.Entities.Subjects;
 using BExIS.Utils.NH.Querying;
 using Microsoft.AspNet.Identity;
@@ -115,12 +116,34 @@ public Task DeleteAsync(User user)
             return Task.CompletedTask;
         }
 
-        public Task DeleteByIdAsync(long userId)
+        public Task<bool> DeleteByIdAsync(long userId)
         {
-            _guow.GetRepository<User>().Delete(userId);
+            var userRepository = _guow.GetRepository<User>();
+            var user = userRepository.Get(userId);
+
+            if(user == null)
+                //return Task.FromException(new Exception());
+                return Task.FromResult(false);
+
+            // EntityPermissions
+            var entityPermissionRepository = _guow.GetRepository<EntityPermission>();
+            foreach (var entityPermission in entityPermissionRepository.Get(e => e.Subject.Id == userId))
+            {
+                entityPermissionRepository.Delete(entityPermission);
+            }
+
+            // FeaturePermissions
+            var featurePermissionRepository = _guow.GetRepository<FeaturePermission>();
+            foreach (var featurePermission in featurePermissionRepository.Get(e => e.Subject.Id == userId))
+            {
+                featurePermissionRepository.Delete(featurePermission);
+            }
+
+            var result = userRepository.Delete(user);
+
             _guow.Commit();
 
-            return Task.CompletedTask;
+            return Task.FromResult(result);
         }
 
         public void Dispose()