Merge branch 'develop' into bugfix/RDMP-259-delta-load-off-by-one-issue

HicServices · Oct 24, 2024 · 1a1c267 · 1a1c267
2 parents eb314ac + 4787dce
commit 1a1c267
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -71,7 +71,7 @@ jobs:
           mv `find coverage -type f` db-ui.lcov
           dotnet test Rdmp.Core.Tests/Rdmp.Core.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release -e AWS_ENDPOINT_URL="http://127.0.0.1:9000" --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
           mv `find coverage -type f` db-core.lcov
-      - uses: coverallsapp/[email protected].0
+      - uses: coverallsapp/[email protected].3
         with:
           github-token: ${{ secrets.github_token }}
           files: ./db-ui.lcov ./db-core.lcov
@@ -137,7 +137,7 @@ jobs:
           mv `find coverage -type f` fs-ui.lcov
           dotnet test Rdmp.Core.Tests/Rdmp.Core.Tests.csproj --nologo --collect:"XPlat Code Coverage" --no-build --verbosity minimal -c Release  -e AWS_ENDPOINT_URL="http://127.0.0.1:9000" --results-directory coverage -- DataCollectionRunSettings.DataCollectors.DataCollector.Configuration.Format=lcov
           mv `find coverage -type f` fs-core.lcov
-      - uses: coverallsapp/[email protected].0
+      - uses: coverallsapp/[email protected].3
         with:
           github-token: ${{ secrets.github_token }}
           files: ./fs-ui.lcov ./fs-core.lcov
@@ -176,7 +176,6 @@ jobs:
           cp -r Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/runtimes ./PublishWinForms
           cp -r Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/x64 ./PublishWinForms
           cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/D3DCompiler_47_cor3.dll ./PublishWinForms
-          cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/mongocrypt.dll ./PublishWinForms
           cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/PenImc_cor3.dll ./PublishWinForms
           cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/PresentationNative_cor3.dll ./PublishWinForms
           cp Application/ResearchDataManagementPlatform/bin/Release/net8.0-windows/win-x64/vcruntime140_cor3.dll ./PublishWinForms

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [8.3.1] - Unreleased
+## [8.3.1] - 2024-10-22
 
 - Improve Performance of regenerating problems with child providers
 - Update UI Tab opening Logic

diff --git a/Directory.Packages.props b/Directory.Packages.props
@@ -1,22 +1,22 @@
 <Project>
   <ItemGroup>
-    <PackageVersion Include="AWSSDK.S3" Version="3.7.404.5" />
-    <PackageVersion Include="AWSSDK.SecurityToken" Version="3.7.400.33" />
-    <PackageVersion Include="AWSSDK.SSO" Version="3.7.400.33" />
-    <PackageVersion Include="AWSSDK.SSOOIDC" Version="3.7.400.33" />
+    <PackageVersion Include="AWSSDK.S3" Version="3.7.405.2" />
+    <PackageVersion Include="AWSSDK.SecurityToken" Version="3.7.400.38" />
+    <PackageVersion Include="AWSSDK.SSO" Version="3.7.400.38" />
+    <PackageVersion Include="AWSSDK.SSOOIDC" Version="3.7.400.38" />
     <PackageVersion Include="CommandLineParser" Version="2.9.1" />
     <PackageVersion Include="Equ" Version="2.3.0" />
     <PackageVersion Include="ExcelNumberFormat" Version="1.1.0" />
     <PackageVersion Include="FluentFTP" Version="51.1.0" />
     <PackageVersion Include="HIC.SynthEHR" Version="2.0.1" />
-    <PackageVersion Include="HIC.FAnsiSql" Version="3.2.6" />
+    <PackageVersion Include="HIC.FAnsiSql" Version="3.2.7" />
     <PackageVersion Include="LibArchive.Net" Version="0.1.5" />
     <PackageVersion Include="Microsoft.SourceLink.GitHub" Version="8.0.0">
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageVersion>
     <PackageVersion Include="Minio" Version="6.0.3" />
-    <PackageVersion Include="MongoDB.Driver" Version="2.29.0" />
+    <PackageVersion Include="MongoDB.Driver" Version="3.0.0" />
     <PackageVersion Include="Newtonsoft.Json" Version="13.0.3" />
     <PackageVersion Include="NPOI" Version="2.7.1" />
     <PackageVersion Include="NLog" Version="5.3.4" />
@@ -30,14 +30,14 @@
     <PackageVersion Include="Autoupdater.NET.Official" Version="1.9.2" />
     <PackageVersion Include="DockPanelSuite.ThemeVS2015" Version="3.1.1" />
     <PackageVersion Include="System.Threading.ThreadPool" Version="4.3.0" />
-    <PackageVersion Include="WeCantSpell.Hunspell" Version="5.0.0" />
+    <PackageVersion Include="WeCantSpell.Hunspell" Version="5.1.0" />
     <PackageVersion Include="NUnit" Version="4.2.2" />
     <PackageVersion Include="ObjectListView.Repack.NET6Plus" Version="2.9.5" />
     <PackageVersion Include="Scintilla.NET" Version="5.3.2.9" />
     <PackageVersion Include="System.Resources.Extensions" Version="8.0.0" />
     <PackageVersion Include="VPKSoft.ScintillaLexers.NET" Version="1.1.16" />
     <PackageVersion Include="HIC.System.Windows.Forms.DataVisualization" Version="1.0.1" />
-    <PackageVersion Include="NunitXml.TestLogger" Version="4.0.254" />
+    <PackageVersion Include="NunitXml.TestLogger" Version="4.1.0" />
     <PackageVersion Include="NUnit3TestAdapter" Version="4.6.0" />
     <PackageVersion Include="NUnit.Analyzers" Version="4.3.0" />
     <PackageVersion Include="NSubstitute" Version="5.1.0" />

diff --git a/Rdmp.Core/Logging/LogManager.cs b/Rdmp.Core/Logging/LogManager.cs
@@ -63,7 +63,8 @@ public string[] ListDataTasks(bool hideTests = false)
 
         using var con = Server.GetConnection();
         con.Open();
-        using var cmd = Server.GetCommand("SELECT * FROM DataLoadTask", con);
+        var sh = Server.GetQuerySyntaxHelper();
+        using var cmd = Server.GetCommand($"SELECT * FROM {sh.EnsureWrapped("DataLoadTask")}", con);
         using var r = cmd.ExecuteReader();
         while (r.Read())
             if (!hideTests || !(bool)r["isTest"])
@@ -113,7 +114,8 @@ public string[] ListDataSets()
         using var con = Server.GetConnection();
         con.Open();
 
-        using var cmd = Server.GetCommand("SELECT * FROM DataSet", con);
+        var sh = Server.GetQuerySyntaxHelper();
+        using var cmd = Server.GetCommand($"SELECT * FROM {sh.EnsureWrapped("DataSet")}", con);
         using var r = cmd.ExecuteReader();
         while (r.Read())
             tasks.Add(r["dataSetID"].ToString());
@@ -133,7 +135,8 @@ public IEnumerable<ArchivalDataLoadInfo> GetArchivalDataLoadInfos(string dataTas
         int? specificDataLoadRunIDOnly = null, int? topX = null)
     {
         var db = Server.GetCurrentDatabase();
-        var run = db.ExpectTable("DataLoadRun");
+        var sh = Server.GetQuerySyntaxHelper();
+        var run = db.ExpectTable(sh.EnsureWrapped("DataLoadRun"));
 
         using var con = Server.GetConnection();
         con.Open();
@@ -144,11 +147,11 @@ public IEnumerable<ArchivalDataLoadInfo> GetArchivalDataLoadInfos(string dataTas
         string where;
         if (specificDataLoadRunIDOnly != null)
         {
-            where = $"WHERE ID={specificDataLoadRunIDOnly.Value}";
+            where = $"WHERE {sh.EnsureWrapped("ID")}={specificDataLoadRunIDOnly.Value}";
         }
         else
         {
-            where = "WHERE dataLoadTaskID = @dataTaskId";
+            where = $"WHERE {sh.EnsureWrapped("dataLoadTaskID")} = @dataTaskId";
             var p = cmd.CreateParameter();
             p.ParameterName = "@dataTaskId";
             p.Value = dataTaskId;
@@ -158,13 +161,13 @@ public IEnumerable<ArchivalDataLoadInfo> GetArchivalDataLoadInfos(string dataTas
         TopXResponse top = null;
 
         if (topX.HasValue)
-            top = Server.GetQuerySyntaxHelper().HowDoWeAchieveTopX(topX.Value);
+            top = sh.HowDoWeAchieveTopX(topX.Value);
 
         var sb = new StringBuilder("SELECT ");
 
         if (top?.Location == QueryComponent.SELECT) sb.AppendLine(top.SQL);
 
-        sb.AppendLine($" * FROM {run.GetFullyQualifiedName()}  {where} ORDER BY ID desc");
+        sb.AppendLine($" * FROM {run.GetFullyQualifiedName()}  {where} ORDER BY {sh.EnsureWrapped("ID")} desc");
 
         if (top?.Location == QueryComponent.Postfix) sb.AppendLine(top.SQL);
 
@@ -204,7 +207,8 @@ public IEnumerable<ArchivalDataLoadInfo> GetArchivalDataLoadInfos(string dataTas
 
     private static int GetDataTaskId(string dataTask, DiscoveredServer server, DbConnection con)
     {
-        using var cmd = server.GetCommand("SELECT ID FROM DataLoadTask WHERE name = @name", con);
+        var sh = server.GetQuerySyntaxHelper();
+        using var cmd = server.GetCommand($"SELECT {sh.EnsureWrapped("ID")} FROM {sh.EnsureWrapped("DataLoadTask")} WHERE name = @name", con);
         var p = cmd.CreateParameter();
         p.ParameterName = "@name";
         p.Value = dataTask;
@@ -236,9 +240,10 @@ public IDataLoadInfo CreateDataLoadInfo(string dataLoadTaskName, string packageN
     public void CreateNewLoggingTask(int id, string dataSetID)
     {
         using var conn = Server.GetConnection();
+        var sh = Server.GetQuerySyntaxHelper();
         conn.Open();
         var sql =
-            $"INSERT INTO DataLoadTask (ID, description, name, createTime, userAccount, statusID, isTest, dataSetID) VALUES ({id}, @dataSetID, @dataSetID, @date, @username, 1, 0, @dataSetID)";
+            $"INSERT INTO {sh.EnsureWrapped("DataLoadTask")} ({sh.EnsureWrapped("ID")}, description, name, {sh.EnsureWrapped("createTime")}, {sh.EnsureWrapped("userAccount")}, {sh.EnsureWrapped("statusID")}, {sh.EnsureWrapped("isTest")}, {sh.EnsureWrapped("dataSetID")}) VALUES ({id}, @dataSetID, @dataSetID, @date, @username, 1, {sh.False}, @dataSetID)";
 
         using var cmd = Server.GetCommand(sql, conn);
         Server.AddParameterWithValueToCommand("@date", cmd, DateTime.Now);
@@ -251,9 +256,10 @@ public void CreateNewLoggingTask(int id, string dataSetID)
     private void CreateNewDataSet(string datasetName)
     {
         using var conn = Server.GetConnection();
+        var sh = Server.GetQuerySyntaxHelper();
         conn.Open();
         {
-            const string sql = "INSERT INTO DataSet (dataSetID,name) VALUES (@datasetName,@datasetName)";
+            var sql = $"INSERT INTO {sh.EnsureWrapped("DataSet")} ({sh.EnsureWrapped("dataSetID")},name) VALUES (@datasetName,@datasetName)";
 
             using var cmd = Server.GetCommand(sql, conn);
             Server.AddParameterWithValueToCommand("@datasetName", cmd, datasetName.Substring(Math.Max(0, datasetName.Length - 150)));
@@ -274,8 +280,9 @@ public void CreateNewLoggingTaskIfNotExists(string toCreate)
     private int GetMaxTaskID()
     {
         using var conn = Server.GetConnection();
+        var sh = Server.GetQuerySyntaxHelper();
         conn.Open();
-        const string sql = "SELECT MAX(ID) FROM DataLoadTask";
+        var sql = $"SELECT MAX({sh.EnsureWrapped("ID")}) FROM {sh.EnsureWrapped("DataLoadTask")}";
 
         using var cmd = Server.GetCommand(sql, conn);
         var result = cmd.ExecuteScalar();
@@ -285,9 +292,10 @@ private int GetMaxTaskID()
     public void ResolveFatalErrors(int[] ids, DataLoadInfo.FatalErrorStates newState, string newExplanation)
     {
         using var conn = Server.GetConnection();
+        var sh = Server.GetQuerySyntaxHelper();
         conn.Open();
         var sql =
-            $"UPDATE FatalError SET explanation =@explanation, statusID=@statusID where ID in ({string.Join(",", ids)})";
+            $"UPDATE {sh.EnsureWrapped("FatalError")} SET explanation =@explanation, {sh.EnsureWrapped("statusID")}=@statusID where {sh.EnsureWrapped("ID")} in ({string.Join(",", ids)})";
 
         using var cmd = Server.GetCommand(sql, conn);
         Server.AddParameterWithValueToCommand("@explanation", cmd, newExplanation);
@@ -298,4 +306,4 @@ public void ResolveFatalErrors(int[] ids, DataLoadInfo.FatalErrorStates newState
             throw new Exception(
                 $"Query {sql} resulted in {affectedRows}, we were expecting there to be {ids.Length} updates because that is how many FatalError IDs that were passed to this method");
     }
-}
+}
diff --git a/SharedAssemblyInfo.cs b/SharedAssemblyInfo.cs
@@ -10,6 +10,6 @@
 [assembly: AssemblyTrademark("")]
 [assembly: AssemblyCulture("")]
 
-[assembly: AssemblyVersion("8.3.0")]
-[assembly: AssemblyFileVersion("8.3.0")]
-[assembly: AssemblyInformationalVersion("8.3.0")]
+[assembly: AssemblyVersion("8.3.1")]
+[assembly: AssemblyFileVersion("8.3.1")]
+[assembly: AssemblyInformationalVersion("8.3.1")]
diff --git a/Tools/rdmp/CommandLine/Gui/ConsoleGuiCohortIdentificationConfigurationUI.cs b/Tools/rdmp/CommandLine/Gui/ConsoleGuiCohortIdentificationConfigurationUI.cs
@@ -140,38 +140,40 @@ private void Tableview1_CellActivated(TableView.CellActivatedEventArgs obj)
         var o = RowObjects[obj.Row];
         if (o == null)
             return;
+
         var col = tableview1.Table.Columns[obj.Col];
 
-        if (col.ColumnName.Equals("Name"))
+        switch (col.ColumnName)
         {
-            var factory = new ConsoleGuiContextMenuFactory(_activator);
-            var menu = factory.Create(Array.Empty<object>(), o);
-
-            if (menu != null)
+            case "Name":
             {
                 var p = tableview1.CellToScreen(obj.Col, obj.Row);
 
                 if (p == null)
                     return;
 
-                menu.Position = p.Value;
-                _contextMenuShowing = true;
-                menu.Show();
-                menu.MenuBar.MenuAllClosed += () => _contextMenuShowing = false;
+                var factory = new ConsoleGuiContextMenuFactory(_activator);
+                var menu = factory.Create(p.Value.X, p.Value.Y, Array.Empty<object>(), o);
+                if (menu != null)
+                {
+                    menu.Position = p.Value;
+                    _contextMenuShowing = true;
+                    menu.Show();
+                    menu.MenuBar.MenuAllClosed += () => _contextMenuShowing = false;
+                }
+
+                break;
             }
-        }
-
-        if (col.ColumnName.Equals("Working"))
-        {
-            var key = Common.GetKey(o);
-            if (key?.CrashMessage != null)
+            case "Working":
             {
-                _activator.ShowException("Task Crashed", key.CrashMessage);
-                return;
+                var key = Common.GetKey(o);
+                if (key?.CrashMessage != null) _activator.ShowException("Task Crashed", key.CrashMessage);
+                break;
             }
+            case "Execute":
+                Common.ExecuteOrCancel(o, int.MaxValue);
+                break;
         }
-
-        if (col.ColumnName.Equals("Execute")) Common.ExecuteOrCancel(o, Common.Timeout);
     }
 
     private bool IsValidSelection(int col, int row)

diff --git a/Tools/rdmp/CommandLine/Gui/ConsoleGuiContextMenuFactory.cs b/Tools/rdmp/CommandLine/Gui/ConsoleGuiContextMenuFactory.cs
@@ -28,7 +28,7 @@ public ConsoleGuiContextMenuFactory(IBasicActivateItems activator)
         this.activator = activator;
     }
 
-    public ContextMenu Create(object[] many, object single)
+    public ContextMenu Create(int x,int y,object[] many, object single)
     {
         var commands = GetCommands(activator, many, single).ToArray();
 
@@ -65,18 +65,16 @@ public ContextMenu Create(object[] many, object single)
             items.Add(bar);
         }
 
-        // we can do nothing if theres no menu items
+        // we can do nothing if there are no menu items
         if (items.Count == 0)
             return null;
 
         var withSpacers = AddSpacers(items, order);
 
-        var menu = new ContextMenu
+        return new ContextMenu(x, y, new MenuBarItem(withSpacers))
         {
-            MenuItems = new MenuBarItem(withSpacers)
+            UseSubMenusSingleFrame = true
         };
-
-        return menu;
     }
 
     private static MenuItem[] AddSpacers(List<MenuItem> items, Dictionary<MenuItem, float> order)

diff --git a/Tools/rdmp/CommandLine/Gui/ConsoleMainWindow.cs b/Tools/rdmp/CommandLine/Gui/ConsoleMainWindow.cs
@@ -17,6 +17,7 @@
 using Rdmp.Core.MapsDirectlyToDatabaseTable;
 using Rdmp.Core.Providers;
 using Rdmp.Core.Providers.Nodes;
+using Rdmp.Core.ReusableLibraryCode.Annotations;
 using Rdmp.Core.ReusableLibraryCode.Settings;
 using Terminal.Gui;
 using Terminal.Gui.Trees;
@@ -27,7 +28,7 @@ internal class ConsoleMainWindow
 {
     private Window _win;
     private TreeView<object> _treeView;
-    private IBasicActivateItems _activator;
+    private readonly IBasicActivateItems _activator;
 
     /// <summary>
     /// The last <see cref="IBasicActivateItems"/> passed to this UI.
@@ -167,7 +168,7 @@ internal void SetUp(Toplevel top)
         var statusBar = new StatusBar(new StatusItem[]
         {
             new(Key.Q | Key.CtrlMask, "~^Q~ Quit", Quit),
-            new(Key.R | Key.CtrlMask, "~^R~ Run", action: Run),
+            new(Key.R | Key.CtrlMask, "~^R~ Run", Run),
             new(Key.F | Key.CtrlMask, "~^F~ Find", Find),
             new(Key.N | Key.CtrlMask, "~^N~ New", New),
             new(Key.F5, "~F5~ Refresh", Publish)
@@ -252,21 +253,18 @@ private void _treeView_ObjectActivated(ObjectActivatedEventArgs<object> obj)
 
     private string AspectGetter(object model)
     {
-        if (model is IContainer container) return $"{container} ({container.Operation})";
-
-        if (model is CohortAggregateContainer setContainer) return $"{setContainer} ({setContainer.Operation})";
-
-        if (model is ExtractionInformation ei) return $"{ei} ({ei.ExtractionCategory})";
-
-        if (model is CatalogueItemsNode cin) return $"{cin} ({cin.CatalogueItems.Length})";
-
-        if (model is TableInfoServerNode server) return $"{server.ServerName} ({server.DatabaseType})";
-
-        if (model is IDisableable d) return d.IsDisabled ? $"{d} (Disabled)" : d.ToString();
-
-        return model is IArgument arg
-            ? $"{arg} ({(string.IsNullOrWhiteSpace(arg.Value) ? "Null" : arg.Value)})"
-            : model?.ToString() ?? "Null Object";
+        return model switch
+        {
+            IContainer container => $"{container} ({container.Operation})",
+            CohortAggregateContainer setContainer => $"{setContainer} ({setContainer.Operation})",
+            ExtractionInformation ei => $"{ei} ({ei.ExtractionCategory})",
+            CatalogueItemsNode cin => $"{cin} ({cin.CatalogueItems.Length})",
+            TableInfoServerNode server => $"{server.ServerName} ({server.DatabaseType})",
+            IDisableable d => d.IsDisabled ? $"{d} (Disabled)" : d.ToString(),
+            _ => model is IArgument arg
+                ? $"{arg} ({(string.IsNullOrWhiteSpace(arg.Value) ? "Null" : arg.Value)})"
+                : model?.ToString() ?? "Null Object"
+        };
     }
 
     private void Publish()
@@ -337,7 +335,7 @@ private void Show(object selected)
         _treeView.SetNeedsDisplay();
     }
 
-    private void _treeView_SelectionChanged(object sender, SelectionChangedEventArgs<object> e)
+    private void _treeView_SelectionChanged(object sender, [NotNull] SelectionChangedEventArgs<object> e)
     {
         if (e.NewValue != null)
             _treeView.RefreshObject(e.NewValue);
@@ -346,13 +344,9 @@ private void _treeView_SelectionChanged(object sender, SelectionChangedEventArgs
     private void Menu()
     {
         var factory = new ConsoleGuiContextMenuFactory(_activator);
-        var menu = factory.Create(_treeView.GetAllSelectedObjects().ToArray(), _treeView.SelectedObject);
-
-        if (menu == null)
-            return;
-
-        menu.Position = DateTime.Now.Subtract(_lastMouseMove).TotalSeconds < 1 ? _lastMousePos : new Point(10, 5);
-        menu.Show();
+        var position = DateTime.Now.Subtract(_lastMouseMove).TotalSeconds < 1 ? _lastMousePos : new Point(10, 5);
+        var menu = factory.Create(position.X,position.Y,_treeView.GetAllSelectedObjects().ToArray(), _treeView.SelectedObject);
+        menu?.Show();
     }