From 77318a45413cb51b8ddf80f2b34728b52179dd9d Mon Sep 17 00:00:00 2001 From: James Friel Date: Mon, 9 Mar 2026 13:39:55 +0000 Subject: [PATCH 1/6] bump for rdmp 9.2.0 --- .github/workflows/dotnet-core.yml | 2 +- RDMP | 2 +- SharedAssemblyInfo.cs | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/dotnet-core.yml b/.github/workflows/dotnet-core.yml index ca690cf..94e52ef 100644 --- a/.github/workflows/dotnet-core.yml +++ b/.github/workflows/dotnet-core.yml @@ -15,7 +15,7 @@ jobs: - uses: actions/checkout@v4 with: repository: HicServices/RDMP - ref: v9.0.0-rc1 + ref: v9.2.0-rc1 path: RDMP - uses: actions/setup-dotnet@v4 with: diff --git a/RDMP b/RDMP index 2d888af..53516e7 160000 --- a/RDMP +++ b/RDMP @@ -1 +1 @@ -Subproject commit 2d888af249bae7208efbef1a73135938edb71c94 +Subproject commit 53516e795a294c5cc9786f7bf339bfd4b26155fb diff --git a/SharedAssemblyInfo.cs b/SharedAssemblyInfo.cs index 07963d1..5395179 100644 --- a/SharedAssemblyInfo.cs +++ b/SharedAssemblyInfo.cs @@ -10,6 +10,6 @@ [assembly: AssemblyCulture("")] // These should be overwritten by release builds -[assembly: AssemblyVersion("6.1.15")] -[assembly: AssemblyFileVersion("6.1.15")] -[assembly: AssemblyInformationalVersion("6.1.15")] +[assembly: AssemblyVersion("6.1.16")] +[assembly: AssemblyFileVersion("6.1.16")] +[assembly: AssemblyInformationalVersion("6.1.16")] From 410db020bdfa557838dc00544746e96aba50f976 Mon Sep 17 00:00:00 2001 From: James Friel Date: Mon, 9 Mar 2026 13:48:49 +0000 Subject: [PATCH 2/6] update deps --- HICPluginTests/HICPluginTests.csproj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HICPluginTests/HICPluginTests.csproj b/HICPluginTests/HICPluginTests.csproj index 58fccdc..6e5297b 100644 --- a/HICPluginTests/HICPluginTests.csproj +++ b/HICPluginTests/HICPluginTests.csproj @@ -11,7 +11,7 @@ - + all From ff290114625a5936b1b16ffd8ca69c6ab7badded Mon Sep 17 00:00:00 2001 From: James Friel Date: Mon, 9 Mar 2026 14:05:01 +0000 Subject: [PATCH 3/6] fix rdmp update --- HICPlugin/DataFlowComponents/CHIColumnFinder.cs | 8 ++++++-- .../ForceHICTableNamingConventionForProjects.cs | 16 ++++++++-------- .../HICCohortManagerDestination.cs | 17 +++++++++-------- 3 files changed, 23 insertions(+), 18 deletions(-) diff --git a/HICPlugin/DataFlowComponents/CHIColumnFinder.cs b/HICPlugin/DataFlowComponents/CHIColumnFinder.cs index 94c678f..8525edc 100644 --- a/HICPlugin/DataFlowComponents/CHIColumnFinder.cs +++ b/HICPlugin/DataFlowComponents/CHIColumnFinder.cs @@ -465,9 +465,13 @@ public void PreInitialize(IExtractCommand value, IDataLoadEventListener listener } } - public void PreInitialize(IBasicActivateItems value, IDataLoadEventListener listener) + public void PreInitialize(IBasicActivateItems activator, IExtractCommand value, IDataLoadEventListener listener) { - _activator = value; + _activator = activator; } + public void PreInitialize(IBasicActivateItems activator, IBasicActivateItems value, IDataLoadEventListener listener) + { + _activator = activator; + } } \ No newline at end of file diff --git a/HICPlugin/DataFlowComponents/ForceHICTableNamingConventionForProjects.cs b/HICPlugin/DataFlowComponents/ForceHICTableNamingConventionForProjects.cs index 14a97ba..d0ba179 100644 --- a/HICPlugin/DataFlowComponents/ForceHICTableNamingConventionForProjects.cs +++ b/HICPlugin/DataFlowComponents/ForceHICTableNamingConventionForProjects.cs @@ -2,6 +2,7 @@ using System.ComponentModel; using System.Data; using System.Text.RegularExpressions; +using Rdmp.Core.CommandExecution; using Rdmp.Core.Curation.Data; using Rdmp.Core.DataFlowPipeline; using Rdmp.Core.DataFlowPipeline.Requirements; @@ -30,14 +31,6 @@ public void Abort(IDataLoadEventListener listener) } - public void PreInitialize(TableInfo target,IDataLoadEventListener listener) - { - if (!NamingConvention.IsMatch(target.GetRuntimeName())) - listener.OnNotify(this,new NotifyEventArgs(ProgressEventType.Error, - $"TableInfo {target} does not match hic regex for naming conventions of project/group data ({NamingConvention})")); - } - - public void Check(ICheckNotifier notifier) { @@ -45,4 +38,11 @@ public void Check(ICheckNotifier notifier) [GeneratedRegex("tt_\\d*", RegexOptions.Compiled)] private static partial Regex TtPrefix(); + + public void PreInitialize(IBasicActivateItems activator, TableInfo value, IDataLoadEventListener listener) + { + if (!NamingConvention.IsMatch(value.GetRuntimeName())) + listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Error, + $"TableInfo {value} does not match hic regex for naming conventions of project/group data ({NamingConvention})")); + } } \ No newline at end of file diff --git a/HICPlugin/DataFlowComponents/HICCohortManagerDestination.cs b/HICPlugin/DataFlowComponents/HICCohortManagerDestination.cs index 0cfb669..265f861 100644 --- a/HICPlugin/DataFlowComponents/HICCohortManagerDestination.cs +++ b/HICPlugin/DataFlowComponents/HICCohortManagerDestination.cs @@ -10,6 +10,7 @@ using Rdmp.Core.DataLoad.Engine.Pipeline.Destinations; using Rdmp.Core.ReusableLibraryCode.Checks; using Rdmp.Core.ReusableLibraryCode.Progress; +using Rdmp.Core.CommandExecution; namespace HICPlugin.DataFlowComponents; @@ -87,7 +88,7 @@ public void Dispose(IDataLoadEventListener listener, Exception pipelineFailureEx dest.AddExplicitWriteType(_privateIdentifier, "varchar(10)"); dest.AllowResizingColumnsAtUploadTime = true; - dest.PreInitialize(cohortDatabase,listener); + dest.PreInitialize(null,cohortDatabase,listener); dest.ProcessPipelineData(AllAtOnceDataTable, listener, new GracefulCancellationToken()); dest.Dispose(listener,null); @@ -167,13 +168,6 @@ public void Abort(IDataLoadEventListener listener) } - public void PreInitialize(ICohortCreationRequest value, IDataLoadEventListener listener) - { - Request = value; - var syntaxHelper = value.NewCohortDefinition.LocationOfCohort.GetQuerySyntaxHelper(); - _privateIdentifier = syntaxHelper.GetRuntimeName(Request.NewCohortDefinition.LocationOfCohort.PrivateIdentifierField); - } - public void Check(ICheckNotifier notifier) { @@ -211,4 +205,11 @@ public void Check(ICheckNotifier notifier) } + + public void PreInitialize(IBasicActivateItems activator, ICohortCreationRequest value, IDataLoadEventListener listener) + { + Request = value; + var syntaxHelper = value.NewCohortDefinition.LocationOfCohort.GetQuerySyntaxHelper(); + _privateIdentifier = syntaxHelper.GetRuntimeName(Request.NewCohortDefinition.LocationOfCohort.PrivateIdentifierField); + } } \ No newline at end of file From b3c58263cb302aad36866ba77d4138187d3f8aea Mon Sep 17 00:00:00 2001 From: James Friel Date: Mon, 9 Mar 2026 14:12:39 +0000 Subject: [PATCH 4/6] update --- HICPlugin/BespokeAttachers/MetIDQAttacher.cs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HICPlugin/BespokeAttachers/MetIDQAttacher.cs b/HICPlugin/BespokeAttachers/MetIDQAttacher.cs index 7edb180..b4998dd 100644 --- a/HICPlugin/BespokeAttachers/MetIDQAttacher.cs +++ b/HICPlugin/BespokeAttachers/MetIDQAttacher.cs @@ -44,7 +44,7 @@ public ExitCodeType Attach(IDataLoadJob job, GracefulCancellationToken token) //Read it all in one go MaxBatchSize = int.MaxValue }; - fromCSV.PreInitialize(new FlatFileToLoad(file),job); + fromCSV.PreInitialize(null,new FlatFileToLoad(file),job); fromCSV.GetChunk(job, new GracefulCancellationToken()); From 1f1b4f476f750fbc4796a4c5718e769dbbb0163e Mon Sep 17 00:00:00 2001 From: James Friel Date: Mon, 9 Mar 2026 14:24:22 +0000 Subject: [PATCH 5/6] fix file --- DrsPlugin/Extraction/ImageExtraction.cs | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/DrsPlugin/Extraction/ImageExtraction.cs b/DrsPlugin/Extraction/ImageExtraction.cs index e41e229..274179c 100644 --- a/DrsPlugin/Extraction/ImageExtraction.cs +++ b/DrsPlugin/Extraction/ImageExtraction.cs @@ -1,4 +1,5 @@ -using Rdmp.Core.Curation.Data; +using Rdmp.Core.CommandExecution; +using Rdmp.Core.Curation.Data; using Rdmp.Core.Curation.Data.DataLoad; using Rdmp.Core.DataExport.DataExtraction.Commands; using Rdmp.Core.DataFlowPipeline; @@ -46,7 +47,7 @@ protected bool PreProcessingCheck(IDataLoadEventListener listener) } - public void PreInitialize(IExtractCommand request, IDataLoadEventListener listener) + public void PreInitialize(IBasicActivateItems activator, IExtractCommand request, IDataLoadEventListener listener) { Request = request as IExtractDatasetCommand; From f333569f12389f9cbe4867f8550f7f1358c854f5 Mon Sep 17 00:00:00 2001 From: James Friel Date: Mon, 9 Mar 2026 14:31:57 +0000 Subject: [PATCH 6/6] fix tests --- HICPluginTests/ExtractionTests.cs | 6 +++--- .../Integration/ChrisHallSpecialExplicitSourceTests.cs | 2 +- HICPluginTests/Integration/HICCohortDestinationTest.cs | 2 +- HICPluginTests/Integration/SCIStoreCacheDestinationTests.cs | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/HICPluginTests/ExtractionTests.cs b/HICPluginTests/ExtractionTests.cs index 0fcb99f..16bfb96 100644 --- a/HICPluginTests/ExtractionTests.cs +++ b/HICPluginTests/ExtractionTests.cs @@ -87,7 +87,7 @@ public void ExtractionTestWithZipArchive() AppendIndexCountToFileName = false }; - extractionComponent.PreInitialize(request, listener); + extractionComponent.PreInitialize(null,request, listener); var cts = new GracefulCancellationTokenSource(); var dt = extractionComponent.ProcessPipelineData(dataset, listener, cts.Token); @@ -165,7 +165,7 @@ public void ExtractionTestWithTarArchive() AppendIndexCountToFileName = false }; - extractionComponent.PreInitialize(request, listener); + extractionComponent.PreInitialize(null,request, listener); var cts = new GracefulCancellationTokenSource(); var dt = extractionComponent.ProcessPipelineData(dataset, listener, cts.Token); @@ -227,7 +227,7 @@ public void ExtractionTestWithNullImageFilename() PathToImageArchive = rootDir.FullName }; - extractionComponent.PreInitialize(request, listener); + extractionComponent.PreInitialize(null,request, listener); var cts = new GracefulCancellationTokenSource(); Assert.DoesNotThrow(() => extractionComponent.ProcessPipelineData(dataset, listener, cts.Token)); diff --git a/HICPluginTests/Integration/ChrisHallSpecialExplicitSourceTests.cs b/HICPluginTests/Integration/ChrisHallSpecialExplicitSourceTests.cs index d68f43b..31c1153 100644 --- a/HICPluginTests/Integration/ChrisHallSpecialExplicitSourceTests.cs +++ b/HICPluginTests/Integration/ChrisHallSpecialExplicitSourceTests.cs @@ -19,7 +19,7 @@ public void TestUse() Collation = "Latin1_General_Bin" }; - source.PreInitialize(_request,ThrowImmediatelyDataLoadEventListener.Quiet); + source.PreInitialize(null, _request,ThrowImmediatelyDataLoadEventListener.Quiet); var chunk = source.GetChunk(ThrowImmediatelyDataLoadEventListener.Quiet, new GracefulCancellationToken()); Assert.That(chunk, Is.Not.Null); diff --git a/HICPluginTests/Integration/HICCohortDestinationTest.cs b/HICPluginTests/Integration/HICCohortDestinationTest.cs index 92d2ce4..5a23728 100644 --- a/HICPluginTests/Integration/HICCohortDestinationTest.cs +++ b/HICPluginTests/Integration/HICCohortDestinationTest.cs @@ -55,7 +55,7 @@ @description varchar(10) NewCohortsStoredProcedure = "fishfishfishproc1", ExistingCohortsStoredProcedure = "fishfishfishproc2" }; - d.PreInitialize(request,ThrowImmediatelyDataLoadEventListener.Quiet); + d.PreInitialize(null,request,ThrowImmediatelyDataLoadEventListener.Quiet); d.CreateExternalCohort = true; var dt = new DataTable("mytbl"); diff --git a/HICPluginTests/Integration/SCIStoreCacheDestinationTests.cs b/HICPluginTests/Integration/SCIStoreCacheDestinationTests.cs index 4ec4b54..8d20be2 100644 --- a/HICPluginTests/Integration/SCIStoreCacheDestinationTests.cs +++ b/HICPluginTests/Integration/SCIStoreCacheDestinationTests.cs @@ -81,7 +81,7 @@ public void ProcessPipelineDataTest() }; - component.PreInitialize(deleteMe,ThrowImmediatelyDataLoadEventListener.Quiet); + component.PreInitialize(null,deleteMe,ThrowImmediatelyDataLoadEventListener.Quiet); component.ProcessPipelineData((ICacheChunk)cacheChunk, ThrowImmediatelyDataLoadEventListener.Quiet, new GracefulCancellationToken()); var downloadDir = Path.Combine(rootDirectory.FullName, "T", "Biochemistry");