Add Catch for Junk CHI in SCI Store Loader (#78)

* add sci update * use specified release * update shared assembly * clone dt columns * add better logging * fix bad error message * throw for bad chi * tidy up code
HicServices · Jul 17, 2024 · fd421e2 · fd421e2
1 parent cadb652
commit fd421e2
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Showing 3 changed files with 10 additions and 10 deletions.
diff --git a/SCIStorePlugin/Attachers/SciStoreAttacher.cs b/SCIStorePlugin/Attachers/SciStoreAttacher.cs
@@ -20,7 +20,7 @@ namespace SCIStorePlugin.Attachers;
 [Description(@"Populates the RAW database from XML files retrieved from the SCI Store web service in the ForLoading directory")]
 public class SciStoreAttacher : Attacher
 {
-    public string HeaderTable ="Header";
+    public string HeaderTable = "Header";
     public string SamplesTable = "SampleDetails";
     public string ResultsTable = "Results";
     private Stopwatch _timer;
@@ -31,7 +31,7 @@ public class SciStoreAttacher : Attacher
 
     [DemandsInitialization(@"Determines behaviour when bad reports are encountered e.g. LabNumbers like 000000000.  
 True - Report warning and continue (not loading file)
-False - Stop the data load with an error",DefaultValue = true)]
+False - Stop the data load with an error", DefaultValue = true)]
     public bool IgnoreBadData { get; set; }
 
     public SciStoreAttacher()
@@ -45,7 +45,7 @@ public SciStoreAttacher()
     /// <param name="job"></param>
     /// <returns></returns>
     /// <exception cref="BadCombinedReportDataException"></exception>
-    public override ExitCodeType Attach(IDataLoadJob job,GracefulCancellationToken token)
+    public override ExitCodeType Attach(IDataLoadJob job, GracefulCancellationToken token)
     {
         // Create the DataTable repository into which the XML files will be loaded into prior to their bulk insert into RAW
         var dataTableSchemaSource = new DataTableSchemaFromDatabase(_dbInfo);
@@ -78,7 +78,7 @@ public override ExitCodeType Attach(IDataLoadJob job,GracefulCancellationToken t
             {
                 labs = reports
                     .Select(report => reportFactory.Create(report, job))
-                    .Where(r=>r != null) //bad reports are null
+                    .Where(r => r != null) //bad reports are null
                     .ToList();
             }
             catch (BadCombinedReportDataException e)
@@ -111,7 +111,6 @@ public override ExitCodeType Attach(IDataLoadJob job,GracefulCancellationToken t
             BulkInsertDataTable(destRepo.HeadersTable, job);
             BulkInsertDataTable(destRepo.SampleDetailsTable, job);
             BulkInsertDataTable(destRepo.ResultsTable, job);
-
             _timer.Stop();
 
             job.OnNotify(this, new NotifyEventArgs(ProgressEventType.Information, "SciStoreAttacher::Attach complete"));
@@ -162,7 +161,7 @@ private void CreateReadCodeConstraint()
         };
     }
 
-    public override void LoadCompletedSoDispose(ExitCodeType exitCode,IDataLoadEventListener postLoadEventListener)
+    public override void LoadCompletedSoDispose(ExitCodeType exitCode, IDataLoadEventListener postLoadEventListener)
     {
     }
 
@@ -172,9 +171,9 @@ private void ResolveTestResultOrderDuplication(List<SciStoreReport> labs, IDataL
         {
             foreach (var sample in lab.Samples)
             {
-                var recordsRemoved  = sample.ResolveTestResultOrderDuplication();
+                var recordsRemoved = sample.ResolveTestResultOrderDuplication();
                 if (recordsRemoved > 0)
-                    job.OnNotify(this,new NotifyEventArgs(ProgressEventType.Warning,
+                    job.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning,
                         $"Resolved duplicate TestResultOrder using method 'ResolveTestResultOrderDuplication' in lab number:{lab.Header.LabNumber}"));
             }
         }

diff --git a/SCIStorePlugin/Data/SciStoreHeader.cs b/SCIStorePlugin/Data/SciStoreHeader.cs
@@ -109,7 +109,8 @@ private static string CleanCHI(string chi)
         // encountered in Fife Haematology load
         if (!string.IsNullOrWhiteSpace(chi) && chi.Equals("Temp Residen"))
             return chi[..10];
-
+        if (chi.Length > 10)
+            throw new Exception($"CHI '{chi}' was too long");
         return chi;
     }
 

diff --git a/SharedAssemblyInfo.cs b/SharedAssemblyInfo.cs
@@ -12,4 +12,4 @@
 // These should be overwritten by release builds
 [assembly: AssemblyVersion("6.1.6")]
 [assembly: AssemblyFileVersion("6.1.6")]
-[assembly: AssemblyInformationalVersion("6.1.6")]
+[assembly: AssemblyInformationalVersion("6.1.7")]