fix console gapfill func for GC (#450)

* fix console gapfill func for GC * Add providerFactory to CoreTestApp process
systemsomicslab · Nov 13, 2024 · 423d925 · 423d925
1 parent 4f4f2c1
commit 423d925
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Showing 5 changed files with 5 additions and 1 deletion.
diff --git a/tests/MSDIAL5/MsdialCoreTestApp/Process/DimsProcess.cs b/tests/MSDIAL5/MsdialCoreTestApp/Process/DimsProcess.cs
@@ -124,6 +124,7 @@ private async Task<int> ExecuteAsync(MsdialDimsDataStorage storage, IDataProvide
             var alignmentFile = storage.AlignmentFiles.First();
             var factory = new DimsAlignmentProcessFactory(storage, evaluator);
             var aligner = factory.CreatePeakAligner();
+            aligner.ProviderFactory = providerFactory;
             var result = aligner.Alignment(files, alignmentFile, serializer);
             result.Save(alignmentFile);
             var align_decResults = LoadRepresentativeDeconvolutions(storage, result.AlignmentSpotProperties).ToList();

diff --git a/tests/MSDIAL5/MsdialCoreTestApp/Process/GcmsProcess.cs b/tests/MSDIAL5/MsdialCoreTestApp/Process/GcmsProcess.cs
@@ -222,6 +222,7 @@ private async Task<int> ExecuteAsync(MsdialGcmsDataStorage storage, string outpu
             var alignmentFile = storage.AlignmentFiles.First();
             var factory = new GcmsAlignmentProcessFactory(files, storage);
             var aligner = factory.CreatePeakAligner();
+            aligner.ProviderFactory = providerFactory;
             var result = aligner.Alignment(files, alignmentFile, serializer);
             result.Save(alignmentFile);
             var decResults = LoadRepresentativeDeconvolutions(storage, result.AlignmentSpotProperties);

diff --git a/tests/MSDIAL5/MsdialCoreTestApp/Process/ImmsProcess.cs b/tests/MSDIAL5/MsdialCoreTestApp/Process/ImmsProcess.cs
@@ -133,6 +133,7 @@ private async Task<int> ExecuteAsync(IMsdialDataStorage<MsdialImmsParameter> sto
             var alignmentFile = storage.AlignmentFiles.First();
             var factory = new ImmsAlignmentProcessFactory(storage, evaluator);
             var aligner = factory.CreatePeakAligner();
+            aligner.ProviderFactory = providerFactory;
             aligner.ProviderFactory = providerFactory; // TODO: I'll remove this later.
             var result = aligner.Alignment(files, alignmentFile, null);
             result.Save(alignmentFile);

diff --git a/tests/MSDIAL5/MsdialCoreTestApp/Process/LcimmsProcess.cs b/tests/MSDIAL5/MsdialCoreTestApp/Process/LcimmsProcess.cs
@@ -123,6 +123,7 @@ private async Task<int> ExecuteAsync(IMsdialDataStorage<MsdialLcImMsParameter> s
             var alignmentFile = storage.AlignmentFiles.First();
             var factory = new LcimmsAlignmentProcessFactory(storage, evaluator, providerFactory, accProviderFactory);
             var aligner = factory.CreatePeakAligner();
+            aligner.ProviderFactory = providerFactory;
             var result = aligner.Alignment(files, alignmentFile, serializer);
             result.Save(alignmentFile);
             var align_decResults = LoadRepresentativeDeconvolutions(storage, result.AlignmentSpotProperties).ToList();

diff --git a/tests/MSDIAL5/MsdialCoreTestApp/Properties/launchSettings.json b/tests/MSDIAL5/MsdialCoreTestApp/Properties/launchSettings.json
@@ -2,7 +2,7 @@
   "profiles": {
     "MsdialCoreTestApp": {
       "commandName": "Project",
-      "commandLineArgs": "gcms -i D:\\MSDIALdemo\\gcms_nominal_metabolomics\\rawdata2 -o D:\\MSDIALdemo\\gcms_nominal_metabolomics\\output -m D:\\MSDIALdemo\\wine\\pramGC.txt -p\r\n"
+      "commandLineArgs": "gcms -i D:\\MSDIALdemo\\gcms_nominal_metabolomics\\rawdata4 -o D:\\MSDIALdemo\\wine\\output2 -m D:\\MSDIALdemo\\wine\\pramGC.txt -p\r\n"
     }
   }
 }