From 9115c35921053e482d16453711aaa5119ffb0822 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Thu, 21 Nov 2024 16:36:07 -0500 Subject: [PATCH 1/3] Change default Koina URL Requested by Koina dev. --- .../Skyline/Model/Koina/Config/KoinaConfig_development.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pwiz_tools/Skyline/Model/Koina/Config/KoinaConfig_development.xml b/pwiz_tools/Skyline/Model/Koina/Config/KoinaConfig_development.xml index c9ac4490f1..4fa997bc7f 100644 --- a/pwiz_tools/Skyline/Model/Koina/Config/KoinaConfig_development.xml +++ b/pwiz_tools/Skyline/Model/Koina/Config/KoinaConfig_development.xml @@ -1,4 +1,4 @@ - koina.proteomicsdb.org:443 - \ No newline at end of file + koina.wilhelmlab.org:443 + From f33125227db13bd3e633c0b1b10f20ffc716d66c Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Fri, 22 Nov 2024 10:49:52 -0500 Subject: [PATCH 2/3] Reduce precision requirement for checking Koina peak intensities --- .../Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs b/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs index 289db7024d..381c9cf3d8 100644 --- a/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs +++ b/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs @@ -277,7 +277,7 @@ void comparePredictionResultsToFile(string intensityModel, string rtModel, bool var expectedPeak = expected.Peaks[i]; var actualPeak = actualPeaks[i]; Assert.AreEqual(expectedPeak.Mz, actualPeak.Mz, 1e-5, $"{testTag}: peak[{i}].Mz not equal"); - Assert.AreEqual(expectedPeak.Intensity, actualPeak.Intensity, 1e-5, $"{testTag}: peak[{i}].Intensity not equal"); + Assert.AreEqual(expectedPeak.Intensity, actualPeak.Intensity, 1e-4, $"{testTag}: peak[{i}].Intensity not equal"); } } } From d922177bab191e5dfa9a52f5dbea77a44032c719 Mon Sep 17 00:00:00 2001 From: Matt Chambers Date: Mon, 25 Nov 2024 11:53:25 -0500 Subject: [PATCH 3/3] Relax RT and intensity epsilon to 1e-2 M/z epsilon is still tight. --- .../Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs b/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs index 381c9cf3d8..9cefc52c8f 100644 --- a/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs +++ b/pwiz_tools/Skyline/TestConnected/KoinaBuildLibraryFromCsvTest.cs @@ -265,7 +265,7 @@ void comparePredictionResultsToFile(string intensityModel, string rtModel, bool var expected = predictionTests[testIndex++]; Assert.AreEqual(expected.PrecursorMz, precursorMz, 1e-8, $"{testTag}: PrecursorMz not equal"); Assert.AreEqual(expected.PrecursorCharge, key.Charge, $"{testTag}: PrecursorCharge not equal"); - Assert.AreEqual(expected.RetentionTime, spectrum.RetentionTime.Value, 1e-5, $"{testTag}: RetentionTime not equal"); + Assert.AreEqual(expected.RetentionTime, spectrum.RetentionTime.Value, 1e-2, $"{testTag}: RetentionTime not equal"); if (!comparePeaks) continue; @@ -277,7 +277,7 @@ void comparePredictionResultsToFile(string intensityModel, string rtModel, bool var expectedPeak = expected.Peaks[i]; var actualPeak = actualPeaks[i]; Assert.AreEqual(expectedPeak.Mz, actualPeak.Mz, 1e-5, $"{testTag}: peak[{i}].Mz not equal"); - Assert.AreEqual(expectedPeak.Intensity, actualPeak.Intensity, 1e-4, $"{testTag}: peak[{i}].Intensity not equal"); + Assert.AreEqual(expectedPeak.Intensity, actualPeak.Intensity, 1e-2, $"{testTag}: peak[{i}].Intensity not equal"); } } }