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Recognize Koina libraries in the spectral library validation step for Panorama Public #460

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Merged
vagisha merged 1 commit into from
Nov 19, 2024
Merged

Recognize Koina libraries in the spectral library validation step for Panorama Public #460

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19 changes: 14 additions & 5 deletions panoramapublic/src/org/labkey/panoramapublic/model/validation/SpecLibValidation.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package org.labkey.panoramapublic.model.validation;

import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.panoramapublic.model.speclib.SpecLibInfo;
Expand Down Expand Up @@ -197,7 +198,7 @@ public String getStatusString()
}
if (isPrositLibrary())
{
return "Prosit Library";
return "Prosit / Koina Library";
}
if (hasSpectrumFiles() && foundSpectrumFiles() && hasIdFiles() && foundIdFiles())
{
Expand Down Expand Up @@ -301,12 +302,20 @@ public List<String> getMissingIdFileNames()

public boolean isPrositLibrary()
{
// For a library based on Prosit we expect only one row in the SpectrumSourceFiles table,
// We expect idFileName to be blank and the value in the fileName column to be "Prositintensity_prosit_publication_v1".
// The value in the fileName column may be different in Skyline 21.1. This code will be have to be updated then.
// For a library based on Prosit/Koina we expect only one row in the SpectrumSourceFiles table,
// We expect idFileName to be blank.
// The value in the fileName column is "Prositintensity_prosit_publication_v1" for versions of Skyline that built
// the library using the legacy Prosit server.
// Skyline switched from Prosit to the new Koina framework (https://github.com/ProteoWizard/pwiz/pull/2900).
// Skyline now prefixes "Koina-" to the model names in the SpectrumSourceFiles.fileName column.
// For example: Koina-Prosit_2020_intensity_HCD-Prosit_2019_irt where
// Prosit_2020_intensity_HCD is the intensity model and Prosit_2019_irt is the retention time model. Skyline
// supports multiple Koina models.
if(isBibliospecLibrary() && getSpectrumFiles().size() == 1 && getIdFiles().size() == 0)
{
return "Prositintensity_prosit_publication_v1".equals(getSpectrumFiles().get(0).getName());
String modelName = getSpectrumFiles().get(0).getName();
return "Prositintensity_prosit_publication_v1".equals(modelName)
|| StringUtils.startsWith(modelName, "Koina-");
}
return false;
}
Expand Down