Remove Mascot search and import support

.gitattributes

@@ -532,8 +532,6 @@ ms2/module.properties -text
 ms2/resources/credits/scripts.txt -text
 ms2/resources/queries/ms2/CometPeptides/ProteinProphet.qview.xml -text
 ms2/resources/queries/ms2/CometPeptides/SearchEngineProtein.qview.xml -text
-ms2/resources/queries/ms2/MascotPeptides/ProteinProphet.qview.xml -text
-ms2/resources/queries/ms2/MascotPeptides/SearchEngineProtein.qview.xml -text
 ms2/resources/queries/ms2/Peptides/ProteinProphet.qview.xml -text
 ms2/resources/queries/ms2/Peptides/SearchEngineProtein.qview.xml -text
 ms2/resources/queries/ms2/PhenyxPeptides/ProteinProphet.qview.xml -text
@@ -584,8 +582,6 @@ ms2/src/org/labkey/ms2/MS2Module.java -text
 ms2/src/org/labkey/ms2/MS2RunType.java -text
 ms2/src/org/labkey/ms2/MS2SearchExperimentRunType.java -text
 ms2/src/org/labkey/ms2/MS2ServiceImpl.java -text
-ms2/src/org/labkey/ms2/MascotDatExperimentDataHandler.java -text
-ms2/src/org/labkey/ms2/MascotDatImporter.java -text
 ms2/src/org/labkey/ms2/PepXmlExperimentDataHandler.java -text
 ms2/src/org/labkey/ms2/PepXmlImporter.java -text
 ms2/src/org/labkey/ms2/PeptideImporter.java -text
@@ -627,7 +623,6 @@ ms2/src/org/labkey/ms2/editElution.jsp -text
 ms2/src/org/labkey/ms2/extraExportOptions.jsp -text
 ms2/src/org/labkey/ms2/filterHeader.jsp -text
 ms2/src/org/labkey/ms2/manageViews.jsp -text
-ms2/src/org/labkey/ms2/mascotConfig.jsp -text
 ms2/src/org/labkey/ms2/ms2Admin.jsp -text
 ms2/src/org/labkey/ms2/peptideChart.jsp -text
 ms2/src/org/labkey/ms2/peptideview/AbstractMS2RunView.java -text
@@ -678,17 +673,6 @@ ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocolFactory.java -text
 ms2/src/org/labkey/ms2/pipeline/comet/CometSearchTask.java -text
 ms2/src/org/labkey/ms2/pipeline/comet/LegacyCometRun.java -text
 ms2/src/org/labkey/ms2/pipeline/comet/setCometDefaults.jsp -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotCPipelineProvider.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotClientImpl.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotConfig.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotDefaults.xml -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotImportPipelineJob.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotPipelineJob.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotRun.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchProtocol.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchProtocolFactory.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchTask.java -text
-ms2/src/org/labkey/ms2/pipeline/mascot/setMascotDefaults.jsp -text
 ms2/src/org/labkey/ms2/pipeline/phenyx/PhenyxRun.java -text
 ms2/src/org/labkey/ms2/pipeline/sequest/AbstractMultipleValueParamsValidator.java -text
 ms2/src/org/labkey/ms2/pipeline/sequest/AbstractSequestParams.java -text
@@ -782,7 +766,6 @@ ms2/src/org/labkey/ms2/reader/MGFDocumentParser.java -text
 ms2/src/org/labkey/ms2/reader/MS2Loader.java -text
 ms2/src/org/labkey/ms2/reader/MS2ModificationList.java -text
 ms2/src/org/labkey/ms2/reader/MS2XmlLoader.java -text
-ms2/src/org/labkey/ms2/reader/MascotDatLoader.java -text
 ms2/src/org/labkey/ms2/reader/ModifiedAminoAcid.java -text
 ms2/src/org/labkey/ms2/reader/MzMLDocumentParser.java -text
 ms2/src/org/labkey/ms2/reader/MzXMLDocumentParser.java -text
@@ -817,24 +800,20 @@ ms2/src/org/labkey/ms2/showPeptideProphetDetails.jsp -text
 ms2/src/org/labkey/ms2/showPeptideQuantitation.jsp -text
 ms2/src/org/labkey/ms2/showProteinGroup.jsp -text
 ms2/src/org/labkey/ms2/showSensitivityDetails.jsp -text
-ms2/src/org/labkey/ms2/testMascot.jsp -text
 ms2/test/src/org/labkey/test/ms2/AbstractMS2SearchEngineTest.java -text
 ms2/test/src/org/labkey/test/ms2/AbstractXTandemTest.java -text
 ms2/test/src/org/labkey/test/ms2/MS2PipelineFolder.java -text
 ms2/test/src/org/labkey/test/ms2/MS2TestBase.java -text
 ms2/test/src/org/labkey/test/ms2/QuantitationTest.java -text
 ms2/test/src/org/labkey/test/ms2/params/MS2EmailSuccessParams.java -text
 ms2/test/src/org/labkey/test/ms2/params/MS2TestParams.java -text
-ms2/test/src/org/labkey/test/pages/ms2/MascotConfigPage.java -text
-ms2/test/src/org/labkey/test/pages/ms2/MascotTestPage.java -text
 ms2/test/src/org/labkey/test/tests/ms2/AbstractMS2ImportTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/CometTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/MS2ExportTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/MS2ExtensionsTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/MS2GZTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/MS2Test.java -text
-ms2/test/src/org/labkey/test/tests/ms2/MascotTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/PipelineTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/SequestImportTest.java -text
 ms2/test/src/org/labkey/test/tests/ms2/XTandemShortTest.java -text

ms2/build.gradle

@@ -18,9 +18,6 @@ dependencies {
          "SQLite JDBC Driver"
       )
    )
-   implementation "net.sf.opencsv:opencsv:${opencsvVersion}"
-   compileOnly "org.projectlombok:lombok:${lombokVersion}"
-   annotationProcessor "org.projectlombok:lombok:${lombokVersion}"
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "assay"), depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: BuildUtils.getCommonAssayModuleProjectPath(project.gradle, "protein"), depProjectConfig: "apiJarFile")
    BuildUtils.addLabKeyDependency(project: project, config: "jspImplementation", depProjectPath: BuildUtils.getCommonAssayModuleProjectPath(project.gradle, "protein"), depProjectConfig: "apiJarFile")

ms2/resources/schemas/dbscripts/postgresql/ms2-26.000-26.001.sql

@@ -0,0 +1,10 @@
+/*
+ * Copyright (c) 2026 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+ALTER TABLE ms2.Runs DROP COLUMN MascotFile;
+ALTER TABLE ms2.Runs DROP COLUMN DistillerRawFile;
+
+DELETE FROM prop.Properties WHERE Set IN (SELECT Set FROM prop.PropertySets WHERE Category = 'MascotConfig');
+DELETE FROM prop.PropertySets WHERE Category = 'MascotConfig';

ms2/resources/schemas/ms2.xml

@@ -441,8 +441,6 @@
         <columnTitle>NegativeHits</columnTitle>
         <formatString>#,##0</formatString>
       </column>
-      <column columnName="MascotFile"/>
-      <column columnName="DistillerRawFile"/>
     </columns>
     <tableTitle>MS2Runs</tableTitle>
     <versionColumnName>_ts</versionColumnName>
@@ -557,8 +555,6 @@
       <column columnName="PeptideCount"/>
       <column columnName="SpectrumCount"/>
       <column columnName="NegativeHitCount"/>
-      <column columnName="MascotFile"/>
-      <column columnName="DistillerRawFile"/>
     </columns>
     <tableTitle>MS2Runs</tableTitle>
     <pkColumnName>Run</pkColumnName>

ms2/resources/views/runsOverview.html

@@ -348,11 +348,6 @@
             filterArray     : runsFilterArray
         };
 
-        if ("MASCOT" == Ext.getCmp('filter-engine').value)
-        {
-            _storeConfig.columns += ", MS2Details/MascotFile, MS2Details/DistillerRawFile";
-        }
-
         var _store = new LABKEY.ext.Store(_storeConfig);
 
         var runsGrid = new LABKEY.ext.EditorGridPanel({
@@ -426,12 +421,6 @@
         }}});
         colItems.push({boxLabel: 'Peptide', name: 'Peptide'});
         colItems.push({boxLabel: 'Protein', name: 'Protein'});
-        if ("MASCOT" == Ext.getCmp('filter-engine').value)
-        {
-            colItems.push({boxLabel: 'Query Number', name: 'QueryNumber'});
-            colItems.push({boxLabel: 'Hit Rank', name: 'HitRank'});
-            colItems.push({boxLabel: 'Decoy', name: 'Decoy'});
-        }
         formItems = [{
             xtype   : 'checkboxgroup',
             columns : 3,

ms2/src/org/labkey/ms2/BibliospecSpectrumRenderer.java

@@ -166,7 +166,7 @@ public void render(SpectrumIterator iter) throws IOException
                                 File spectraSource;
                                 if (fraction.getMzXmlURL() == null)
                                 {
-                                    // Likely a direct Mascot .dat import, with no .mzXML available. The .dat
+                                    // No .mzXML available, so point at the run instead
                                     spectraSource = new File(run.getPath());
                                 }
                                 else