diff --git a/src/org/labkey/targetedms/SkylineAuditLogManager.java b/src/org/labkey/targetedms/SkylineAuditLogManager.java
index f6f293d8c..9b203f9d8 100644
--- a/src/org/labkey/targetedms/SkylineAuditLogManager.java
+++ b/src/org/labkey/targetedms/SkylineAuditLogManager.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.targetedms;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.AfterClass;
 import org.junit.Assert;
 import org.junit.BeforeClass;
@@ -80,7 +81,7 @@ private class AuditLogImportContext{
     }
 
     public SkylineAuditLogManager(@NotNull Container pContainer, @NotNull User pUser) throws AuditLogException{
-        _logger = Logger.getLogger(this.getClass());
+        _logger = LogManager.getLogger(this.getClass());
         _securityMgr = new SkylineAuditLogSecurityManager(pContainer, pUser);
     }
 
@@ -448,7 +449,7 @@ public static class TestCase extends Assert
         @BeforeClass
         public static void InitTest(){
 
-            _logger = Logger.getLogger(SkylineAuditLogManager.TestCase.class.getPackageName() + ".test");
+            _logger = LogManager.getLogger(SkylineAuditLogManager.TestCase.class.getPackageName() + ".test");
             UnitTestUtil.cleanupDatabase(_docGUID);
             _user = TestContext.get().getUser();
             _container = ContainerManager.ensureContainer(JunitUtil.getTestContainer(), FOLDER_NAME);
diff --git a/src/org/labkey/targetedms/SkylineBinaryDataHandler.java b/src/org/labkey/targetedms/SkylineBinaryDataHandler.java
index 58b56a62a..a381eae2b 100644
--- a/src/org/labkey/targetedms/SkylineBinaryDataHandler.java
+++ b/src/org/labkey/targetedms/SkylineBinaryDataHandler.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.targetedms;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.Handler;
diff --git a/src/org/labkey/targetedms/SkylineDocImporter.java b/src/org/labkey/targetedms/SkylineDocImporter.java
index 523098230..b834c6fc3 100644
--- a/src/org/labkey/targetedms/SkylineDocImporter.java
+++ b/src/org/labkey/targetedms/SkylineDocImporter.java
@@ -19,7 +19,8 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
@@ -128,7 +129,7 @@ public class SkylineDocImporter
     private ProgressMonitor _progressMonitor;
 
     // Use system logger for bugs & system problems, and in cases where we don't have a pipeline logger
-    protected static final Logger _systemLog = Logger.getLogger(SkylineDocImporter.class);
+    protected static final Logger _systemLog = LogManager.getLogger(SkylineDocImporter.class);
     protected final XarContext _context;
     private int blankLabelIndex;
 
diff --git a/src/org/labkey/targetedms/SkylineFileUtils.java b/src/org/labkey/targetedms/SkylineFileUtils.java
index 477b5f8d0..fb33da6a1 100644
--- a/src/org/labkey/targetedms/SkylineFileUtils.java
+++ b/src/org/labkey/targetedms/SkylineFileUtils.java
@@ -15,18 +15,17 @@
  */
 package org.labkey.targetedms;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.api.ExpData;
-import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.util.FileUtil;
 
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.List;
 
 /**
  * User: vsharma
@@ -43,7 +42,7 @@ public class SkylineFileUtils
     public static final String EXT_BLIB = "blib";
     public static final String EXT_SKY_LOG = "skyl";
 
-    private static final Logger LOG = Logger.getLogger(SkylineFileUtils.class);
+    private static final Logger LOG = LogManager.getLogger(SkylineFileUtils.class);
 
     public static String getBaseName(String fileName)
     {
diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java b/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java
index c1c8da97e..a0768a3cd 100644
--- a/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java
+++ b/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java
@@ -1,12 +1,11 @@
 package org.labkey.targetedms.SkylinePort.Irt;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.targetedms.IrtPeptide;
 
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedHashMap;
-import java.util.List;
 
 /**
  * User: tgaluhn
diff --git a/src/org/labkey/targetedms/TargetedMSController.java b/src/org/labkey/targetedms/TargetedMSController.java
index cadf17134..6d010e010 100644
--- a/src/org/labkey/targetedms/TargetedMSController.java
+++ b/src/org/labkey/targetedms/TargetedMSController.java
@@ -20,45 +20,55 @@
 import com.keypoint.PngEncoder;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.jfree.chart.ChartFactory;
 import org.jfree.chart.ChartUtilities;
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.plot.PlotOrientation;
-import org.labkey.api.action.*;
-import org.labkey.api.analytics.AnalyticsService;
-import org.labkey.api.pipeline.PipelineJob;
-import org.labkey.api.pipeline.PipelineValidationException;
-import org.labkey.api.query.QueryDefinition;
-import org.labkey.api.security.permissions.ApplicationAdminPermission;
-import org.labkey.api.settings.AppProps;
-import org.labkey.api.targetedms.TargetedMSService;
-import org.labkey.api.targetedms.TargetedMSUrls;
-import org.labkey.api.targetedms.model.SampleFileInfo;
-import org.labkey.api.util.Button;
-import org.labkey.api.util.DOM;
-import org.labkey.api.util.DateUtil;
-import org.labkey.api.util.StringUtilsLabKey;
-import org.labkey.api.util.UnexpectedException;
-import org.labkey.api.view.*;
-import org.labkey.api.view.PopupMenu;
-import org.labkey.api.view.template.ClientDependency;
-import org.labkey.targetedms.model.GuideSet;
-import org.labkey.targetedms.model.GuideSetKey;
-import org.labkey.targetedms.model.GuideSetStats;
-import org.labkey.targetedms.model.QCPlotFragment;
-import org.labkey.targetedms.model.RawMetricDataSet;
-import org.labkey.targetedms.outliers.OutlierGenerator;
 import org.jfree.chart.title.TextTitle;
 import org.jfree.data.category.DefaultCategoryDataset;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.junit.Assert;
 import org.junit.Test;
-import org.labkey.api.data.*;
+import org.labkey.api.action.ApiResponse;
+import org.labkey.api.action.ApiSimpleResponse;
+import org.labkey.api.action.ApiUsageException;
+import org.labkey.api.action.CustomApiForm;
+import org.labkey.api.action.ExportAction;
+import org.labkey.api.action.FormHandlerAction;
+import org.labkey.api.action.FormViewAction;
+import org.labkey.api.action.HasViewContext;
+import org.labkey.api.action.LabKeyError;
+import org.labkey.api.action.Marshal;
+import org.labkey.api.action.Marshaller;
+import org.labkey.api.action.MutatingApiAction;
+import org.labkey.api.action.QueryViewAction;
+import org.labkey.api.action.ReadOnlyApiAction;
+import org.labkey.api.action.ReturnUrlForm;
+import org.labkey.api.action.SimpleErrorView;
+import org.labkey.api.action.SimpleViewAction;
+import org.labkey.api.action.SpringActionController;
+import org.labkey.api.analytics.AnalyticsService;
+import org.labkey.api.data.ButtonBar;
+import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.DataRegion;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.Table;
+import org.labkey.api.data.TableCustomizer;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
@@ -71,8 +81,10 @@
 import org.labkey.api.ms2.MS2Urls;
 import org.labkey.api.pipeline.LocalDirectory;
 import org.labkey.api.pipeline.PipeRoot;
+import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.pipeline.PipelineUrls;
+import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.pipeline.browse.PipelinePathForm;
 import org.labkey.api.portal.ProjectUrls;
 import org.labkey.api.protein.ProteinService;
@@ -80,6 +92,7 @@
 import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.FilteredTable;
+import org.labkey.api.query.QueryDefinition;
 import org.labkey.api.query.QueryParam;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QuerySettings;
@@ -96,15 +109,41 @@
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.AdminPermission;
+import org.labkey.api.security.permissions.ApplicationAdminPermission;
 import org.labkey.api.security.permissions.InsertPermission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
+import org.labkey.api.settings.AppProps;
+import org.labkey.api.targetedms.TargetedMSService;
+import org.labkey.api.targetedms.TargetedMSUrls;
+import org.labkey.api.targetedms.model.SampleFileInfo;
+import org.labkey.api.util.Button;
 import org.labkey.api.util.ContainerContext;
+import org.labkey.api.util.DOM;
+import org.labkey.api.util.DateUtil;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.HelpTopic;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
+import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.URLHelper;
+import org.labkey.api.util.UnexpectedException;
+import org.labkey.api.view.ActionURL;
+import org.labkey.api.view.DetailsView;
+import org.labkey.api.view.GridView;
+import org.labkey.api.view.HtmlView;
+import org.labkey.api.view.HttpView;
+import org.labkey.api.view.JspView;
+import org.labkey.api.view.NavTree;
+import org.labkey.api.view.NotFoundException;
+import org.labkey.api.view.PopupMenu;
+import org.labkey.api.view.Portal;
+import org.labkey.api.view.RedirectException;
+import org.labkey.api.view.VBox;
+import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.api.view.ViewContext;
+import org.labkey.api.view.WebPartView;
+import org.labkey.api.view.template.ClientDependency;
 import org.labkey.api.view.template.PageConfig;
 import org.labkey.targetedms.chart.ChromatogramChartMakerFactory;
 import org.labkey.targetedms.chart.ComparisonChartMaker;
@@ -115,7 +154,13 @@
 import org.labkey.targetedms.conflict.ConflictPrecursor;
 import org.labkey.targetedms.conflict.ConflictProtein;
 import org.labkey.targetedms.conflict.ConflictTransition;
+import org.labkey.targetedms.model.GuideSet;
+import org.labkey.targetedms.model.GuideSetKey;
+import org.labkey.targetedms.model.GuideSetStats;
 import org.labkey.targetedms.model.QCMetricConfiguration;
+import org.labkey.targetedms.model.QCPlotFragment;
+import org.labkey.targetedms.model.RawMetricDataSet;
+import org.labkey.targetedms.outliers.OutlierGenerator;
 import org.labkey.targetedms.parser.GeneralMolecule;
 import org.labkey.targetedms.parser.GeneralMoleculeChromInfo;
 import org.labkey.targetedms.parser.Molecule;
@@ -136,9 +181,26 @@
 import org.labkey.targetedms.parser.TransitionChromInfo;
 import org.labkey.targetedms.parser.blib.BlibSpectrumReader;
 import org.labkey.targetedms.parser.list.ListDefinition;
-import org.labkey.targetedms.pipeline.ChromatogramCrawlerJob;
 import org.labkey.targetedms.parser.skyaudit.AuditLogEntry;
-import org.labkey.targetedms.query.*;
+import org.labkey.targetedms.pipeline.ChromatogramCrawlerJob;
+import org.labkey.targetedms.query.ChromatogramDisplayColumnFactory;
+import org.labkey.targetedms.query.ConflictResultsManager;
+import org.labkey.targetedms.query.IsotopeLabelManager;
+import org.labkey.targetedms.query.LibraryManager;
+import org.labkey.targetedms.query.ModificationManager;
+import org.labkey.targetedms.query.ModifiedSequenceDisplayColumn;
+import org.labkey.targetedms.query.MoleculeManager;
+import org.labkey.targetedms.query.MoleculePrecursorManager;
+import org.labkey.targetedms.query.PeptideChromatogramsTableInfo;
+import org.labkey.targetedms.query.PeptideGroupManager;
+import org.labkey.targetedms.query.PeptideManager;
+import org.labkey.targetedms.query.PrecursorChromatogramsTableInfo;
+import org.labkey.targetedms.query.PrecursorManager;
+import org.labkey.targetedms.query.ReplicateManager;
+import org.labkey.targetedms.query.SkylineListManager;
+import org.labkey.targetedms.query.SkylineListSchema;
+import org.labkey.targetedms.query.TargetedMSTable;
+import org.labkey.targetedms.query.TransitionManager;
 import org.labkey.targetedms.search.ModificationSearchWebPart;
 import org.labkey.targetedms.view.CalibrationCurveChart;
 import org.labkey.targetedms.view.CalibrationCurvesView;
@@ -163,7 +225,6 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-
 import javax.servlet.http.HttpServletResponse;
 import java.awt.*;
 import java.awt.image.BufferedImage;
@@ -194,10 +255,11 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
+import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME;
+import static org.labkey.api.targetedms.TargetedMSService.FolderType;
 import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME;
-import static org.labkey.api.targetedms.TargetedMSService.RAW_FILES_TAB;
 import static org.labkey.api.targetedms.TargetedMSService.RAW_FILES_DIR;
-import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME;
+import static org.labkey.api.targetedms.TargetedMSService.RAW_FILES_TAB;
 import static org.labkey.api.util.DOM.Attribute.method;
 import static org.labkey.api.util.DOM.Attribute.src;
 import static org.labkey.api.util.DOM.DIV;
@@ -207,14 +269,13 @@
 import static org.labkey.api.util.DOM.at;
 import static org.labkey.api.util.DOM.cl;
 import static org.labkey.targetedms.TargetedMSModule.EXPERIMENT_FOLDER_WEB_PARTS;
-import static org.labkey.api.targetedms.TargetedMSService.FolderType;
 import static org.labkey.targetedms.TargetedMSModule.LIBRARY_FOLDER_WEB_PARTS;
 import static org.labkey.targetedms.TargetedMSModule.PROTEIN_LIBRARY_FOLDER_WEB_PARTS;
 import static org.labkey.targetedms.TargetedMSModule.QC_FOLDER_WEB_PARTS;
 
 public class TargetedMSController extends SpringActionController
 {
-    private static final Logger LOG = Logger.getLogger(TargetedMSController.class);
+    private static final Logger LOG = LogManager.getLogger(TargetedMSController.class);
 
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(TargetedMSController.class);
     public static final String CONFIGURE_TARGETED_MS_FOLDER = "Configure Panorama Folder";
diff --git a/src/org/labkey/targetedms/TargetedMSDataHandler.java b/src/org/labkey/targetedms/TargetedMSDataHandler.java
index 56b54d605..95de1cbb2 100644
--- a/src/org/labkey/targetedms/TargetedMSDataHandler.java
+++ b/src/org/labkey/targetedms/TargetedMSDataHandler.java
@@ -17,7 +17,8 @@
 package org.labkey.targetedms;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.exp.ExperimentException;
@@ -58,7 +59,7 @@
  */
 public class TargetedMSDataHandler extends AbstractExperimentDataHandler
 {
-    private static final Logger _log = Logger.getLogger(TargetedMSDataHandler.class);
+    private static final Logger _log = LogManager.getLogger(TargetedMSDataHandler.class);
 
     @Override
     public DataType getDataType()
diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java
index a7970c336..5124b4778 100644
--- a/src/org/labkey/targetedms/TargetedMSManager.java
+++ b/src/org/labkey/targetedms/TargetedMSManager.java
@@ -19,7 +19,8 @@
 import com.google.common.base.Joiner;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -123,7 +124,7 @@ public class TargetedMSManager
 {
     private static final TargetedMSManager _instance = new TargetedMSManager();
 
-    private static Logger _log = Logger.getLogger(TargetedMSManager.class);
+    private static Logger _log = LogManager.getLogger(TargetedMSManager.class);
 
     private TargetedMSManager()
     {
diff --git a/src/org/labkey/targetedms/TargetedMSServiceImpl.java b/src/org/labkey/targetedms/TargetedMSServiceImpl.java
index fca7cd7d7..ab9d82290 100644
--- a/src/org/labkey/targetedms/TargetedMSServiceImpl.java
+++ b/src/org/labkey/targetedms/TargetedMSServiceImpl.java
@@ -23,14 +23,14 @@
 import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
+import org.labkey.api.targetedms.BlibSourceFiles;
 import org.labkey.api.targetedms.IModification;
 import org.labkey.api.targetedms.ITargetedMSRun;
-import org.labkey.api.targetedms.SkylineDocumentImportListener;
 import org.labkey.api.targetedms.SkylineAnnotation;
+import org.labkey.api.targetedms.SkylineDocumentImportListener;
 import org.labkey.api.targetedms.TargetedMSFolderTypeListener;
 import org.labkey.api.targetedms.TargetedMSService;
 import org.labkey.api.targetedms.model.SampleFileInfo;
-import org.labkey.api.targetedms.BlibSourceFiles;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.targetedms.parser.blib.BlibSpectrumReader;
 import org.labkey.targetedms.query.ModificationManager;
diff --git a/src/org/labkey/targetedms/TargetedMSUpgradeCode.java b/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
index 998be85a5..066ddffde 100644
--- a/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
+++ b/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
@@ -15,9 +15,9 @@
  */
 package org.labkey.targetedms;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.CompareType;
-import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbScope;
@@ -39,7 +39,6 @@
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
-import org.labkey.api.view.Portal;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -52,8 +51,6 @@
 import java.util.List;
 import java.util.Set;
 
-import static org.labkey.api.targetedms.TargetedMSService.RAW_FILES_TAB;
-
 
 /**
  * User: jeckels
@@ -61,7 +58,7 @@
  */
 public class TargetedMSUpgradeCode implements UpgradeCode
 {
-    private static final Logger LOG = Logger.getLogger(TargetedMSUpgradeCode.class);
+    private static final Logger LOG = LogManager.getLogger(TargetedMSUpgradeCode.class);
 
     // called at every bootstrap to initialize annotation types
     @SuppressWarnings({"UnusedDeclaration"})
diff --git a/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java b/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java
index 98c6096cf..0eeb54b71 100644
--- a/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java
+++ b/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java
@@ -15,8 +15,6 @@
 package org.labkey.targetedms.calculations;
 
 import org.jetbrains.annotations.NotNull;
-import org.labkey.targetedms.calculations.quantification.ReplicateData;
-import org.labkey.targetedms.calculations.quantification.TransitionAreas;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableSelector;
@@ -24,6 +22,8 @@
 import org.labkey.api.security.User;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSSchema;
+import org.labkey.targetedms.calculations.quantification.ReplicateData;
+import org.labkey.targetedms.calculations.quantification.TransitionAreas;
 import org.labkey.targetedms.parser.GeneralMolecule;
 import org.labkey.targetedms.parser.GeneralMoleculeChromInfo;
 import org.labkey.targetedms.parser.GeneralPrecursor;
diff --git a/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java b/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java
index de2ab8a1f..ee0d32e42 100644
--- a/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java
+++ b/src/org/labkey/targetedms/calculations/NormalizationMethodAreas.java
@@ -14,13 +14,13 @@
  */
 package org.labkey.targetedms.calculations;
 
-import org.labkey.targetedms.calculations.quantification.NormalizationMethod;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.security.User;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSRun;
+import org.labkey.targetedms.calculations.quantification.NormalizationMethod;
 import org.labkey.targetedms.parser.GeneralMolecule;
 import org.labkey.targetedms.parser.PeptideSettings;
 import org.labkey.targetedms.parser.StandardType;
diff --git a/src/org/labkey/targetedms/calculations/RunQuantifier.java b/src/org/labkey/targetedms/calculations/RunQuantifier.java
index 996858971..821888512 100644
--- a/src/org/labkey/targetedms/calculations/RunQuantifier.java
+++ b/src/org/labkey/targetedms/calculations/RunQuantifier.java
@@ -14,16 +14,6 @@
  */
 package org.labkey.targetedms.calculations;
 
-import org.labkey.targetedms.SkylineDocImporter.IProgressStatus;
-import org.labkey.targetedms.calculations.quantification.CalibrationCurve;
-import org.labkey.targetedms.calculations.quantification.CalibrationCurveDataSet;
-import org.labkey.targetedms.calculations.quantification.GroupComparisonDataSet;
-import org.labkey.targetedms.calculations.quantification.LinearFitResult;
-import org.labkey.targetedms.calculations.quantification.NormalizationMethod;
-import org.labkey.targetedms.calculations.quantification.PValues;
-import org.labkey.targetedms.calculations.quantification.RegressionFit;
-import org.labkey.targetedms.calculations.quantification.RegressionWeighting;
-import org.labkey.targetedms.calculations.quantification.SampleType;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
@@ -31,9 +21,19 @@
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
 import org.labkey.api.util.Tuple3;
+import org.labkey.targetedms.SkylineDocImporter.IProgressStatus;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSRun;
 import org.labkey.targetedms.TargetedMSSchema;
+import org.labkey.targetedms.calculations.quantification.CalibrationCurve;
+import org.labkey.targetedms.calculations.quantification.CalibrationCurveDataSet;
+import org.labkey.targetedms.calculations.quantification.GroupComparisonDataSet;
+import org.labkey.targetedms.calculations.quantification.LinearFitResult;
+import org.labkey.targetedms.calculations.quantification.NormalizationMethod;
+import org.labkey.targetedms.calculations.quantification.PValues;
+import org.labkey.targetedms.calculations.quantification.RegressionFit;
+import org.labkey.targetedms.calculations.quantification.RegressionWeighting;
+import org.labkey.targetedms.calculations.quantification.SampleType;
 import org.labkey.targetedms.parser.CalibrationCurveEntity;
 import org.labkey.targetedms.parser.FoldChange;
 import org.labkey.targetedms.parser.GeneralMolecule;
diff --git a/src/org/labkey/targetedms/calculations/quantification/NameValueCollection.java b/src/org/labkey/targetedms/calculations/quantification/NameValueCollection.java
index 0594e6f7f..d655cc4dd 100644
--- a/src/org/labkey/targetedms/calculations/quantification/NameValueCollection.java
+++ b/src/org/labkey/targetedms/calculations/quantification/NameValueCollection.java
@@ -15,6 +15,7 @@
 package org.labkey.targetedms.calculations.quantification;
 
 import org.apache.commons.lang3.StringUtils;
+
 import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
 import java.net.URLEncoder;
diff --git a/src/org/labkey/targetedms/chart/ComparisonAxis.java b/src/org/labkey/targetedms/chart/ComparisonAxis.java
index 8fc5d5afd..18ff4bbb6 100644
--- a/src/org/labkey/targetedms/chart/ComparisonAxis.java
+++ b/src/org/labkey/targetedms/chart/ComparisonAxis.java
@@ -21,8 +21,12 @@
 import org.jfree.ui.RectangleEdge;
 
 import java.awt.*;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
 /**
 * User: vsharma
diff --git a/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java b/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java
index 6b2848e1d..4212a4b5e 100644
--- a/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java
+++ b/src/org/labkey/targetedms/chart/RetentionTimeBoxAndWhiskerRenderer.java
@@ -27,8 +27,6 @@
 import java.awt.*;
 import java.awt.geom.Line2D;
 import java.awt.geom.Rectangle2D;
-import java.util.List;
-import java.util.Map;
 
 /**
  * User: vsharma
diff --git a/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java b/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java
index 77831c1e9..953f843b3 100644
--- a/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java
+++ b/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.targetedms.chromlib;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.targetedms.chromlib.Constants.ColumnDef;
 
 import java.sql.Connection;
@@ -32,7 +33,7 @@
  */
 public abstract class BaseDaoImpl<T extends ObjectWithId> implements Dao<T>
 {
-    private static final Logger _log = Logger.getLogger(BaseDaoImpl.class);
+    private static final Logger _log = LogManager.getLogger(BaseDaoImpl.class);
 
     public PreparedStatement getPreparedStatement(Connection connection, String sql) throws SQLException
     {
diff --git a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
index 9c9868f78..ea0af10fa 100644
--- a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
+++ b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
@@ -26,8 +26,8 @@
 import org.labkey.api.view.NotFoundException;
 import org.labkey.targetedms.TargetedMSManager;
 
-import java.io.IOException;
 import java.io.File;
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.sql.SQLException;
diff --git a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java
index 3f1bb1850..21e6c6f01 100644
--- a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java
+++ b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.targetedms.chromlib;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.util.FileUtil;
 
 import java.nio.file.Files;
@@ -50,7 +51,7 @@ public class ChromatogramLibraryWriter
 
     private Path _libFile;
 
-    private static final Logger _log = Logger.getLogger(ChromatogramLibraryWriter.class);
+    private static final Logger _log = LogManager.getLogger(ChromatogramLibraryWriter.class);
 
     public void setMaxCacheSize(int maxCacheSize)
     {
diff --git a/src/org/labkey/targetedms/model/GuideSetStats.java b/src/org/labkey/targetedms/model/GuideSetStats.java
index d162b442a..0bbafc065 100644
--- a/src/org/labkey/targetedms/model/GuideSetStats.java
+++ b/src/org/labkey/targetedms/model/GuideSetStats.java
@@ -17,7 +17,6 @@
 
 import org.labkey.api.visualization.Stats;
 
-import java.rmi.server.RMIClassLoader;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
diff --git a/src/org/labkey/targetedms/model/PrecursorChromInfoPlus.java b/src/org/labkey/targetedms/model/PrecursorChromInfoPlus.java
index 6f5b8748f..d50ec2d1f 100644
--- a/src/org/labkey/targetedms/model/PrecursorChromInfoPlus.java
+++ b/src/org/labkey/targetedms/model/PrecursorChromInfoPlus.java
@@ -17,8 +17,6 @@
 
 import org.labkey.targetedms.parser.PrecursorChromInfo;
 
-import java.util.Comparator;
-
 /**
  * User: vsharma
  * Date: 5/8/12
diff --git a/src/org/labkey/targetedms/parser/AbstractChromInfo.java b/src/org/labkey/targetedms/parser/AbstractChromInfo.java
index 51f797428..130e2f538 100644
--- a/src/org/labkey/targetedms/parser/AbstractChromInfo.java
+++ b/src/org/labkey/targetedms/parser/AbstractChromInfo.java
@@ -15,7 +15,8 @@
 
 package org.labkey.targetedms.parser;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.cache.BlockingCache;
 import org.labkey.api.cache.CacheManager;
@@ -53,7 +54,7 @@ public abstract class AbstractChromInfo extends ChromInfo<PrecursorChromInfoAnno
     private Integer _chromatogramLength;
     private int _chromatogramFormat;
 
-    private static final Logger LOG = Logger.getLogger(AbstractChromInfo.class);
+    private static final Logger LOG = LogManager.getLogger(AbstractChromInfo.class);
 
     private static final BlockingCache<Tuple3<Path, Long, Integer>, byte[]> ON_DEMAND_CHROM_CACHE = new BlockingCache<>(CacheManager.getCache(100, CacheManager.HOUR, "SKYD chromatogram cache"), (key, argument) -> {
         Path path = key.first;
diff --git a/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java b/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java
index 4de8b6754..3faf2904b 100644
--- a/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java
+++ b/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.targetedms.parser;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.targetedms.SkylineDocImporter;
 import org.labkey.targetedms.query.IsotopeLabelManager;
 import org.labkey.targetedms.query.ReplicateManager;
@@ -34,7 +35,7 @@ public class PeakAreaRatioCalculator
     private final Peptide _peptide;
     private Map<Integer, PeptideAreaRatioCalculator> _peptideAreaRatioCalculatorMap;
 
-    private static Logger _log = Logger.getLogger(SkylineDocImporter.class);
+    private static Logger _log = LogManager.getLogger(SkylineDocImporter.class);
 
     // All the precursors and transitions and chrom infos for this peptide must already have database IDs.
     public PeakAreaRatioCalculator(Peptide peptide)
diff --git a/src/org/labkey/targetedms/parser/SkylineBinaryParser.java b/src/org/labkey/targetedms/parser/SkylineBinaryParser.java
index 11a3b21f3..d3003e641 100644
--- a/src/org/labkey/targetedms/parser/SkylineBinaryParser.java
+++ b/src/org/labkey/targetedms/parser/SkylineBinaryParser.java
@@ -16,8 +16,7 @@
 package org.labkey.targetedms.parser;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.jetbrains.annotations.Nullable;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.exp.api.DataType;
 import org.labkey.targetedms.parser.skyd.CacheFormat;
 import org.labkey.targetedms.parser.skyd.CacheFormatVersion;
diff --git a/src/org/labkey/targetedms/parser/SkylineDocumentParser.java b/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
index 440f59aa8..52a92cc54 100644
--- a/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
+++ b/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
@@ -19,7 +19,7 @@
 import com.google.common.collect.Iterables;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
diff --git a/src/org/labkey/targetedms/parser/blib/BlibSpectrumReader.java b/src/org/labkey/targetedms/parser/blib/BlibSpectrumReader.java
index 95eb8e164..949b0ee8a 100644
--- a/src/org/labkey/targetedms/parser/blib/BlibSpectrumReader.java
+++ b/src/org/labkey/targetedms/parser/blib/BlibSpectrumReader.java
@@ -16,7 +16,8 @@
 package org.labkey.targetedms.parser.blib;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.cache.BlockingCache;
@@ -25,8 +26,8 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.RuntimeSQLException;
 import org.labkey.api.pipeline.LocalDirectory;
-import org.labkey.api.targetedms.ITargetedMSRun;
 import org.labkey.api.targetedms.BlibSourceFiles;
+import org.labkey.api.targetedms.ITargetedMSRun;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.targetedms.parser.Peptide;
@@ -80,7 +81,7 @@ private BlibSpectrumReader() {}
         }
     }
 
-    private static final Logger LOG = Logger.getLogger(BlibSpectrumReader.class);
+    private static final Logger LOG = LogManager.getLogger(BlibSpectrumReader.class);
 
     @Nullable
     public static BlibSpectrum getSpectrum(Container container, Path blibPath,
diff --git a/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java b/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java
index 0e780ea47..ce0e516a6 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java
@@ -21,7 +21,6 @@
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.query.FieldKey;
-import org.labkey.api.query.QueryDefinition;
 import org.labkey.api.util.GUID;
 import org.labkey.api.view.ViewContext;
 import org.labkey.targetedms.TargetedMSManager;
@@ -37,13 +36,10 @@
 import java.time.ZoneId;
 import java.time.ZoneOffset;
 import java.time.format.DateTimeParseException;
-import java.util.ArrayList;
 import java.util.Base64;
 import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
 import java.util.LinkedList;
-import java.util.Map;
+import java.util.List;
 
 public class AuditLogEntry
 {
diff --git a/src/org/labkey/targetedms/parser/skyaudit/AuditLogMessageExpander.java b/src/org/labkey/targetedms/parser/skyaudit/AuditLogMessageExpander.java
index 23066e765..966d3952c 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/AuditLogMessageExpander.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/AuditLogMessageExpander.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.targetedms.parser.skyaudit;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.resource.FileResource;
diff --git a/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java b/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java
index a1299f490..e2d5f40d9 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.targetedms.parser.skyaudit;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.util.GUID;
 
@@ -29,7 +30,7 @@ public class AuditLogTree implements Iterable<AuditLogTree>
 {
     public static final String NULL_STRING = "(null)";
 
-    private static final Logger LOG = Logger.getLogger(AuditLogTree.class);
+    private static final Logger LOG = LogManager.getLogger(AuditLogTree.class);
 
     private final Map<String, AuditLogTree> _children = new HashMap<>();
     private final String _entryHash;
diff --git a/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogParser.java b/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogParser.java
index 58362f571..2ec9c47d4 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogParser.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogParser.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.targetedms.parser.skyaudit;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -307,7 +308,7 @@ public static class TestCase extends Assert{
         @BeforeClass
         public static void getTestFile(){
 
-            _logger = Logger.getLogger(TestCase.class.getPackageName() + ".test");
+            _logger = LogManager.getLogger(TestCase.class.getPackageName() + ".test");
             UnitTestUtil.cleanupDatabase(_docGUID);
         }
 
diff --git a/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogSecurityManager.java b/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogSecurityManager.java
index 367cb4226..d8af55475 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogSecurityManager.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/SkylineAuditLogSecurityManager.java
@@ -16,7 +16,8 @@
 package org.labkey.targetedms.parser.skyaudit;
 
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleProperty;
@@ -47,7 +48,7 @@ public enum INTEGRITY_LEVEL
     public SkylineAuditLogSecurityManager(Container pContainer, User pUser) throws AuditLogException
     {
         _container = pContainer;
-        _logger = Logger.getLogger(this.getClass());
+        _logger = LogManager.getLogger(this.getClass());
 
         TargetedMSModule targetedMSModule = null;
         for (Module m : _container.getActiveModules())
diff --git a/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java b/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java
index 8901f8a14..e20d09439 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java
@@ -16,7 +16,7 @@
 package org.labkey.targetedms.parser.skyaudit;
 
 import org.apache.commons.io.FileExistsException;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.BaseSelector;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Filter;
diff --git a/src/org/labkey/targetedms/parser/skyd/CacheFormat.java b/src/org/labkey/targetedms/parser/skyd/CacheFormat.java
index 45ef51215..c98aa6217 100644
--- a/src/org/labkey/targetedms/parser/skyd/CacheFormat.java
+++ b/src/org/labkey/targetedms/parser/skyd/CacheFormat.java
@@ -16,7 +16,6 @@
 
 import org.apache.poi.util.LittleEndianByteArrayInputStream;
 
-import java.io.IOException;
 import java.nio.charset.Charset;
 import java.nio.charset.StandardCharsets;
 
diff --git a/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java b/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java
index 480b332ee..0a74ab259 100644
--- a/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java
+++ b/src/org/labkey/targetedms/parser/skyd/CachedFileHeaderStruct.java
@@ -16,7 +16,6 @@
 
 import org.apache.poi.util.LittleEndianInput;
 
-import java.io.IOException;
 import java.util.Arrays;
 import java.util.EnumSet;
 import java.util.stream.Collectors;
diff --git a/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java b/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java
index 31e60115f..a80c8d7bd 100644
--- a/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java
+++ b/src/org/labkey/targetedms/parser/skyd/ChromGroupHeaderInfo.java
@@ -19,7 +19,6 @@
 import org.labkey.targetedms.parser.ChromatogramBinaryFormat;
 import org.labkey.targetedms.parser.SignedMz;
 
-import java.io.IOException;
 import java.util.EnumSet;
 
 /**
diff --git a/src/org/labkey/targetedms/parser/skyd/ChromPeak.java b/src/org/labkey/targetedms/parser/skyd/ChromPeak.java
index 5e835b9cb..6cad12e5d 100644
--- a/src/org/labkey/targetedms/parser/skyd/ChromPeak.java
+++ b/src/org/labkey/targetedms/parser/skyd/ChromPeak.java
@@ -16,8 +16,6 @@
 
 import org.apache.poi.util.LittleEndianInput;
 
-import java.io.IOException;
-
 /**
  * Structure which describes a candidate peak in a chromatogram for a transition.
  */
diff --git a/src/org/labkey/targetedms/parser/skyd/ChromTransition.java b/src/org/labkey/targetedms/parser/skyd/ChromTransition.java
index 2a0924ab7..354230158 100644
--- a/src/org/labkey/targetedms/parser/skyd/ChromTransition.java
+++ b/src/org/labkey/targetedms/parser/skyd/ChromTransition.java
@@ -17,8 +17,6 @@
 import org.apache.poi.util.LittleEndianInput;
 import org.labkey.targetedms.parser.SignedMz;
 
-import java.io.IOException;
-
 /**
  * Structure for a transition within a ChromGroupHeaderInfo.
  */
diff --git a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java
index 0704dda3a..06b770d16 100644
--- a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java
+++ b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java
@@ -18,8 +18,6 @@
 
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import org.apache.log4j.Logger;
-import org.junit.Test;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.pipeline.LocalDirectory;
 import org.labkey.api.pipeline.PipeRoot;
@@ -32,7 +30,6 @@
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.targetedms.SkylineDocImporter;
 import org.labkey.targetedms.TargetedMSController;
-import org.labkey.targetedms.TargetedMSModule;
 import org.labkey.targetedms.TargetedMSRun;
 
 import java.util.List;
diff --git a/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java b/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java
index 09d3e328d..6dfc01c51 100644
--- a/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java
+++ b/src/org/labkey/targetedms/pipeline/TargetedMSImportTask.java
@@ -19,7 +19,6 @@
 import org.labkey.api.data.DbScope;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.XarContext;
-import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.pipeline.AbstractTaskFactory;
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipelineJob;
@@ -37,7 +36,6 @@
 import java.io.IOException;
 import java.util.Collections;
 import java.util.List;
-import java.util.zip.DataFormatException;
 
 /**
  * Import a Skyline document, create an experiment run wrapper around it, and wire up to the experiment, if present.
diff --git a/src/org/labkey/targetedms/query/CalibrationCurveTable.java b/src/org/labkey/targetedms/query/CalibrationCurveTable.java
index 15ecd51a7..37c42cac7 100644
--- a/src/org/labkey/targetedms/query/CalibrationCurveTable.java
+++ b/src/org/labkey/targetedms/query/CalibrationCurveTable.java
@@ -14,7 +14,6 @@
  */
 package org.labkey.targetedms.query;
 
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
diff --git a/src/org/labkey/targetedms/query/GeneralMoleculeAnnotationTableInfo.java b/src/org/labkey/targetedms/query/GeneralMoleculeAnnotationTableInfo.java
index 8f7cee485..942a4dc33 100644
--- a/src/org/labkey/targetedms/query/GeneralMoleculeAnnotationTableInfo.java
+++ b/src/org/labkey/targetedms/query/GeneralMoleculeAnnotationTableInfo.java
@@ -15,7 +15,6 @@
  */
 package org.labkey.targetedms.query;
 
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.targetedms.TargetedMSSchema;
diff --git a/src/org/labkey/targetedms/query/GuideSetTable.java b/src/org/labkey/targetedms/query/GuideSetTable.java
index 52c09b40f..7cdc3c14d 100644
--- a/src/org/labkey/targetedms/query/GuideSetTable.java
+++ b/src/org/labkey/targetedms/query/GuideSetTable.java
@@ -18,7 +18,6 @@
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerForeignKey;
 import org.labkey.api.data.JdbcType;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
@@ -29,7 +28,6 @@
 import org.labkey.api.query.FilteredTable;
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.RowIdQueryUpdateService;
-import org.labkey.api.query.UserIdQueryForeignKey;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserPrincipal;
@@ -38,8 +36,6 @@
 import org.labkey.targetedms.TargetedMSSchema;
 import org.labkey.targetedms.model.GuideSet;
 
-import java.sql.SQLException;
-
 /**
  * Created by cnathe on 4/9/2015.
  */
diff --git a/src/org/labkey/targetedms/query/IconColumn.java b/src/org/labkey/targetedms/query/IconColumn.java
index 66bed94c3..c91532b00 100644
--- a/src/org/labkey/targetedms/query/IconColumn.java
+++ b/src/org/labkey/targetedms/query/IconColumn.java
@@ -17,7 +17,6 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
-import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.DataColumn;
 import org.labkey.api.data.RenderContext;
diff --git a/src/org/labkey/targetedms/query/LibraryManager.java b/src/org/labkey/targetedms/query/LibraryManager.java
index e75dae909..f352c6340 100644
--- a/src/org/labkey/targetedms/query/LibraryManager.java
+++ b/src/org/labkey/targetedms/query/LibraryManager.java
@@ -15,7 +15,6 @@
 
 package org.labkey.targetedms.query;
 
-import org.labkey.api.collections.CsvSet;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
diff --git a/src/org/labkey/targetedms/query/PeptideIsotopeModificationTableInfo.java b/src/org/labkey/targetedms/query/PeptideIsotopeModificationTableInfo.java
index 55356c9fc..0df756e88 100644
--- a/src/org/labkey/targetedms/query/PeptideIsotopeModificationTableInfo.java
+++ b/src/org/labkey/targetedms/query/PeptideIsotopeModificationTableInfo.java
@@ -15,11 +15,8 @@
  */
 package org.labkey.targetedms.query;
 
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.TableInfo;
 import org.labkey.api.query.FilteredTable;
-import org.labkey.api.query.LookupForeignKey;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSSchema;
 
diff --git a/src/org/labkey/targetedms/query/PeptideManager.java b/src/org/labkey/targetedms/query/PeptideManager.java
index 5b68a7031..07b48b7eb 100644
--- a/src/org/labkey/targetedms/query/PeptideManager.java
+++ b/src/org/labkey/targetedms/query/PeptideManager.java
@@ -28,8 +28,6 @@
 import org.labkey.targetedms.parser.Peptide;
 
 import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
diff --git a/src/org/labkey/targetedms/query/PeptideStructuralModificationTableInfo.java b/src/org/labkey/targetedms/query/PeptideStructuralModificationTableInfo.java
index 8ffabbab4..41b89f9a7 100644
--- a/src/org/labkey/targetedms/query/PeptideStructuralModificationTableInfo.java
+++ b/src/org/labkey/targetedms/query/PeptideStructuralModificationTableInfo.java
@@ -15,11 +15,8 @@
  */
 package org.labkey.targetedms.query;
 
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.TableInfo;
 import org.labkey.api.query.FilteredTable;
-import org.labkey.api.query.LookupForeignKey;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSSchema;
 
diff --git a/src/org/labkey/targetedms/query/QCAnnotationTable.java b/src/org/labkey/targetedms/query/QCAnnotationTable.java
index f20ce0398..3e6e44dd8 100644
--- a/src/org/labkey/targetedms/query/QCAnnotationTable.java
+++ b/src/org/labkey/targetedms/query/QCAnnotationTable.java
@@ -17,9 +17,6 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerForeignKey;
-import org.labkey.api.data.TableInfo;
-import org.labkey.api.exp.query.ExpSchema;
 import org.labkey.api.query.DefaultQueryUpdateService;
 import org.labkey.api.query.FilteredTable;
 import org.labkey.api.query.QueryForeignKey;
diff --git a/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java b/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java
index edee23e52..7c2663c83 100644
--- a/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java
+++ b/src/org/labkey/targetedms/query/QCAnnotationTypeTable.java
@@ -21,7 +21,6 @@
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerForeignKey;
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.DisplayColumnFactory;
 import org.labkey.api.data.SqlExecutor;
diff --git a/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java b/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java
index b20fb3f76..8cd1119d1 100644
--- a/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java
+++ b/src/org/labkey/targetedms/query/QCMetricConfigurationTable.java
@@ -20,7 +20,6 @@
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.query.DefaultQueryUpdateService;
-import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.FilteredTable;
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.security.UserPrincipal;
diff --git a/src/org/labkey/targetedms/query/SampleFileTable.java b/src/org/labkey/targetedms/query/SampleFileTable.java
index 6c48dde05..95fe502b0 100644
--- a/src/org/labkey/targetedms/query/SampleFileTable.java
+++ b/src/org/labkey/targetedms/query/SampleFileTable.java
@@ -17,7 +17,6 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.assay.AssayUrls;
 import org.labkey.api.data.Aggregate;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
@@ -37,7 +36,6 @@
 import org.labkey.api.security.permissions.Permission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.targetedms.TargetedMSService;
-import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.targetedms.TargetedMSController;
 import org.labkey.targetedms.TargetedMSManager;
diff --git a/src/org/labkey/targetedms/query/SkylineListSchema.java b/src/org/labkey/targetedms/query/SkylineListSchema.java
index 43ddba0cb..454addd18 100644
--- a/src/org/labkey/targetedms/query/SkylineListSchema.java
+++ b/src/org/labkey/targetedms/query/SkylineListSchema.java
@@ -1,7 +1,6 @@
 package org.labkey.targetedms.query;
 
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.collections.CaseInsensitiveHashSet;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/targetedms/search/ModificationSearchBean.java b/src/org/labkey/targetedms/search/ModificationSearchBean.java
index c06a190c3..c2ab67807 100644
--- a/src/org/labkey/targetedms/search/ModificationSearchBean.java
+++ b/src/org/labkey/targetedms/search/ModificationSearchBean.java
@@ -15,7 +15,6 @@
  */
 package org.labkey.targetedms.search;
 
-import org.labkey.api.view.ViewContext;
 import org.labkey.targetedms.TargetedMSController;
 
 /**
diff --git a/src/org/labkey/targetedms/search/ModificationSearchWebPart.java b/src/org/labkey/targetedms/search/ModificationSearchWebPart.java
index 952ad76b5..9c45664f9 100644
--- a/src/org/labkey/targetedms/search/ModificationSearchWebPart.java
+++ b/src/org/labkey/targetedms/search/ModificationSearchWebPart.java
@@ -17,7 +17,6 @@
 
 import org.labkey.api.view.JspView;
 import org.labkey.targetedms.TargetedMSController;
-import org.labkey.targetedms.TargetedMSModule;
 
 /**
  * User: cnathe
diff --git a/src/org/labkey/targetedms/view/AnnotationUIDisplayColumn.java b/src/org/labkey/targetedms/view/AnnotationUIDisplayColumn.java
index 0be029ff7..9aa4a88c8 100644
--- a/src/org/labkey/targetedms/view/AnnotationUIDisplayColumn.java
+++ b/src/org/labkey/targetedms/view/AnnotationUIDisplayColumn.java
@@ -17,14 +17,10 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.ColumnInfo;
-import org.labkey.api.data.Container;
 import org.labkey.api.data.DataColumn;
 import org.labkey.api.data.RenderContext;
 import org.labkey.api.query.FieldKey;
-import org.labkey.api.security.User;
 
-import java.io.IOException;
-import java.io.Writer;
 import java.util.Set;
 
 /**
diff --git a/src/org/labkey/targetedms/view/CalibrationCurvesView.java b/src/org/labkey/targetedms/view/CalibrationCurvesView.java
index e90ccda6f..3bb812d6a 100644
--- a/src/org/labkey/targetedms/view/CalibrationCurvesView.java
+++ b/src/org/labkey/targetedms/view/CalibrationCurvesView.java
@@ -15,24 +15,23 @@
 package org.labkey.targetedms.view;
 
 import org.labkey.api.data.SimpleDisplayColumn;
-import org.labkey.api.data.Sort;
-import org.labkey.api.data.UrlColumn;
-import org.labkey.api.view.DataView;
-import org.labkey.targetedms.calculations.quantification.RegressionFit;
 import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.data.UrlColumn;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.view.ActionURL;
+import org.labkey.api.view.DataView;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.ViewContext;
 import org.labkey.targetedms.TargetedMSController;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSSchema;
+import org.labkey.targetedms.calculations.quantification.RegressionFit;
 import org.labkey.targetedms.parser.QuantificationSettings;
 import org.labkey.targetedms.query.CalibrationCurveTable;
 
-import java.sql.SQLException;
 import java.util.Collection;
 
 /**
diff --git a/src/org/labkey/targetedms/view/DocumentPrecursorsView.java b/src/org/labkey/targetedms/view/DocumentPrecursorsView.java
index 827f90f88..25b51e449 100644
--- a/src/org/labkey/targetedms/view/DocumentPrecursorsView.java
+++ b/src/org/labkey/targetedms/view/DocumentPrecursorsView.java
@@ -19,8 +19,6 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.targetedms.TargetedMSSchema;
 
-import java.sql.SQLException;
-
 /**
  * User: vsharma
  * Date: 4/17/12
diff --git a/src/org/labkey/targetedms/view/DocumentTransitionsView.java b/src/org/labkey/targetedms/view/DocumentTransitionsView.java
index 1d72bcb7a..04b577ffb 100644
--- a/src/org/labkey/targetedms/view/DocumentTransitionsView.java
+++ b/src/org/labkey/targetedms/view/DocumentTransitionsView.java
@@ -20,8 +20,6 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.targetedms.TargetedMSSchema;
 
-import java.sql.SQLException;
-
 /**
  * User: vsharma
  * Date: 4/17/12
diff --git a/src/org/labkey/targetedms/view/DocumentView.java b/src/org/labkey/targetedms/view/DocumentView.java
index 04c0ffe31..08f230b91 100644
--- a/src/org/labkey/targetedms/view/DocumentView.java
+++ b/src/org/labkey/targetedms/view/DocumentView.java
@@ -21,8 +21,6 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.targetedms.TargetedMSSchema;
 
-import java.sql.SQLException;
-
 /**
  * User: binalpatel
  * Date: 2/27/2016
diff --git a/src/org/labkey/targetedms/view/GroupComparisonView.java b/src/org/labkey/targetedms/view/GroupComparisonView.java
index a6d194519..125fb2a46 100644
--- a/src/org/labkey/targetedms/view/GroupComparisonView.java
+++ b/src/org/labkey/targetedms/view/GroupComparisonView.java
@@ -27,7 +27,6 @@
 import org.labkey.targetedms.parser.GroupComparisonSettings;
 import org.labkey.targetedms.query.FoldChangeTable;
 
-import java.sql.SQLException;
 import java.util.Collection;
 import java.util.Objects;
 
diff --git a/src/org/labkey/targetedms/view/PeptidePrecursorsView.java b/src/org/labkey/targetedms/view/PeptidePrecursorsView.java
index 71297cd9d..031a1cc1e 100644
--- a/src/org/labkey/targetedms/view/PeptidePrecursorsView.java
+++ b/src/org/labkey/targetedms/view/PeptidePrecursorsView.java
@@ -23,8 +23,6 @@
 import org.labkey.targetedms.TargetedMSSchema;
 import org.labkey.targetedms.query.PrecursorTableInfo;
 
-import java.sql.SQLException;
-
 /**
  * User: binalpatel
  * Date: 2/26/2016
diff --git a/src/org/labkey/targetedms/view/PeptideTransitionsView.java b/src/org/labkey/targetedms/view/PeptideTransitionsView.java
index 2fac902a8..6aa40aee1 100644
--- a/src/org/labkey/targetedms/view/PeptideTransitionsView.java
+++ b/src/org/labkey/targetedms/view/PeptideTransitionsView.java
@@ -22,8 +22,6 @@
 import org.labkey.targetedms.TargetedMSSchema;
 import org.labkey.targetedms.query.DocTransitionsTableInfo;
 
-import java.sql.SQLException;
-
 /**
  * User: binalpatel
  * Date: 2/27/2016
diff --git a/src/org/labkey/targetedms/view/QuantificationView.java b/src/org/labkey/targetedms/view/QuantificationView.java
index 2577ec44f..eff181606 100644
--- a/src/org/labkey/targetedms/view/QuantificationView.java
+++ b/src/org/labkey/targetedms/view/QuantificationView.java
@@ -23,8 +23,6 @@
 import org.labkey.targetedms.TargetedMSController;
 import org.labkey.targetedms.TargetedMSSchema;
 
-import java.sql.SQLException;
-
 /**
  * Base class for displaying peptide/molecule level calculations (i.e. fold changes and calibration curves).
  */
diff --git a/src/org/labkey/targetedms/view/SmallMoleculePrecursorsView.java b/src/org/labkey/targetedms/view/SmallMoleculePrecursorsView.java
index 25b567ddc..89880e3f6 100644
--- a/src/org/labkey/targetedms/view/SmallMoleculePrecursorsView.java
+++ b/src/org/labkey/targetedms/view/SmallMoleculePrecursorsView.java
@@ -22,8 +22,6 @@
 import org.labkey.targetedms.TargetedMSSchema;
 import org.labkey.targetedms.query.MoleculePrecursorTableInfo;
 
-import java.sql.SQLException;
-
 /**
  * User: binalpatel
  * Date: 2/26/2016
diff --git a/src/org/labkey/targetedms/view/SmallMoleculeTransitionsView.java b/src/org/labkey/targetedms/view/SmallMoleculeTransitionsView.java
index a58b96998..b9b21eba1 100644
--- a/src/org/labkey/targetedms/view/SmallMoleculeTransitionsView.java
+++ b/src/org/labkey/targetedms/view/SmallMoleculeTransitionsView.java
@@ -22,8 +22,6 @@
 import org.labkey.targetedms.TargetedMSSchema;
 import org.labkey.targetedms.query.MoleculeTransitionsTableInfo;
 
-import java.sql.SQLException;
-
 /**
  * User: binalpatel
  * Date: 2/27/2016
diff --git a/src/org/labkey/targetedms/view/archivedRevisionsDownload.jsp b/src/org/labkey/targetedms/view/archivedRevisionsDownload.jsp
index 56bd8a7e3..4ab09aec0 100644
--- a/src/org/labkey/targetedms/view/archivedRevisionsDownload.jsp
+++ b/src/org/labkey/targetedms/view/archivedRevisionsDownload.jsp
@@ -18,6 +18,7 @@
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page import="org.apache.commons.io.FileUtils" %>
 <%@ page import="org.labkey.api.data.Container" %>
+<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.targetedms.TargetedMSManager" %>
@@ -25,7 +26,6 @@
 <%@ page import="java.nio.file.Files" %>
 <%@ page import="java.nio.file.Path" %>
 <%@ page import="java.util.Date" %>
-<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     Container c = getContainer();
diff --git a/src/org/labkey/targetedms/view/chromatogramLibraryDownload.jsp b/src/org/labkey/targetedms/view/chromatogramLibraryDownload.jsp
index 65426ef05..88b741c63 100644
--- a/src/org/labkey/targetedms/view/chromatogramLibraryDownload.jsp
+++ b/src/org/labkey/targetedms/view/chromatogramLibraryDownload.jsp
@@ -19,6 +19,7 @@
 <%@ page import="org.apache.commons.io.FileUtils" %>
 <%@ page import="org.labkey.api.data.Container" %>
 <%@ page import="org.labkey.api.security.User" %>
+<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.targetedms.TargetedMSManager" %>
@@ -27,7 +28,6 @@
 <%@ page import="java.nio.file.Files" %>
 <%@ page import="java.nio.file.Path" %>
 <%@ page import="java.text.DecimalFormat" %>
-<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     Container c = getContainer();
diff --git a/src/org/labkey/targetedms/view/conflictSummary.jsp b/src/org/labkey/targetedms/view/conflictSummary.jsp
index 9114fb761..2bfa45095 100644
--- a/src/org/labkey/targetedms/view/conflictSummary.jsp
+++ b/src/org/labkey/targetedms/view/conflictSummary.jsp
@@ -16,11 +16,11 @@
  */
 %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
+<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.targetedms.TargetedMSManager" %>
 <%@ page import="org.labkey.targetedms.query.ConflictResultsManager" %>
-<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
 
diff --git a/src/org/labkey/targetedms/view/folderSetup.jsp b/src/org/labkey/targetedms/view/folderSetup.jsp
index e554df1cd..e0d09bce6 100644
--- a/src/org/labkey/targetedms/view/folderSetup.jsp
+++ b/src/org/labkey/targetedms/view/folderSetup.jsp
@@ -16,10 +16,10 @@
  */
 %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
+<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.targetedms.TargetedMSManager" %>
-<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     TargetedMSService.FolderType folderType = TargetedMSManager.getFolderType(getContainer());
diff --git a/src/org/labkey/targetedms/view/peptideSummaryView.jsp b/src/org/labkey/targetedms/view/peptideSummaryView.jsp
index a923de60d..b0feb2c82 100644
--- a/src/org/labkey/targetedms/view/peptideSummaryView.jsp
+++ b/src/org/labkey/targetedms/view/peptideSummaryView.jsp
@@ -22,11 +22,11 @@
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.targetedms.parser.PeptideSettings" %>
 <%@ page import="org.labkey.targetedms.parser.Precursor" %>
+<%@ page import="org.labkey.targetedms.view.IconFactory" %>
+<%@ page import="org.labkey.targetedms.view.ModifiedPeptideHtmlMaker" %>
 <%@ page import="org.labkey.targetedms.view.PrecursorHtmlMaker" %>
 <%@ page import="java.util.HashMap" %>
 <%@ page import="java.util.Map" %>
-<%@ page import="org.labkey.targetedms.view.ModifiedPeptideHtmlMaker" %>
-<%@ page import="org.labkey.targetedms.view.IconFactory" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     JspView<TargetedMSController.PeptideChromatogramsViewBean> me = (JspView<TargetedMSController.PeptideChromatogramsViewBean>) HttpView.currentView();
diff --git a/src/org/labkey/targetedms/view/pharmacokinetics.jsp b/src/org/labkey/targetedms/view/pharmacokinetics.jsp
index 0c9e681f6..122793889 100644
--- a/src/org/labkey/targetedms/view/pharmacokinetics.jsp
+++ b/src/org/labkey/targetedms/view/pharmacokinetics.jsp
@@ -15,10 +15,10 @@
      * limitations under the License.
      */
 %>
-<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
-<%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
+<%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ taglib prefix="h" uri="http://www.labkey.org/taglib" %>
diff --git a/src/org/labkey/targetedms/view/precursorChromatogramsView.jsp b/src/org/labkey/targetedms/view/precursorChromatogramsView.jsp
index 25d0b1d6a..1a826cbaf 100644
--- a/src/org/labkey/targetedms/view/precursorChromatogramsView.jsp
+++ b/src/org/labkey/targetedms/view/precursorChromatogramsView.jsp
@@ -18,8 +18,8 @@
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.JspView" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
-<%@ page import="java.text.DecimalFormat" %>
 <%@ page import="org.labkey.targetedms.parser.PeptideSettings" %>
+<%@ page import="java.text.DecimalFormat" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%
     JspView<TargetedMSController.PrecursorChromatogramsViewBean> me = (JspView<TargetedMSController.PrecursorChromatogramsViewBean>) HttpView.currentView();
diff --git a/src/org/labkey/targetedms/view/precursorConflictResolutionView.jsp b/src/org/labkey/targetedms/view/precursorConflictResolutionView.jsp
index 98ebba2d8..be2c4b6b7 100644
--- a/src/org/labkey/targetedms/view/precursorConflictResolutionView.jsp
+++ b/src/org/labkey/targetedms/view/precursorConflictResolutionView.jsp
@@ -19,13 +19,13 @@
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
+<%@ page import="org.labkey.targetedms.TargetedMSSchema" %>
 <%@ page import="org.labkey.targetedms.conflict.ConflictPrecursor" %>
 <%@ page import="org.labkey.targetedms.query.PrecursorManager" %>
 <%@ page import="org.labkey.targetedms.view.ModifiedPeptideHtmlMaker" %>
 <%@ page import="org.labkey.targetedms.view.PrecursorHtmlMaker" %>
-<%@ page import="org.labkey.targetedms.TargetedMSSchema" %>
-<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%!
     @Override
diff --git a/src/org/labkey/targetedms/view/proteinConflictResolutionView.jsp b/src/org/labkey/targetedms/view/proteinConflictResolutionView.jsp
index ec7189e25..0c515b952 100644
--- a/src/org/labkey/targetedms/view/proteinConflictResolutionView.jsp
+++ b/src/org/labkey/targetedms/view/proteinConflictResolutionView.jsp
@@ -19,9 +19,9 @@
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.targetedms.conflict.ConflictProtein" %>
-<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%!
diff --git a/src/org/labkey/targetedms/view/runSummaryView.jsp b/src/org/labkey/targetedms/view/runSummaryView.jsp
index 1dda4d0f4..cda242f72 100644
--- a/src/org/labkey/targetedms/view/runSummaryView.jsp
+++ b/src/org/labkey/targetedms/view/runSummaryView.jsp
@@ -15,26 +15,18 @@
  * limitations under the License.
  */
 %>
-<%@ page import="org.apache.commons.io.FileUtils" %>
 <%@ page import="org.labkey.api.data.Container" %>
 <%@ page import="org.labkey.api.security.permissions.UpdatePermission" %>
+<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
+<%@ page import="org.labkey.api.util.StringUtilsLabKey" %>
 <%@ page import="org.labkey.api.view.ActionURL" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.JspView" %>
-<%@ page import="org.labkey.targetedms.SkylineFileUtils" %>
+<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
-<%@ page import="org.labkey.targetedms.TargetedMSRun" %>
-<%@ page import="java.nio.file.Path" %>
-<%@ page import="java.nio.file.Files" %>
 <%@ page import="org.labkey.targetedms.TargetedMSManager" %>
+<%@ page import="org.labkey.targetedms.TargetedMSRun" %>
 <%@ page import="org.labkey.targetedms.TargetedMSSchema" %>
-<%@ page import="org.labkey.api.util.StringUtilsLabKey" %>
-<%@ page import="org.labkey.api.targetedms.TargetedMSService" %>
-<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
-<%@ page import="org.labkey.api.view.PopupMenu" %>
-<%@ page import="org.labkey.api.view.template.ClientDependency" %>
-<%@ page import="org.labkey.api.util.Pair" %>
-<%@ page import="java.io.IOException" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 
 <%!
diff --git a/src/org/labkey/targetedms/view/skylineAuditLogExtraInfoView.jsp b/src/org/labkey/targetedms/view/skylineAuditLogExtraInfoView.jsp
index 0aab0e9f7..187dac604 100644
--- a/src/org/labkey/targetedms/view/skylineAuditLogExtraInfoView.jsp
+++ b/src/org/labkey/targetedms/view/skylineAuditLogExtraInfoView.jsp
@@ -1,7 +1,6 @@
-<%@ page import="org.labkey.targetedms.TargetedMSController" %>
-<%@ page import="org.labkey.api.view.JspView" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
-<%@ page import="org.labkey.targetedms.TargetedMSRun" %>
+<%@ page import="org.labkey.api.view.JspView" %>
+<%@ page import="org.labkey.targetedms.TargetedMSController" %>
 <%@ page import="org.labkey.targetedms.parser.skyaudit.AuditLogEntry" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 
diff --git a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java
index 1f7c9c3fc..30c0f1e43 100644
--- a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java
+++ b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java
@@ -22,7 +22,6 @@
 import org.labkey.api.cache.CacheLoader;
 import org.labkey.api.cache.CacheManager;
 import org.labkey.api.data.Container;
-import org.labkey.api.pipeline.LocalDirectory;
 import org.labkey.api.security.User;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSRun;
diff --git a/src/org/labkey/targetedms/view/summaryChartsView.jsp b/src/org/labkey/targetedms/view/summaryChartsView.jsp
index 468146047..42955c74c 100644
--- a/src/org/labkey/targetedms/view/summaryChartsView.jsp
+++ b/src/org/labkey/targetedms/view/summaryChartsView.jsp
@@ -20,11 +20,11 @@
 <%@ page import="org.labkey.api.view.JspView" %>
 <%@ page import="org.labkey.api.view.template.ClientDependencies" %>
 <%@ page import="org.labkey.targetedms.TargetedMSController" %>
+<%@ page import="org.labkey.targetedms.parser.Molecule" %>
 <%@ page import="org.labkey.targetedms.parser.Peptide" %>
 <%@ page import="org.labkey.targetedms.parser.Replicate" %>
-<%@ page import="java.util.List" %>
 <%@ page import="org.labkey.targetedms.parser.ReplicateAnnotation" %>
-<%@ page import="org.labkey.targetedms.parser.Molecule" %>
+<%@ page import="java.util.List" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%!
     @Override