diff --git a/src/org/labkey/panoramapremium/PanoramaPremiumController.java b/src/org/labkey/panoramapremium/PanoramaPremiumController.java
index c435ed067..1dcc2c2b8 100644
--- a/src/org/labkey/panoramapremium/PanoramaPremiumController.java
+++ b/src/org/labkey/panoramapremium/PanoramaPremiumController.java
@@ -118,7 +118,7 @@ else if(isMolecule)
         //skip selected precursors that are already excluded
         selectedRowsKeys.forEach(id -> {
             List<ExcludedPrecursor> prec = precursorsList.stream().filter(p -> p.getId() == id).toList();
-            ExcludedPrecursor precursor = prec.get(0);
+            ExcludedPrecursor precursor = prec.getFirst();
             precursor.setIsPeptide(isPeptide);
 
             if (isExcluding)
diff --git a/src/org/labkey/targetedms/SkylineAuditLogManager.java b/src/org/labkey/targetedms/SkylineAuditLogManager.java
index 646ef18ad..b3a0de4ce 100644
--- a/src/org/labkey/targetedms/SkylineAuditLogManager.java
+++ b/src/org/labkey/targetedms/SkylineAuditLogManager.java
@@ -198,7 +198,7 @@ private int persistAuditLog(User user, AuditLogImportContext pContext, SkylineAu
                 ent.setDocumentGUID(pContext._documentGUID);
                 pContext._rootHash.update(ent.getEntryHash().getBytes(StandardCharsets.UTF_8));
                 // Insert at the beginning of the list so we can quickly iterate in reverse order for validation
-                entries.add(0, ent);
+                entries.addFirst(ent);
             }
             catch (XMLStreamException e)
             {
@@ -247,7 +247,7 @@ private int persistAuditLog(User user, AuditLogImportContext pContext, SkylineAu
         }
 
         if (pContext._runId != null)       //set the document version id on the chronologically last log entry.
-            entries.get(entries.size() - 1).setVersionId(pContext._runId);
+            entries.getLast().setVersionId(pContext._runId);
 
         AuditLogTree treePointer = pContext._logTree;
         int persistedEntriesCount = 0;
@@ -280,7 +280,7 @@ private int persistAuditLog(User user, AuditLogImportContext pContext, SkylineAu
             }
         }
         if (persistedEntriesCount == 0)      //if no entries were actually saved into the database we are uploading an earlier document version
-            entries.get(entries.size() - 1).insertRunAuditLogEntry(user, pContext._runId);   //and still need to update the terminal entry with the versionId.
+            entries.getLast().insertRunAuditLogEntry(user, pContext._runId);   //and still need to update the terminal entry with the versionId.
 
         return entries.size();
     }
@@ -304,7 +304,8 @@ private void verifyPostRequisites(AuditLogImportContext pContext, SkylineAuditLo
      * Builds a tree of audit log entry tokens representing the document versioning tree
      * @return the root node of the tree
      */
-    private AuditLogTree buildLogTree(@NotNull GUID pDocumentGUID) throws AuditLogException {
+    private AuditLogTree buildLogTree(@NotNull GUID pDocumentGUID)
+    {
 
         TableInfo entryTbl = TargetedMSManager.getTableInfoSkylineAuditLogEntry();
 
@@ -440,7 +441,7 @@ private TargetedMSRun getNewRun(GUID pDocumentGUID, Container container)
             run.setContainer(container);
             run.setDocumentGUID(pDocumentGUID);
             Table.insert(_user, TargetedMSManager.getTableInfoRuns(), run);
-            _logger.info(String.format("new run is inserted with id %d", run.getId()));
+            _logger.info("new run is inserted with id {}", run.getId());
             return run;
         }
 
@@ -564,7 +565,7 @@ public void addAVersionTest() throws IOException, AuditLogException
 
             for(String fileName : testFileNames)
             {
-                _logger.info("AuditLogFiles/" + fileName);
+                _logger.info("AuditLogFiles/{}", fileName);
                 runs.push(getNewRun(_docGUID));
                 tree = persistALogFile("AuditLogFiles/" + fileName, runs.peek());
             }
diff --git a/src/org/labkey/targetedms/SkylineBinaryDataHandler.java b/src/org/labkey/targetedms/SkylineBinaryDataHandler.java
index e75d35792..99ff247b3 100644
--- a/src/org/labkey/targetedms/SkylineBinaryDataHandler.java
+++ b/src/org/labkey/targetedms/SkylineBinaryDataHandler.java
@@ -50,7 +50,7 @@ public DataType getDataType()
     }
 
     @Override
-    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context) throws ExperimentException
+    public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNull ViewBackgroundInfo info, @NotNull Logger log, @NotNull XarContext context)
     {
     }
 
diff --git a/src/org/labkey/targetedms/SkylineDocImporter.java b/src/org/labkey/targetedms/SkylineDocImporter.java
index 8a1e1afd5..d0b4e4297 100644
--- a/src/org/labkey/targetedms/SkylineDocImporter.java
+++ b/src/org/labkey/targetedms/SkylineDocImporter.java
@@ -214,7 +214,7 @@ public TargetedMSRun importRun(RunInfo runInfo, PipelineJob job) throws IOExcept
         // Skip if run was already fully imported
         if (run.getStatusId() == SkylineDocImporter.STATUS_SUCCESS)
         {
-            _log.info(_expData.getName() + " has already been imported so it does not need to be imported again");
+            _log.info("{} has already been imported so it does not need to be imported again", _expData.getName());
             return run;
         }
 
@@ -249,9 +249,9 @@ public TargetedMSRun importRun(RunInfo runInfo, PipelineJob job) throws IOExcept
             saveRunDocumentSize(run);
 
             updateRunStatus(IMPORT_STARTED);
-            _log.info("Starting to import Skyline document from " + run.getFileName());
+            _log.info("Starting to import Skyline document from {}", run.getFileName());
             importSkylineDoc(run, inputFile.toNioPathForRead().toFile());
-            _log.info("Completed import of Skyline document from " + run.getFileName());
+            _log.info("Completed import of Skyline document from {}", run.getFileName());
 
             updateRunStatus(IMPORT_SUCCEEDED, STATUS_SUCCESS);
 
@@ -401,17 +401,14 @@ private void importSkylineDoc(TargetedMSRun run, File f) throws XMLStreamExcepti
                         modInfo, libraryNameIdMap, pepGroup, parser, peptides, smallMolecules, parser.getTransitionSettings());
                 if (++peptideGroupCount % 100 == 0)
                 {
-                    _log.info("Imported " + peptideGroupCount + " peptide groups.");
+                    _log.info("Imported {} peptide groups.", peptideGroupCount);
                 }
             }
 
             if (!_shouldSaveTransitionChromInfos)
             {
                 TargetedMSModule targetedMSModule = ModuleLoader.getInstance().getModule(TargetedMSModule.class);
-                _log.info("None of the " + parser.getTransitionChromInfoCount() + " TransitionChromInfos in the file " +
-                        "were imported because they exceed the limit of " +
-                        targetedMSModule.MAX_TRANSITION_CHROM_INFOS_PROPERTY.getEffectiveValue(_container) + " and there are more than " +
-                        targetedMSModule.MAX_PRECURSORS_PROPERTY.getEffectiveValue(_container) + " precursors");
+                _log.info("None of the {} TransitionChromInfos in the file were imported because they exceed the limit of {} and there are more than {} precursors", parser.getTransitionChromInfoCount(), targetedMSModule.MAX_TRANSITION_CHROM_INFOS_PROPERTY.getEffectiveValue(_container), targetedMSModule.MAX_PRECURSORS_PROPERTY.getEffectiveValue(_container));
             }
 
             // Done parsing document
@@ -546,7 +543,7 @@ private void calculateSampleFileIRTStats(TargetedMSRun run, ReplicateInfo replic
             return;
         }
 
-        _log.info("Calculating iRT correlations for " + replicateInfo.skylineIdSampleFileIdMap.size() + " sample(s)");
+        _log.info("Calculating iRT correlations for {} sample(s)", replicateInfo.skylineIdSampleFileIdMap.size());
 
         // Get the iRT scale to which we are comparing each sample
         SimpleFilter iRTFilter = new SimpleFilter(FieldKey.fromParts("iRTScaleId"), run.getiRTscaleId());
@@ -600,7 +597,7 @@ private void calculateSampleFileIRTStats(TargetedMSRun run, ReplicateInfo replic
                 updatedCount++;
             }
         }
-        _log.info("Finished calculating iRT correlations for all samples. " + updatedCount + " had a regression line calculated.");
+        _log.info("Finished calculating iRT correlations for all samples. {} had a regression line calculated.", updatedCount);
 
     }
 
@@ -691,9 +688,9 @@ private void deleteOldSampleFiles(ReplicateInfo replicateInfo)
             return;
         }
 
-        _log.info(String.format("Updating previously imported data for %d old sample files.", total));
+        _log.info("Updating previously imported data for {} old sample files.", total);
         _log.debug("Found data for the following old sample files in the QC folder:");
-        replicateInfo.oldSamplesToDelete.keySet().forEach(key -> _log.debug(String.format("  %s", key)));
+        replicateInfo.oldSamplesToDelete.keySet().forEach(key -> _log.debug("  {}", key));
 
         List<Long> existingSamples = new LongArrayList(total);
         replicateInfo.oldSamplesToDelete.forEach((key, value) -> value.forEach(existingSample -> existingSamples.add(existingSample.getId())));
@@ -709,7 +706,7 @@ private void deleteOldSampleFiles(ReplicateInfo replicateInfo)
                 }
                 catch (URISyntaxException e)
                 {
-                    _log.error("Unable to delete file " + srcFile + ". May be an invalid path. This file is no longer needed on the server.");
+                    _log.error("Unable to delete file {}. May be an invalid path. This file is no longer needed on the server.", srcFile);
                 }
             }
         }
@@ -819,7 +816,7 @@ private void insertDigestSettings(PeptideSettings pepSettings)
             }
             else
             {
-                enzyme = existingEnzymes.get(0);
+                enzyme = existingEnzymes.getFirst();
             }
 
             PeptideSettings.EnzymeDigestionSettings digestSettings = pepSettings.getEnzymeDigestionSettings();
@@ -988,9 +985,9 @@ private void handleReplicateExclusions(Replicate replicate, ReplicateAnnotation
                 // If there is an ignore_in_QC annotation and we already have existing exclusions, don't insert but compare and
                 // give a warning if there is a mismatch.
                 if (!shouldExcludeFromAnnot)
-                    _log.warn("Replicate " + replicate.getName() + " has an ignore_in_QC=false annotation but there are existing exclusions that were added within Panorama or from a previous import.");
+                    _log.warn("Replicate {} has an ignore_in_QC=false annotation but there are existing exclusions that were added within Panorama or from a previous import.", replicate.getName());
                 else if (!hasExistingExcludeAllMetrics)
-                    _log.warn("Replicate " + replicate.getName() + " has an ignore_in_QC=true annotation but there are existing metric specific exclusions that were added within Panorama.");
+                    _log.warn("Replicate {} has an ignore_in_QC=true annotation but there are existing metric specific exclusions that were added within Panorama.", replicate.getName());
             }
         }
     }
@@ -1074,7 +1071,7 @@ else if (SkylineFileUtils.EXT_SKY_LOG.equalsIgnoreCase(ext))
                 newScale = true;
             else
             {
-                iRTScaleId = scaleIds.get(0);
+                iRTScaleId = scaleIds.getFirst();
                 SimpleFilter iRTFilter = new SimpleFilter(FieldKey.fromParts("iRTScaleId"), iRTScaleId);
                 List<IrtPeptide> existingScale = new TableSelector(TargetedMSManager.getTableInfoiRTPeptide(), iRTFilter, null).getArrayList(IrtPeptide.class);
 
@@ -1123,7 +1120,7 @@ private ArrayList<IrtPeptide> normalizeIrtImportAndReweighValues(List<IrtPeptide
         IRegressionFunction regressionLine = IrtRegressionCalculator.calcRegressionLine(new RetentionTimeProviderImpl(importScale), new ArrayList<>(existingStandards.values()), new ArrayList<>(existingLibrary.values()), _log);
 
         if (regressionLine == null)
-            throw new PipelineJobException(makeIrtStandardsErrorMsg(existingScale.get(0).getiRTScaleId(), new ArrayList<>(existingStandards.values()), importScale));
+            throw new PipelineJobException(makeIrtStandardsErrorMsg(existingScale.getFirst().getiRTScaleId(), new ArrayList<>(existingStandards.values()), importScale));
 
         applyIrtRegressionLine(regressionLine, importScale);
 
@@ -1284,7 +1281,7 @@ else if(!pepGroup.isDecoy())
         }
 
         // CONSIDER: If there is already an identical entry in the PeptideGroup table re-use it.
-        _log.info("Inserting " + pepGroup.getLabel());
+        _log.info("Inserting {}", pepGroup.getLabel());
         pepGroup = Table.insert(_user, TargetedMSManager.getTableInfoPeptideGroup(), pepGroup);
 
         for (Protein protein : pepGroup.getProteins())
@@ -1332,7 +1329,7 @@ else if(!pepGroup.isDecoy())
                     peptideCount++;
                     if (peptideCount % 50 == 0)
                     {
-                        _log.debug(String.format("Inserted %d peptides", peptideCount));
+                        _log.debug("Inserted {} peptides", peptideCount);
                     }
                 }
                 case MOLECULE -> {
@@ -1346,7 +1343,7 @@ else if(!pepGroup.isDecoy())
                     moleculeCount++;
                     if (moleculeCount % 50 == 0)
                     {
-                        _log.debug(String.format("Inserted %d molecules", moleculeCount));
+                        _log.debug("Inserted {} molecules", moleculeCount);
                     }
                 }
             }
@@ -1356,11 +1353,11 @@ else if(!pepGroup.isDecoy())
         }
         if(peptideCount > 0)
         {
-            _log.debug(String.format("Total peptides inserted: %d", peptideCount));
+            _log.debug("Total peptides inserted: {}", peptideCount);
         }
         if(moleculeCount > 0)
         {
-            _log.debug(String.format("Total molecules inserted: %d", moleculeCount));
+            _log.debug("Total molecules inserted: {}", moleculeCount);
         }
     }
 
@@ -1726,7 +1723,7 @@ private void insertLibInfo(Precursor.LibraryInfo libraryInfo, Precursor precurso
                 if (_missingLibraries.add(libraryInfo.getLibraryName()))
                 {
                     // Only log the first time
-                    _log.warn("'" + libraryInfo.getLibraryName() + "' library was not found in settings.");
+                    _log.warn("'{}' library was not found in settings.", libraryInfo.getLibraryName());
                 }
             }
             else
@@ -2304,7 +2301,7 @@ private void insertSampleFiles(ReplicateInfo replicateInfo, Map<Instrument, Long
 
             if (pathToSampleFile.containsKey(sampleFile.getFilePath()))
             {
-                _log.warn("Duplicate entries found for file path " + sampleFile.getFilePath() + ", may not resolve sample file-scoped chromatograms correctly");
+                _log.warn("Duplicate entries found for file path {}, may not resolve sample file-scoped chromatograms correctly", sampleFile.getFilePath());
             }
             else
             {
@@ -2362,7 +2359,7 @@ private Path copyFileToCloud(Path sourcePath, Path targetParentPath) throws IOEx
     {
         Path dest = targetParentPath.resolve(FileUtil.getFileName(sourcePath));
         Files.copy(sourcePath, dest, StandardCopyOption.REPLACE_EXISTING);
-        _log.info("Copied " + FileUtil.getFileName(sourcePath) + " to cloud storage.");
+        _log.info("Copied {} to cloud storage.", FileUtil.getFileName(sourcePath));
         return dest;
     }
 
@@ -2616,7 +2613,7 @@ public RunInfo prepareRun()
             TargetedMSRun run = getRun();
             if (run == null)
             {
-                _log.info("Starting import from " + _expData.getName());
+                _log.info("Starting import from {}", _expData.getName());
                 run = createRun();
             }
 
@@ -2685,7 +2682,7 @@ int quantifyRun(TargetedMSRun run, PeptideSettings pepSettings, Collection<Group
         }
         for (GroupComparisonSettings groupComparison : groupComparisons)
         {
-            _log.debug(String.format("Calculating fold change for group comparison %s, %d of %d", groupComparison.getName(), ++i, groupComparisons.size()));
+            _log.debug("Calculating fold change for group comparison {}, {} of {}", groupComparison.getName(), ++i, groupComparisons.size());
             for (FoldChange foldChange : quantifier.calculateFoldChanges(groupComparison))
             {
                 Table.insert(_user, TargetedMSManager.getTableInfoFoldChange(), foldChange);
@@ -2928,7 +2925,7 @@ private void doUpdate(int percDone)
             {
                 _job.setStatus(PipelineJob.TaskStatus.running + ", " + percDone + "%"); // This will throw a CancelledException if the job was cancelled.
             }
-            _log.info(percDone + "% Done");
+            _log.info("{}% Done", percDone);
         }
 
 
@@ -3043,7 +3040,7 @@ private boolean documentIsWithinLimits(File file, Container container, Logger lo
         // To prevent giant DIA documents from overwhelming the DB, we skip importing TransitionChromInfos if the document
         // has more than 100,000 AND has more than 1,000 precursors. We use both because a document may have a lot of
         // replicates, so the TransitionChromInfo count by itself isn't sufficient to do the desired screening
-        log.info("Reading Skyline file, " + file.getName() + ", to determine if the TransitionChromInfos in the document should be stored...");
+        log.info("Reading Skyline file, {}, to determine if the TransitionChromInfos in the document should be stored...", file.getName());
         boolean documentWithinLimits = new TransitionChromInfoAndPrecursorTally(maxTransitionChromInfos, maxPrecursors).isWithinLimits(file, log);
         if (documentWithinLimits)
         {
@@ -3051,9 +3048,7 @@ private boolean documentIsWithinLimits(File file, Container container, Logger lo
         }
         else
         {
-            log.info("TransitionChromInfos in the document exceed the limit of " + maxTransitionChromInfos +
-                            ", and there are more than " + maxPrecursors + " precursors." +
-                            " TransitionChromInfos will not be stored.");
+            log.info("TransitionChromInfos in the document exceed the limit of {}, and there are more than {} precursors. TransitionChromInfos will not be stored.", maxTransitionChromInfos, maxPrecursors);
         }
         return documentWithinLimits;
     }
diff --git a/src/org/labkey/targetedms/SkylineFileUtils.java b/src/org/labkey/targetedms/SkylineFileUtils.java
index fb33da6a1..4d9bdbcb5 100644
--- a/src/org/labkey/targetedms/SkylineFileUtils.java
+++ b/src/org/labkey/targetedms/SkylineFileUtils.java
@@ -65,7 +65,7 @@ public static Path getSkylineFile(@Nullable String runLSID, @NotNull Container c
         TargetedMSRun run = TargetedMSManager.getRunByLsid(runLSID, container);
         if (run == null)
         {
-            LOG.warn("Run with experimentRunLSID " + runLSID + " does not exist in container " + container.getPath());
+            LOG.warn("Run with experimentRunLSID {} does not exist in container {}", runLSID, container.getPath());
             return null;
         }
 
@@ -79,11 +79,11 @@ public static Path getSkylineFile(@Nullable String runLSID, @NotNull Container c
             }
             else
             {
-                LOG.warn("Skyline file does not exist: " + (skyDocfile != null ? FileUtil.getFileName(skyDocfile) : null) + ", referenced from " + container.getPath());
+                LOG.warn("Skyline file does not exist: {}, referenced from {}", skyDocfile != null ? FileUtil.getFileName(skyDocfile) : null, container.getPath());
                 return null;
             }
         }
-        LOG.warn("No input data found for targetedms run " + run.getId() + " in container " + container.getPath());
+        LOG.warn("No input data found for targetedms run {} in container {}", run.getId(), container.getPath());
         return null;
     }
 }
diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java b/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java
index f5cd223ba..005cec3e9 100644
--- a/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java
+++ b/src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java
@@ -85,7 +85,7 @@ public static RegressionLine calcRegressionLine(IRetentionTimeProvider retention
                     correlation = statIrts.R(statTimes);
                     if (correlation >= MIN_IRT_TO_TIME_CORRELATION)
                     {
-                        pipelineLog.info("Calculated iRT regression line by ignoring import value for standard: " + standardPeptideList.get(i).getModifiedSequence());
+                        pipelineLog.info("Calculated iRT regression line by ignoring import value for standard: {}", standardPeptideList.get(i).getModifiedSequence());
                         break;
                     }
                 }
@@ -121,7 +121,7 @@ public static RegressionLine calcRegressionLine(IRetentionTimeProvider retention
                 }
                 Statistics statTimes = new Statistics(regressionTimes);
                 Statistics statIrts = new Statistics(regressionScores);
-                pipelineLog.info("Successfully calculated iRT regression line from " + Integer.toString(regression.getPeptideTimes().size()) + " shared peptides.");
+                pipelineLog.info("Successfully calculated iRT regression line from {} shared peptides.", Integer.toString(regression.getPeptideTimes().size()));
                 return new RegressionLine(statIrts.Slope(statTimes), statIrts.Intercept(statTimes));
             }
         }
diff --git a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java
index 01d410bf8..d08b367fa 100644
--- a/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java
+++ b/src/org/labkey/targetedms/SkylinePort/Irt/RetentionTimeRegression.java
@@ -525,7 +525,7 @@ public static RetentionTimeRegression CalcRegression(String name, ArrayList<Rete
             listPeptides.add(mrt.getPeptideSequence());
 
         // Set these now so that we can return null on some conditions
-        calculatorSpec.set(calculators.get(0));
+        calculatorSpec.set(calculators.getFirst());
         statistics.set(null);
 
         int count = listPeptides.size();
diff --git a/src/org/labkey/targetedms/TargetedMSController.java b/src/org/labkey/targetedms/TargetedMSController.java
index 952c0285c..bf012b987 100644
--- a/src/org/labkey/targetedms/TargetedMSController.java
+++ b/src/org/labkey/targetedms/TargetedMSController.java
@@ -2841,7 +2841,7 @@ public List<Integer> getReplicatesFilterList()
                     }
                     catch (NumberFormatException e)
                     {
-                        LOG.debug("Error parsing replicate Id: "+rep,e);
+                        LOG.debug("Error parsing replicate Id: {}", rep, e);
                     }
                 }
 
@@ -3284,7 +3284,7 @@ private void addSpectrumViews(TargetedMSRun run, VBox vbox, List<LibrarySpectrum
             HtmlView view = new HtmlView(DIV("Annotated spectra cannot be displayed from the following unsupported "
                             + (unsupportedLibraries.size() == 1 ? "library" : "libraries") + ": ",
                     (unsupportedLibraries.size() == 1 ?
-                            SPAN(cl("labkey-error"), unsupportedLibraries.get(0))
+                            SPAN(cl("labkey-error"), unsupportedLibraries.getFirst())
                             : DIV(cl("labkey-error"), UL(unsupportedLibraries.stream().map(DOM::LI)))
                     )
             ));
@@ -5216,7 +5216,7 @@ public ModelAndView getView(IdForm form, BindException errors)
             List<? extends ExpMaterial> materials = ExperimentService.get().getExpMaterialsByName(sampleName, null, getUser());
             if (materials.size() == 1)
             {
-                ExpMaterial material = materials.get(0);
+                ExpMaterial material = materials.getFirst();
                 materialURL = material.detailsURL(material.getContainer(), true);
             }
 
@@ -5590,7 +5590,7 @@ private static Protein selectProtein(List<Protein> proteins, @Nullable Long prot
     {
         if (proteinId == null && !proteins.isEmpty())
         {
-            return proteins.get(0);
+            return proteins.getFirst();
         }
         if (proteinId != null)
         {
@@ -7342,8 +7342,7 @@ public static ChromLibAnalyteCounts getChromLibAnalyteCounts(User user, Containe
             }
             catch (IOException | SQLException e)
             {
-                LOG.error("Error reading from chromatogram library file " + ChromatogramLibraryUtils.getDownloadFileName(container, libRevision)
-                        + " in container " + container.getPath(), e);
+                LOG.error("Error reading from chromatogram library file {} in container {}", ChromatogramLibraryUtils.getDownloadFileName(container, libRevision), container.getPath(), e);
             }
             return counts == null ? ChromLibAnalyteCounts.NOT_EXISTS : counts;
         }
@@ -7724,7 +7723,7 @@ else if (!run.getReplacesRuns().isEmpty() && run.getReplacesRuns().size() > 1)
         public Object execute(RowIdForm form, BindException errors) throws BatchValidationException
         {
             ExpRun run = ExperimentService.get().getExpRun(form.getRowId());
-            ExpRun replaces = run.getReplacesRuns().isEmpty() ? null : run.getReplacesRuns().get(0);
+            ExpRun replaces = run.getReplacesRuns().isEmpty() ? null : run.getReplacesRuns().getFirst();
             ExpRun replacedBy = run.getReplacedByRun();
 
             DbScope scope = ExperimentService.get().getSchema().getScope();
diff --git a/src/org/labkey/targetedms/TargetedMSDataHandler.java b/src/org/labkey/targetedms/TargetedMSDataHandler.java
index 5580b2942..ffcc5d66d 100644
--- a/src/org/labkey/targetedms/TargetedMSDataHandler.java
+++ b/src/org/labkey/targetedms/TargetedMSDataHandler.java
@@ -30,7 +30,6 @@
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.pipeline.PipeRoot;
-import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.security.User;
@@ -377,7 +376,7 @@ private boolean zipContainsSkyFile(Path f)
         catch (IOException | IllegalArgumentException e)
         {
             //ignore - see issue 29485 for IllegalArgumentException case
-            _log.warn("Failed to open zip file " + f + " to check if it contains .sky files" + e.getMessage());
+            _log.warn("Failed to open zip file {} to check if it contains .sky files{}", f, e.getMessage());
         }
 
         return false;
diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java
index 8e9fda0fd..02e41b83c 100644
--- a/src/org/labkey/targetedms/TargetedMSManager.java
+++ b/src/org/labkey/targetedms/TargetedMSManager.java
@@ -2788,7 +2788,7 @@ public static void populatePTMPercentsGroupedPrepivotCache(@NotNull TargetedMSRu
             return;
         }
 
-        _log.info("Populating PTMPercentsGroupedPrepivotCache for run " + run.getId());
+        _log.info("Populating PTMPercentsGroupedPrepivotCache for run {}", run.getId());
 
         String labkeySql = "SELECT\n" +
                 "  Modification,\n" +
@@ -2826,7 +2826,7 @@ public static void populatePTMPercentsGroupedPrepivotCache(@NotNull TargetedMSRu
         insertSql.add(run.getId());
         new SqlExecutor(getSchema()).execute(insertSql);
 
-        _log.info("Finished populating PTMPercentsGroupedPrepivotCache for run " + run.getId());
+        _log.info("Finished populating PTMPercentsGroupedPrepivotCache for run {}", run.getId());
     }
 
     /**
diff --git a/src/org/labkey/targetedms/TargetedMSUpgradeCode.java b/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
index 3c95c2dbe..e781278ea 100644
--- a/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
+++ b/src/org/labkey/targetedms/TargetedMSUpgradeCode.java
@@ -101,7 +101,7 @@ public void populatePTMPercentsGroupedPrepivotCache(final ModuleContext moduleCo
                 }
                 catch (Exception e)
                 {
-                    LOG.error("Error populating PTMPercentsGroupedPrepivotCache for run " + run.getId() + " in " + container.getPath(), e);
+                    LOG.error("Error populating PTMPercentsGroupedPrepivotCache for run {} in {}", run.getId(), container.getPath(), e);
                 }
             }
         }
@@ -129,7 +129,7 @@ public void reparentOrphanedTargetedMSData(final ModuleContext moduleContext)
             int deletedCount = executor.execute(deleteSql);
             if (deletedCount > 0)
             {
-                LOG.info("Deleted " + deletedCount + " orphaned rows from targetedms." + tableName);
+                LOG.info("Deleted {} orphaned rows from targetedms.{}", deletedCount, tableName);
             }
         }
 
@@ -142,7 +142,7 @@ public void reparentOrphanedTargetedMSData(final ModuleContext moduleContext)
             int updatedCount = executor.execute(updateSql);
             if (updatedCount > 0)
             {
-                LOG.info("Reparented " + updatedCount + " orphaned rows from targetedms." + tableName + " to /Shared");
+                LOG.info("Reparented {} orphaned rows from targetedms.{} to /Shared", updatedCount, tableName);
             }
         }
     }
diff --git a/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java b/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java
index b047d3a1e..ec92c923a 100644
--- a/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java
+++ b/src/org/labkey/targetedms/calculations/GeneralMoleculeResultDataSet.java
@@ -39,7 +39,6 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
diff --git a/src/org/labkey/targetedms/calculations/RunQuantifier.java b/src/org/labkey/targetedms/calculations/RunQuantifier.java
index e8e089ada..7734052a2 100644
--- a/src/org/labkey/targetedms/calculations/RunQuantifier.java
+++ b/src/org/labkey/targetedms/calculations/RunQuantifier.java
@@ -52,7 +52,6 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
diff --git a/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java b/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java
index a262d04a2..1771d8715 100644
--- a/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java
+++ b/src/org/labkey/targetedms/calculations/quantification/GroupComparisonDataSet.java
@@ -86,7 +86,7 @@ public LinearFitResult calculateFoldChange(String label) {
         DesignMatrix designMatrix = DesignMatrix.getDesignMatrix(foldChangeDataSet, false);
         try
         {
-            LinearFitResult linearFitResult = designMatrix.performLinearFit().get(0);
+            LinearFitResult linearFitResult = designMatrix.performLinearFit().getFirst();
             return linearFitResult;
         }
         catch (Exception x)
diff --git a/src/org/labkey/targetedms/calculations/quantification/TransitionKeys.java b/src/org/labkey/targetedms/calculations/quantification/TransitionKeys.java
index 72d0bbf41..c87a5edcb 100644
--- a/src/org/labkey/targetedms/calculations/quantification/TransitionKeys.java
+++ b/src/org/labkey/targetedms/calculations/quantification/TransitionKeys.java
@@ -14,6 +14,8 @@
  */
 package org.labkey.targetedms.calculations.quantification;
 
+import org.jetbrains.annotations.NotNull;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -76,7 +78,7 @@ public List<String> asList() {
     }
 
     @Override
-    public Iterator<String> iterator() {
+    public @NotNull Iterator<String> iterator() {
         return Arrays.asList(_keys).iterator();
     }
 
diff --git a/src/org/labkey/targetedms/chart/ChromatogramDataset.java b/src/org/labkey/targetedms/chart/ChromatogramDataset.java
index afeba8579..25bcbef23 100644
--- a/src/org/labkey/targetedms/chart/ChromatogramDataset.java
+++ b/src/org/labkey/targetedms/chart/ChromatogramDataset.java
@@ -67,7 +67,6 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -912,7 +911,7 @@ protected List<LibrarySpectrumMatchGetter.PeptideIdRtInfo> getPeptideIdRetention
             }
             else
             {
-                LOG.warn("Could not find pipeline root for container " + _container.getPath());
+                LOG.warn("Could not find pipeline root for container {}", _container.getPath());
                 return Collections.emptyList();
             }
 
diff --git a/src/org/labkey/targetedms/chart/ComparisonCategory.java b/src/org/labkey/targetedms/chart/ComparisonCategory.java
index 6c65b27e8..db77c7de1 100644
--- a/src/org/labkey/targetedms/chart/ComparisonCategory.java
+++ b/src/org/labkey/targetedms/chart/ComparisonCategory.java
@@ -281,7 +281,7 @@ private static void makeUniquePrefixes(List<PeptideCategory> peptideCategories,
 
             if(peptideCategories.size() == 1)
             {
-                ComparisonCategory.PeptideCategory category = peptideCategories.get(0);
+                ComparisonCategory.PeptideCategory category = peptideCategories.getFirst();
                 String sequence = category.getSequence();
                 prefixLen = Math.max(3, prefixLen - 1);
                 category.setSeqPrefix(sequence.substring(0, Math.min(prefixLen, sequence.length())));
@@ -296,7 +296,7 @@ private static void makeUniquePrefixes(List<PeptideCategory> peptideCategories,
             if(uniqSequences.size() == 1)
             {
                 prefixLen = Math.max(3, prefixLen - 1);
-                prefixLen = Math.min(prefixLen, peptideCategories.get(0).getSequence().length());
+                prefixLen = Math.min(prefixLen, peptideCategories.getFirst().getSequence().length());
 
                 // If all the given categories have the same sequence, set the
                 for(ComparisonCategory.PeptideCategory category: peptideCategories)
diff --git a/src/org/labkey/targetedms/chart/ComparisonDataset.java b/src/org/labkey/targetedms/chart/ComparisonDataset.java
index abcbc9a08..e9166a09b 100644
--- a/src/org/labkey/targetedms/chart/ComparisonDataset.java
+++ b/src/org/labkey/targetedms/chart/ComparisonDataset.java
@@ -634,7 +634,7 @@ public BarChartSeriesItemData make(List<PrecursorChromInfoLitePlus> pciPlusList,
 
             if(pciPlusList.size() == 1)
             {
-                Double pciVal = getValue(pciPlusList.get(0));
+                Double pciVal = getValue(pciPlusList.getFirst());
                 if(pciVal != null && !cvValues)
                 {
                     value = pciVal;
@@ -683,7 +683,7 @@ public BoxAndWhiskerSeriesItemData make(List<PrecursorChromInfoLitePlus> pciPlus
         {
             if(pciPlusList.size() == 1)
             {
-                PrecursorChromInfoLitePlus pciPlus = pciPlusList.get(0);
+                PrecursorChromInfoLitePlus pciPlus = pciPlusList.getFirst();
                 if(pciPlus.getBestRetentionTime() == null || pciPlus.getMinStartTime() == null || pciPlus.getMaxEndTime() == null)
                 {
                     return null;
diff --git a/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java b/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java
index fa3bcc2a7..fb3482653 100644
--- a/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java
+++ b/src/org/labkey/targetedms/chart/ReplicateLabelMinimizer.java
@@ -48,7 +48,7 @@ public static Map<String, String> minimize(List<String> labels)
 
         List<String> normalizedLabels = normalizeLabels(labels);
 
-        String[] labelParts = normalizedLabels.get(0).split(String.valueOf(LABEL_SEP_CHAR));
+        String[] labelParts = normalizedLabels.getFirst().split(String.valueOf(LABEL_SEP_CHAR));
         if(labelParts.length == 1)
         {
             return originalLabels(labels);
diff --git a/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java b/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java
index 2de74c513..64549a92b 100644
--- a/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java
+++ b/src/org/labkey/targetedms/chromlib/BaseDaoImpl.java
@@ -61,7 +61,7 @@ public void save(T t, Connection connection) throws SQLException
     @Override
     public void saveAll(Collection<T> list, Connection connection) throws SQLException
     {
-        _log.debug("Batch insert of " + list.size() + " objects");
+        _log.debug("Batch insert of {} objects", list.size());
         if (!list.isEmpty())
         {
             String sql = getInsertSql();
@@ -172,7 +172,7 @@ public T queryForId(int id, Connection connection) throws SQLException
         {
             throw new SQLException("More than one entries found in "+getTableName()+" for Id "+id);
         }
-        return results.get(0);
+        return results.getFirst();
     }
 
     @Override
diff --git a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
index 5a39d9823..498855095 100644
--- a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
+++ b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
@@ -36,7 +36,6 @@
 import org.labkey.vfs.FileLike;
 import org.sqlite.SQLiteConfig;
 
-import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
diff --git a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java
index ecbbfc8c3..a5a787d1b 100644
--- a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java
+++ b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryWriter.java
@@ -63,7 +63,7 @@ public class ChromatogramLibraryWriter
 
     public void openLibrary(Path libFile) throws SQLException
     {
-        _log.info("Writing chromatogram library " + FileUtil.getFileName(libFile));
+        _log.info("Writing chromatogram library {}", FileUtil.getFileName(libFile));
         if(Files.exists(libFile))
         {
             throw new IllegalStateException("Chromatogram library file "+ FileUtil.pathToString(libFile) +" already exists.");
@@ -113,7 +113,7 @@ public void closeLibrary() throws SQLException
         {
             _connectionSource.close();
         }
-        _log.info("Done writing chromatogram library " + FileUtil.pathToString(_libFile));
+        _log.info("Done writing chromatogram library {}", FileUtil.pathToString(_libFile));
     }
 
     private void flushCache() throws SQLException
@@ -196,7 +196,7 @@ private <T> void saveEntry(Dao<T> dao, T object) throws SQLException
         }
         catch(SQLException e)
         {
-            _log.error("Error saving to " + dao.getTableName(), e);
+            _log.error("Error saving to {}", dao.getTableName(), e);
             throw e;
         }
     }
@@ -209,7 +209,7 @@ private <T> void flush(Dao<T> dao, Collection<T> list) throws SQLException
         }
         catch(SQLException e)
         {
-            _log.error("Error saving list to " + dao.getTableName(), e);
+            _log.error("Error saving list to {}", dao.getTableName(), e);
             throw e;
         }
     }
diff --git a/src/org/labkey/targetedms/chromlib/LibProtein.java b/src/org/labkey/targetedms/chromlib/LibProtein.java
index dd74870a4..023985c6a 100644
--- a/src/org/labkey/targetedms/chromlib/LibProtein.java
+++ b/src/org/labkey/targetedms/chromlib/LibProtein.java
@@ -44,7 +44,7 @@ public LibProtein(PeptideGroup pepGroup)
         List<Protein> proteins = PeptideGroupManager.getProteinsForPeptideGroup(pepGroup.getId(), false);
         if (!proteins.isEmpty())
         {
-            setSequence(proteins.get(0).getSequence());
+            setSequence(proteins.getFirst().getSequence());
         }
     }
 
diff --git a/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java b/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java
index dddf2fac6..ff9ab4641 100644
--- a/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java
+++ b/src/org/labkey/targetedms/datasource/MsDataSourceUtil.java
@@ -207,7 +207,7 @@ private MsDataSource getMsDataSource(ISampleFile sampleFile)
         List<MsDataSource> sourceTypes = MsDataSourceTypes.getSourceForName(sampleFile.getFileName());
         if(sourceTypes.size() == 1)
         {
-            return sourceTypes.get(0);
+            return sourceTypes.getFirst();
         }
         else if(sourceTypes.size() > 1)
         {
@@ -685,9 +685,9 @@ public void testGetMsDataSource()
             assertTrue(sourceType instanceof MsMultiDataSource);
             MsMultiDataSource multiSourceType = (MsMultiDataSource) sourceType;
             assertEquals("Expected one directory source", 1, multiSourceType.getDirSources().size());
-            assertEquals("Expected Waters source", MsDataSourceTypes.WATERS, multiSourceType.getDirSources().get(0));
+            assertEquals("Expected Waters source", MsDataSourceTypes.WATERS, multiSourceType.getDirSources().getFirst());
             assertEquals("Expected one file source", 1, multiSourceType.getFileSources().size());
-            assertEquals("Expected Thermo source", MsDataSourceTypes.THERMO, multiSourceType.getFileSources().get(0));
+            assertEquals("Expected Thermo source", MsDataSourceTypes.THERMO, multiSourceType.getFileSources().getFirst());
 
             // .d
             sampleFile.setFilePath("C:\\RawData\\file.d");
diff --git a/src/org/labkey/targetedms/datasource/PsiInstruments.java b/src/org/labkey/targetedms/datasource/PsiInstruments.java
index 6c87570e6..003029fee 100644
--- a/src/org/labkey/targetedms/datasource/PsiInstruments.java
+++ b/src/org/labkey/targetedms/datasource/PsiInstruments.java
@@ -84,7 +84,7 @@ public static List<PsiInstrument> getInstruments()
         }
         catch (ParserConfigurationException | SAXException | IOException e)
         {
-            LOG.error("Error parsing psi-ms-PARSED.xml. " + e.getMessage(), e);
+            LOG.error("Error parsing psi-ms-PARSED.xml. {}", e.getMessage(), e);
             return Collections.emptyList();
         }
 
diff --git a/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java b/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java
index c5b101c6c..2ad839683 100644
--- a/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java
+++ b/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java
@@ -389,7 +389,7 @@ protected void getReplicateDataWithoutDuplicates(FolderImportContext ctx, TableI
         Integer replicateId = getNullableRowIdFromName(TargetedMSSchema.TABLE_REPLICATE, Collections.singleton("Id"), filter, ctx.getUser(), ctx.getContainer(), null);
         if (replicateId == null)
         {
-            ctx.getLogger().info("No replicate '" + replicateName + "' found for exclusion. Skipping.");
+            ctx.getLogger().info("No replicate '{}' found for exclusion. Skipping.", replicateName);
         }
         else
         {
diff --git a/src/org/labkey/targetedms/folderImport/QCFolderImporter.java b/src/org/labkey/targetedms/folderImport/QCFolderImporter.java
index a2620b90d..d52bf5900 100644
--- a/src/org/labkey/targetedms/folderImport/QCFolderImporter.java
+++ b/src/org/labkey/targetedms/folderImport/QCFolderImporter.java
@@ -62,7 +62,7 @@ public void process(@Nullable PipelineJob job, FolderImportContext ctx, VirtualF
                             {
                                 ctx.getLogger().info("Starting QC Plot settings import");
                                 numRows = qcSetting.importSettingsFromFile(ctx, panoramaQCDir, null, null, null, null);
-                                ctx.getLogger().info("Finished importing " + numRows + " QC Plot settings from " + qcSetting.getSettingsFileName() + " as properties.");
+                                ctx.getLogger().info("Finished importing {} QC Plot settings from {} as properties.", numRows, qcSetting.getSettingsFileName());
                             }
                             else
                             {
@@ -70,9 +70,9 @@ public void process(@Nullable PipelineJob job, FolderImportContext ctx, VirtualF
                                 QueryUpdateService qus = ti.getUpdateService();
                                 BatchValidationException errors = new BatchValidationException();
 
-                                ctx.getLogger().info("Starting data import from " + qcSetting.getSettingsFileName() + " into targetedms." + qcSetting.getTableName());
+                                ctx.getLogger().info("Starting data import from {} into targetedms.{}", qcSetting.getSettingsFileName(), qcSetting.getTableName());
                                 numRows = qcSetting.importSettingsFromFile(ctx, panoramaQCDir, schema, ti, qus, errors);
-                                ctx.getLogger().info("Finished importing " + numRows + " rows from " + qcSetting.getSettingsFileName() + " into targetedms." + qcSetting.getTableName());
+                                ctx.getLogger().info("Finished importing {} rows from {} into targetedms.{}", numRows, qcSetting.getSettingsFileName(), qcSetting.getTableName());
                             }
                         }
                         catch (IOException e)
diff --git a/src/org/labkey/targetedms/model/QCPlotFragment.java b/src/org/labkey/targetedms/model/QCPlotFragment.java
index f03f47b8c..d8dfcc1e4 100644
--- a/src/org/labkey/targetedms/model/QCPlotFragment.java
+++ b/src/org/labkey/targetedms/model/QCPlotFragment.java
@@ -195,7 +195,7 @@ public JSONObject toJSON(boolean includeLJ, boolean includeMR, boolean includeMe
         return jsonObject;
     }
 
-    public void setSeriesColor(Color seriesColor)
+    public void setSeriesColor(@Nullable Color seriesColor)
     {
         _seriesColor = seriesColor;
     }
diff --git a/src/org/labkey/targetedms/model/passport/IProtein.java b/src/org/labkey/targetedms/model/passport/IProtein.java
index 25ead6f7a..d1ce744bf 100644
--- a/src/org/labkey/targetedms/model/passport/IProtein.java
+++ b/src/org/labkey/targetedms/model/passport/IProtein.java
@@ -236,7 +236,7 @@ public List<HtmlString> getProtSeqHTML()
             htmlStrings[i] = HtmlString.of(str[i]);
         }
         List<HtmlString> groups = new ArrayList<>();
-        if (features != null && !features.isEmpty() && features.get(features.size() - 1).getEndIndex() < str.length)
+        if (features != null && !features.isEmpty() && features.getLast().getEndIndex() < str.length)
         {
             for (int i = 0; i < features.size(); i++)
             {
diff --git a/src/org/labkey/targetedms/outliers/OutlierGenerator.java b/src/org/labkey/targetedms/outliers/OutlierGenerator.java
index e133136ea..80f8cdadf 100644
--- a/src/org/labkey/targetedms/outliers/OutlierGenerator.java
+++ b/src/org/labkey/targetedms/outliers/OutlierGenerator.java
@@ -529,7 +529,7 @@ public List<QCPlotFragment> getQCPlotFragment(List<RawMetricDataSet> rawMetricDa
         {
             QCPlotFragment qcPlotFragment = new QCPlotFragment();
 
-            RawMetricDataSet firstValue = entry.getValue().get(0);
+            RawMetricDataSet firstValue = entry.getValue().getFirst();
 
             /* Common values for the whole peptide */
             qcPlotFragment.setDataType(firstValue.getDataType());
@@ -620,7 +620,7 @@ public List<PeptideOutliers> getPeptideOutliers(List<RawMetricDataSet> rawMetric
                     outlierCountsPerMetric.put(rawMetricDataSet.getMetric().getName(), outlierCountsPerMetric.get(rawMetricDataSet.getMetric().getName()) + 1);
                 }
             }
-            peptideOutlier.setPrecursorId(entry.getValue().get(0).getPrecursorChromInfoId());
+            peptideOutlier.setPrecursorId(entry.getValue().getFirst().getPrecursorChromInfoId());
             peptideOutlier.setOutlierCountsPerMetric(outlierCountsPerMetric);
             peptideOutlier.setTotalOutliers(totalOutliers);
             peptideOutliers.add(peptideOutlier);
diff --git a/src/org/labkey/targetedms/parser/AbstractChromInfo.java b/src/org/labkey/targetedms/parser/AbstractChromInfo.java
index cec984e0f..4b38e0ac4 100644
--- a/src/org/labkey/targetedms/parser/AbstractChromInfo.java
+++ b/src/org/labkey/targetedms/parser/AbstractChromInfo.java
@@ -62,7 +62,7 @@ public abstract class AbstractChromInfo extends ChromInfo<PrecursorChromInfoAnno
         int length = key.third;
 
         long startTime = System.currentTimeMillis();
-        LOG.debug("Loading chromatogram from " + path + ", offset " + offset + ", length " + length);
+        LOG.debug("Loading chromatogram from {}, offset {}, length {}", path, offset, length);
         try (SeekableByteChannel channel = Files.newByteChannel(path, StandardOpenOption.READ, StandardOpenOption.SPARSE))
         {
             channel.position(offset);
@@ -70,13 +70,13 @@ public abstract class AbstractChromInfo extends ChromInfo<PrecursorChromInfoAnno
             channel.read(byteBuffer);
             byteBuffer.position(0);
             byte[] results = byteBuffer.array();
-            LOG.debug("Finished loading from " + path + ", offset " + offset + ", length " + length + " in " + (System.currentTimeMillis() - startTime) + "ms");
+            LOG.debug("Finished loading from {}, offset {}, length {} in {}ms", path, offset, length, System.currentTimeMillis() - startTime);
             return new CachedBytes(results);
         }
         catch (NoSuchFileException e)
         {
             // Avoid a separate call to Files.exists() as it adds ~1 second overhead
-            LOG.debug("Could not find SKYD file to get chromatogram at path " + path);
+            LOG.debug("Could not find SKYD file to get chromatogram at path {}", path);
             return null;
         }
         catch (RuntimeException e)
@@ -84,14 +84,14 @@ public abstract class AbstractChromInfo extends ChromInfo<PrecursorChromInfoAnno
             if (e.getMessage() != null && e.getMessage().contains("The specified key does not exist"))
             {
                 // Avoid a separate call to Files.exists() as it adds ~1 second overhead
-                LOG.debug("Could not find SKYD file to get chromatogram at path " + path + ": " + e.getMessage());
+                LOG.debug("Could not find SKYD file to get chromatogram at path {}: {}", path, e.getMessage());
                 return null;
             }
             throw e;
         }
         catch (IOException e)
         {
-            LOG.warn("Unable to fetch chromatogram from " + path, e);
+            LOG.warn("Unable to fetch chromatogram from {}", path, e);
             return null;
         }
     });
@@ -237,11 +237,11 @@ private CompressedBytesAndStatus getCompressedBytesAndStatus(TargetedMSRun run)
                 if (skydPath == null)
                 {
                     status = Chromatogram.SourceStatus.skydMissing;
-                    LOG.debug("No path available for " + this + ", bucket may be unavailable for URL " + skydData.getDataFileUrl());
+                    LOG.debug("No path available for {}, bucket may be unavailable for URL {}", this, skydData.getDataFileUrl());
                 }
                 else
                 {
-                    LOG.debug("Attempting to fetch chromatogram bytes (possibly cached) from " + skydPath + " for " + this);
+                    LOG.debug("Attempting to fetch chromatogram bytes (possibly cached) from {} for {}", skydPath, this);
                     CachedBytes diskBytes = ON_DEMAND_CHROM_CACHE.get(new Tuple3<>(skydPath, _chromatogramOffset, _chromatogramLength));
                     if (diskBytes == null)
                     {
@@ -249,7 +249,7 @@ private CompressedBytesAndStatus getCompressedBytesAndStatus(TargetedMSRun run)
                     }
                     else if (databaseBytes != null && !Arrays.equals(databaseBytes, diskBytes._bytes))
                     {
-                        LOG.error("Chromatogram bytes for " + this + " do not match between .skyd and DB. Using database copy. Lengths: " + diskBytes._bytes.length + " vs " + databaseBytes.length);
+                        LOG.error("Chromatogram bytes for {} do not match between .skyd and DB. Using database copy. Lengths: {} vs {}", this, diskBytes._bytes.length, databaseBytes.length);
                         status = Chromatogram.SourceStatus.mismatch;
                     }
                     else
@@ -266,7 +266,7 @@ else if (databaseBytes != null && !Arrays.equals(databaseBytes, diskBytes._bytes
         }
         else
         {
-            LOG.debug("No length, offset, and/or SKYD DataId for " + this);
+            LOG.debug("No length, offset, and/or SKYD DataId for {}", this);
             status = Chromatogram.SourceStatus.dbOnly;
         }
 
diff --git a/src/org/labkey/targetedms/parser/Chromatogram.java b/src/org/labkey/targetedms/parser/Chromatogram.java
index 6187bf589..d33c483cf 100644
--- a/src/org/labkey/targetedms/parser/Chromatogram.java
+++ b/src/org/labkey/targetedms/parser/Chromatogram.java
@@ -78,7 +78,7 @@ public float[] getTimes()
     {
         if (_mergedTimes == null) {
             if (allSameTimes()) {
-                _mergedTimes = getTransitionTimeIntensities().get(0).getTimes();
+                _mergedTimes = getTransitionTimeIntensities().getFirst().getTimes();
             } else {
                 _mergedTimes = getAllTimesMerged();
             }
diff --git a/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java b/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java
index 5fabd3e4e..30d6d0399 100644
--- a/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java
+++ b/src/org/labkey/targetedms/parser/PeakAreaRatioCalculator.java
@@ -276,13 +276,7 @@ PrecursorChromInfo getChromInfo(long isotopeLabelId)
         TransitionAreaRatioCalculator getTransitionAreaRatioCalculator(TransitionType transition, PrecursorType precursor)
         {
             String transitionKey = getTransitionKey(transition, precursor);
-            TransitionAreaRatioCalculator calculator = _calculatorMap.get(transitionKey);
-            if(calculator == null)
-            {
-                calculator = new TransitionAreaRatioCalculator();
-                _calculatorMap.put(transitionKey, calculator);
-            }
-            return calculator;
+            return _calculatorMap.computeIfAbsent(transitionKey, _ -> new TransitionAreaRatioCalculator());
         }
     }
 
diff --git a/src/org/labkey/targetedms/parser/PeptideSettingsParser.java b/src/org/labkey/targetedms/parser/PeptideSettingsParser.java
index 4e37d9522..665659d94 100644
--- a/src/org/labkey/targetedms/parser/PeptideSettingsParser.java
+++ b/src/org/labkey/targetedms/parser/PeptideSettingsParser.java
@@ -226,7 +226,7 @@ else if(XmlUtil.isStartElement(reader, evtType, HEAVY_MODIFICATIONS))
         }
 
         // Mark the label types that were used as an internal standard
-        isotopeLabelNames.add(0, PeptideSettings.IsotopeLabel.LIGHT);
+        isotopeLabelNames.addFirst(PeptideSettings.IsotopeLabel.LIGHT);
 
         // If we did not find either the "internal_standard" attribute or elements, check if we have
         // a "heavy" isotope label.  If we do, set "heavy" as the internal standard
diff --git a/src/org/labkey/targetedms/parser/PrecursorChromInfo.java b/src/org/labkey/targetedms/parser/PrecursorChromInfo.java
index 472fe1b6f..45a6cb375 100644
--- a/src/org/labkey/targetedms/parser/PrecursorChromInfo.java
+++ b/src/org/labkey/targetedms/parser/PrecursorChromInfo.java
@@ -461,7 +461,7 @@ public void setTransitionChromatogramIndices(byte[] bytes)
             }
             catch (IOException e)
             {
-                LOG.error("Unable to read " + bytes.length + " of transition chromatogram indices");
+                LOG.error("Unable to read {} of transition chromatogram indices", bytes.length);
             }
 
         }
diff --git a/src/org/labkey/targetedms/parser/Protein.java b/src/org/labkey/targetedms/parser/Protein.java
index c514758c0..20fb8653b 100644
--- a/src/org/labkey/targetedms/parser/Protein.java
+++ b/src/org/labkey/targetedms/parser/Protein.java
@@ -179,7 +179,7 @@ public void setCdrRanges(String cdrRangesString)
                 }
                 catch (NumberFormatException e)
                 {
-                    LOG.debug("Invalid protein CDR value: " + cdrRangesString);
+                    LOG.debug("Invalid protein CDR value: {}", cdrRangesString);
                 }
             }
         }
diff --git a/src/org/labkey/targetedms/parser/SampleFile.java b/src/org/labkey/targetedms/parser/SampleFile.java
index b3c24c25b..82649f70d 100644
--- a/src/org/labkey/targetedms/parser/SampleFile.java
+++ b/src/org/labkey/targetedms/parser/SampleFile.java
@@ -281,8 +281,8 @@ public void testGetFileName()
             String path = "C:\\Users\\lab\\Data\\2017-Geoduck-SRM-raw\\" + fileName;
             String pathWithParams = path + "?centroid_ms1=true&centroid_ms2=true";
 
-            assertTrue(fileName.equals(getFileName(path)));
-            assertTrue(fileName.equals(getFileName(pathWithParams)));
+            assertEquals(fileName, getFileName(path));
+            assertEquals(fileName, getFileName(pathWithParams));
 
             // Skyline stores multi-injection wiff file paths as: <wiff_file_path>|<sample_name>|<sample_index>
             // Example: C:\Analyst Data\Projects\CPTAC\Site54_STUDY9S_PHASE1_6ProtMix_090919\Site54_190909_Study9S_PHASE-1.wiff|Site54_STUDY9S_PHASE1_6ProtMix_QC_03|2
@@ -290,14 +290,14 @@ public void testGetFileName()
             path = "C:\\Analyst Data\\Projects\\CPTAC\\Site54_STUDY9S_PHASE1_6ProtMix_090919\\" + fileName;
             String pathWithSampleInfo = path + "|Site54_STUDY9S_PHASE1_6ProtMix_QC_03|2";
 
-            assertTrue(fileName.equals(getFileName(path)));
-            assertTrue(fileName.equals(getFileName(pathWithSampleInfo)));
+            assertEquals(fileName, getFileName(path));
+            assertEquals(fileName, getFileName(pathWithSampleInfo));
 
             // Add a bogus param with a '|' character
             String pathWithSampleInfoAndParams = pathWithSampleInfo + "?centroid_ms1=true&centroid_ms2=true&madeup_param=a|b";
 
-            assertTrue(fileName.equals(getFileName(path)));
-            assertTrue(fileName.equals(getFileName(pathWithSampleInfoAndParams)));
+            assertEquals(fileName, getFileName(path));
+            assertEquals(fileName, getFileName(pathWithSampleInfoAndParams));
         }
     }
 }
diff --git a/src/org/labkey/targetedms/parser/SkylineBinaryParser.java b/src/org/labkey/targetedms/parser/SkylineBinaryParser.java
index 6e14a143c..c472405f2 100644
--- a/src/org/labkey/targetedms/parser/SkylineBinaryParser.java
+++ b/src/org/labkey/targetedms/parser/SkylineBinaryParser.java
@@ -116,7 +116,7 @@ public void close()
         {
             if (!_file.delete())
             {
-                _log.warn("Failed to delete temp copy of SKYD file: " + _file.getAbsolutePath());
+                _log.warn("Failed to delete temp copy of SKYD file: {}", _file.getAbsolutePath());
             }
             else
             {
@@ -133,11 +133,11 @@ public void parse() throws IOException
         _cacheFormat = new CacheFormat(_cacheHeaderStruct);
 
         if (_cacheFormat.getFormatVersion().compareTo(CacheFormatVersion.Two) < 0) {
-            _log.warn("Version " + _cacheFormat.getFormatVersion() + " is not supported for .skyd files. The earliest supported version is " + CacheFormatVersion.Two + ". Skipping chromatogram import.");
+            _log.warn("Version {} is not supported for .skyd files. The earliest supported version is {}. Skipping chromatogram import.", _cacheFormat.getFormatVersion(), CacheFormatVersion.Two);
             return;
         }
         if (_cacheFormat.getVersionRequired().compareTo(FORMAT_VERSION_CACHE) > 0) {
-            _log.warn("Version " + _cacheFormat.getVersionRequired() + " is not supported for .skyd files. The newest supported version is " + FORMAT_VERSION_CACHE + ". Skipping chromatogram import.");
+            _log.warn("Version {} is not supported for .skyd files. The newest supported version is {}. Skipping chromatogram import.", _cacheFormat.getVersionRequired(), FORMAT_VERSION_CACHE);
             return;
         }
 
diff --git a/src/org/labkey/targetedms/parser/SkylineDocumentParser.java b/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
index 104c4f589..810fdb8e6 100644
--- a/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
+++ b/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
@@ -45,7 +45,6 @@
 import org.labkey.targetedms.parser.proto.SkylineDocument;
 import org.labkey.targetedms.parser.skyd.ChromGroupHeaderInfo;
 
-import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
 import java.io.File;
@@ -286,7 +285,7 @@ private void parseOptDbFiles()
             String optDbFileName = FilenameUtils.getName(optDbPath);
             File optDbFile = new File(_file.getParent(), optDbFileName);
             if (! optDbFile.exists() ) {
-                _log.warn("Input OPTDB database does not exist " + optDbFileName);
+                _log.warn("Input OPTDB database does not exist {}", optDbFileName);
             }
             else
             {
@@ -303,7 +302,7 @@ private void parseOptDbFiles()
                                 schemaVersion = rs.getInt("SchemaVersion");
                                 if (schemaVersion > 3)
                                 {
-                                    _log.warn("Unsupported OPTDB version: " + schemaVersion + " in OPTDB file " + optDbFile + ", attempting to continue");
+                                    _log.warn("Unsupported OPTDB version: {} in OPTDB file {}, attempting to continue", schemaVersion, optDbFile);
                                 }
                             }
                             else
@@ -358,7 +357,7 @@ private void parseiRTFile()
             String iRTFileName = FilenameUtils.getName(irtDatabasePath);
             File iRTFile = new File(_file.getParent(), iRTFileName);
             if (! iRTFile.exists() ) {
-                _log.warn("Input iRT database does not exist " + iRTFileName);
+                _log.warn("Input iRT database does not exist {}", iRTFileName);
             }
             else
             {
@@ -412,7 +411,7 @@ private ExpData parseChromatograms(@NotNull Container container, @NotNull User u
         }
         else
         {
-            _log.warn("Unable to find file " + skydFile + ", unable to import chromatograms");
+            _log.warn("Unable to find file {}, unable to import chromatograms", skydFile);
         }
         return null;
     }
@@ -460,8 +459,7 @@ private void readDocumentVersion(XMLStreamReader reader) throws XMLStreamExcepti
                 else if(version > MAX_SUPPORTED_VERSION)
                 {
                     // We will log a warning but continue with the import.
-                    _log.warn("The version of this Skyline document is " + version +
-                              ". This is newer than the highest supported version " + MAX_SUPPORTED_VERSION);
+                    _log.warn("The version of this Skyline document is {}. This is newer than the highest supported version " + MAX_SUPPORTED_VERSION, version);
                 }
 
                 _formatVersion = String.valueOf(version);
@@ -1054,7 +1052,7 @@ else if(XmlUtil.isStartElement(reader, evtType, ANNOTATION))
             if(sampleFileList.size() == 1)
             {
                 // Only for replicates with single sample files, store the id given by Skyline to the sample file.
-                _replicateSampleFileIdMap.put(replicate.getName(), sampleFileList.get(0).getSkylineId());
+                _replicateSampleFileIdMap.put(replicate.getName(), sampleFileList.getFirst().getSkylineId());
             }
         }
 
@@ -1391,7 +1389,7 @@ public void logMissingChromatogramCounts()
     {
         for (Map.Entry<String, AtomicInteger> entry : _missingChromatograms.entrySet())
         {
-            _log.warn("Missed importing " + entry.getValue().intValue() + " chromatograms from sample file " + entry.getKey());
+            _log.warn("Missed importing {} chromatograms from sample file {}", entry.getValue().intValue(), entry.getKey());
         }
     }
 
diff --git a/src/org/labkey/targetedms/parser/Target.java b/src/org/labkey/targetedms/parser/Target.java
index bae200fd4..d7f7685e2 100644
--- a/src/org/labkey/targetedms/parser/Target.java
+++ b/src/org/labkey/targetedms/parser/Target.java
@@ -131,7 +131,7 @@ public static Target fromChromatogramTextId(String textId)
 
         if (!parts.isEmpty())
         {
-            target.name = parts.get(0);
+            target.name = parts.getFirst();
         }
         if (parts.size() > 1)
         {
diff --git a/src/org/labkey/targetedms/parser/TransitionSettings.java b/src/org/labkey/targetedms/parser/TransitionSettings.java
index e1d3e4902..d7ace095e 100644
--- a/src/org/labkey/targetedms/parser/TransitionSettings.java
+++ b/src/org/labkey/targetedms/parser/TransitionSettings.java
@@ -667,7 +667,7 @@ public int hashCode()
         }
 
         @Override
-        public int compareTo(PredictorSettings o)
+        public int compareTo(@NotNull PredictorSettings o)
         {
             return o == null ? -1 : this.toString().compareTo(o.toString());
         }
diff --git a/src/org/labkey/targetedms/parser/list/ListData.java b/src/org/labkey/targetedms/parser/list/ListData.java
index 600ed89dc..4c62aed5c 100644
--- a/src/org/labkey/targetedms/parser/list/ListData.java
+++ b/src/org/labkey/targetedms/parser/list/ListData.java
@@ -37,7 +37,7 @@ public int getItemCount()
         if (_columnDatas.isEmpty()) {
             return 0;
         }
-        return _columnDatas.get(0).size();
+        return _columnDatas.getFirst().size();
     }
 
     public int getColumnCount() {
diff --git a/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java b/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java
index e609ce1d2..24b437afc 100644
--- a/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java
+++ b/src/org/labkey/targetedms/parser/proto/ChromatogramGroupDataOuterClass.java
@@ -9315,7 +9315,7 @@ public FilterOperation findValueByNumber(int number)
       }
       public static final com.google.protobuf.Descriptors.EnumDescriptor
           getDescriptor() {
-        return org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.getDescriptor().getEnumTypes().get(0);
+        return org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.ChromatogramGroupIdsProto.getDescriptor().getEnumTypes().getFirst();
       }
 
       private static final FilterOperation[] VALUES = values();
@@ -15982,7 +15982,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma
         new com.google.protobuf.Descriptors.FileDescriptor[] {
         });
     internal_static_ChromatogramGroupData_descriptor =
-      getDescriptor().getMessageTypes().get(0);
+      getDescriptor().getMessageTypes().getFirst();
     internal_static_ChromatogramGroupData_fieldAccessorTable = new
       com.google.protobuf.GeneratedMessageV3.FieldAccessorTable(
         internal_static_ChromatogramGroupData_descriptor,
@@ -16060,7 +16060,7 @@ public org.labkey.targetedms.parser.proto.ChromatogramGroupDataOuterClass.Chroma
         internal_static_ChromatogramGroupIdsProto_SpectrumFilter_descriptor,
         new java.lang.String[] { "Predicates", });
     internal_static_ChromatogramGroupIdsProto_SpectrumFilter_Predicate_descriptor =
-      internal_static_ChromatogramGroupIdsProto_SpectrumFilter_descriptor.getNestedTypes().get(0);
+      internal_static_ChromatogramGroupIdsProto_SpectrumFilter_descriptor.getNestedTypes().getFirst();
     internal_static_ChromatogramGroupIdsProto_SpectrumFilter_Predicate_fieldAccessorTable = new
       com.google.protobuf.GeneratedMessageV3.FieldAccessorTable(
         internal_static_ChromatogramGroupIdsProto_SpectrumFilter_Predicate_descriptor,
diff --git a/src/org/labkey/targetedms/parser/proto/SkylineDocument.java b/src/org/labkey/targetedms/parser/proto/SkylineDocument.java
index 92a6f382b..fa23c53d8 100644
--- a/src/org/labkey/targetedms/parser/proto/SkylineDocument.java
+++ b/src/org/labkey/targetedms/parser/proto/SkylineDocument.java
@@ -169,7 +169,7 @@ public UserSet findValueByNumber(int number)
       }
       public static final com.google.protobuf.Descriptors.EnumDescriptor
           getDescriptor() {
-        return org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.getDescriptor().getEnumTypes().get(0);
+        return org.labkey.targetedms.parser.proto.SkylineDocument.SkylineDocumentProto.getDescriptor().getEnumTypes().getFirst();
       }
 
       private static final UserSet[] VALUES = values();
@@ -18724,7 +18724,7 @@ public KeyType findValueByNumber(int number)
       }
       public static final com.google.protobuf.Descriptors.EnumDescriptor
           getDescriptor() {
-        return org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.getDescriptor().getEnumTypes().get(0);
+        return org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto.getDescriptor().getEnumTypes().getFirst();
       }
 
       private static final KeyType[] VALUES = values();
@@ -22554,7 +22554,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto getDef
           com.google.protobuf.WrappersProto.getDescriptor(),
         });
     internal_static_SkylineDocumentProto_descriptor =
-      getDescriptor().getMessageTypes().get(0);
+      getDescriptor().getMessageTypes().getFirst();
     internal_static_SkylineDocumentProto_fieldAccessorTable = new
       com.google.protobuf.GeneratedMessageV3.FieldAccessorTable(
         internal_static_SkylineDocumentProto_descriptor,
@@ -22578,7 +22578,7 @@ public org.labkey.targetedms.parser.proto.SkylineDocument.LibraryKeyProto getDef
         internal_static_SkylineDocumentProto_TransitionPeak_descriptor,
         new java.lang.String[] { "ReplicateIndex", "FileIndexInReplicate", "MassError", "RetentionTime", "StartRetentionTime", "EndRetentionTime", "IonMobility", "IonMobilityWindow", "Area", "BackgroundArea", "Height", "Fwhm", "IsFwhmDegenerate", "Truncated", "Identified", "Rank", "RankByLevel", "PointsAcrossPeak", "UserSet", "OptimizationStep", "Annotations", "ForcedIntegration", "PeakShapeValues", "IonMobilityCollisionCrossSection", });
     internal_static_SkylineDocumentProto_TransitionPeak_PeakShapeValues_descriptor =
-      internal_static_SkylineDocumentProto_TransitionPeak_descriptor.getNestedTypes().get(0);
+      internal_static_SkylineDocumentProto_TransitionPeak_descriptor.getNestedTypes().getFirst();
     internal_static_SkylineDocumentProto_TransitionPeak_PeakShapeValues_fieldAccessorTable = new
       com.google.protobuf.GeneratedMessageV3.FieldAccessorTable(
         internal_static_SkylineDocumentProto_TransitionPeak_PeakShapeValues_descriptor,
diff --git a/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java b/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java
index 2d0e35445..d42f04e9a 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/AuditLogEntry.java
@@ -76,7 +76,7 @@ public static AuditLogEntry retrieve(int pEntryId)
         List<AuditLogEntry> results = sel.getArrayList(AuditLogEntry.class);
         // Possible to get more than one match if two documents share an audit history. In this case, we don't care
         // which we use
-        return results.isEmpty() ? null : results.get(0);
+        return results.isEmpty() ? null : results.getFirst();
     }
 
     public AuditLogTree getTreeEntry(){
diff --git a/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java b/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java
index 2ac567cf1..c0f2cae7a 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/AuditLogTree.java
@@ -119,7 +119,7 @@ public int getTreeSize()
 
         while (!stack.isEmpty())
         {
-            AuditLogTree current = stack.remove(0);
+            AuditLogTree current = stack.removeFirst();
             result += current._children.size();
             stack.addAll(current._children.values());
         }
@@ -176,7 +176,7 @@ public Set<AuditLogTree> deleteList(long versionId)
                 {
                     if (currentEntry._entryId != 0)                  //No need to check for the root node.
                     {
-                        LOG.warn(String.format("Audit log entry with ID %d is a leaf but has no version ID. This might be a data corruption.", this._entryId));
+                        LOG.warn("Audit log entry with ID {} is a leaf but has no version ID. This might be a data corruption.", this._entryId);
                     }
                 }
                 else if (versionId == currentEntry._versionId)      //check if it is the right version id
@@ -232,7 +232,7 @@ public AuditLogTree findVersionEntry(long pVersionId)
 
         while (!stack.isEmpty())
         {
-            AuditLogTree currentEntry = stack.remove(0);
+            AuditLogTree currentEntry = stack.removeFirst();
             // check if it is the right version id
             if (currentEntry._versionId != null && currentEntry._versionId == pVersionId)
             {
diff --git a/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java b/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java
index ab050b3aa..725b8bd21 100644
--- a/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java
+++ b/src/org/labkey/targetedms/parser/skyaudit/UnitTestUtil.java
@@ -38,7 +38,6 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.io.UnsupportedEncodingException;
 import java.net.URL;
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
diff --git a/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java b/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java
index db436891a..d178bb297 100644
--- a/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java
+++ b/src/org/labkey/targetedms/parser/speclib/BlibSpectrumReader.java
@@ -127,7 +127,7 @@ private static boolean malformedBlibFileError(String blibFilePath, SQLException
     {
         if(e.getMessage().contains("no such table") || e.getMessage().contains("no such column") || e.getMessage().contains("File opened that is not a database file"))
         {
-            LOG.error("Malformed .blib file " + blibFilePath + ". Error was: " + e.getMessage());
+            LOG.error("Malformed .blib file {}. Error was: {}", blibFilePath, e.getMessage());
             return true;
         }
         return false;
@@ -415,7 +415,7 @@ private static void addRedundantSpectrumInfo(Connection conn, BlibSpectrum spect
                 if (rSpec.isBestSpectrum())
                 {
                     // If this is the reference spectrum keep it in front of the list.
-                    redundantSpectra.add(0, rSpec);
+                    redundantSpectra.addFirst(rSpec);
                 }
                 else
                 {
diff --git a/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java b/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java
index 182839d81..dcb350074 100644
--- a/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java
+++ b/src/org/labkey/targetedms/parser/speclib/ElibSpectrumReader.java
@@ -106,7 +106,7 @@ private ElibSpectrum readElibSpectrum(Connection conn, SpectrumKey spectrumKey,
         if(!spectra.isEmpty())
         {
             sortElibSpectra(spectra);
-            ElibSpectrum bestSpectrum = spectra.get(0);
+            ElibSpectrum bestSpectrum = spectra.getFirst();
             readPeaks(conn, bestSpectrum);
 
             if(getRedundant)
diff --git a/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java b/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java
index fcf7f2e7b..f58728715 100644
--- a/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java
+++ b/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java
@@ -218,7 +218,7 @@ static String getNonEmptyLocalLibPath(Container container, Path libPath)
             }
             else
             {
-                LOG.debug("Unable to copy " + libPath + " to local file, referenced from " + container.getPath());
+                LOG.debug("Unable to copy {} to local file, referenced from {}", libPath, container.getPath());
                 return null;
             }
         }
@@ -229,12 +229,12 @@ static String getNonEmptyLocalLibPath(Container container, Path libPath)
         File f = new File(libPathString);
         if(!f.exists())
         {
-            LOG.debug("Library file not found: " + libPathString + ", referenced from container " + container.getPath());
+            LOG.debug("Library file not found: {}, referenced from container {}", libPathString, container.getPath());
             return null;
         }
         if(f.length() == 0)
         {
-            LOG.debug("Found 0 byte library file: " + libPathString + ", referenced from container " + container.getPath());
+            LOG.debug("Found 0 byte library file: {}, referenced from container {}", libPathString, container.getPath());
             return null;
         }
         return libPathString;
diff --git a/src/org/labkey/targetedms/passport/PassportController.java b/src/org/labkey/targetedms/passport/PassportController.java
index 0e8afed5c..7cb653b50 100644
--- a/src/org/labkey/targetedms/passport/PassportController.java
+++ b/src/org/labkey/targetedms/passport/PassportController.java
@@ -61,7 +61,6 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
diff --git a/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java b/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java
index 950139b66..5c32636a0 100644
--- a/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java
+++ b/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java
@@ -47,7 +47,7 @@ public ChromatogramCrawlerJob(ViewBackgroundInfo info, @NotNull PipeRoot root)
         getLogger().info("Description of key statuses:");
         for (Chromatogram.SourceStatus value : Chromatogram.SourceStatus.values())
         {
-            getLogger().info("\t" + value.toString() + ": " + value.getDescription());
+            getLogger().info("\t{}: {}", value.toString(), value.getDescription());
         }
         getLogger().info("\n");
     }
@@ -81,7 +81,7 @@ public void run()
         setStatus(TaskStatus.running);
         var containers = ContainerManager.getAllChildren(getContainer(), getUser());
 
-        getLogger().info("Starting to process chromatogram rows over " + containers.size() + " containers");
+        getLogger().info("Starting to process chromatogram rows over {} containers", containers.size());
 
         CrawlSummary crawlSummary = new CrawlSummary();
 
@@ -99,11 +99,11 @@ public void run()
 
             if (containerPCICount == 0)
             {
-                getLogger().info("Skipping container " + container.getPath() + " - no chromatogram rows to process");
+                getLogger().info("Skipping container {} - no chromatogram rows to process", container.getPath());
             }
             else
             {
-                getLogger().info("Starting processing of container " + container.getPath() + " (" + containerCount + " of " + containers.size() + ") with " + containerPCICount + " chromatogram rows to process");
+                getLogger().info("Starting processing of container {} ({} of {}) with {} chromatogram rows to process", container.getPath(), containerCount, containers.size(), containerPCICount);
 
                 var handler = new PrecursorChromInfoHandler(container);
                 try
diff --git a/src/org/labkey/targetedms/query/AnnotatedTargetedMSTable.java b/src/org/labkey/targetedms/query/AnnotatedTargetedMSTable.java
index f462dc497..f1a718f0e 100644
--- a/src/org/labkey/targetedms/query/AnnotatedTargetedMSTable.java
+++ b/src/org/labkey/targetedms/query/AnnotatedTargetedMSTable.java
@@ -140,7 +140,7 @@ protected void addAnnotationsColumns(TableInfo annotationTableInfo, String annot
                 listDefs = listDefs.stream().filter((l) -> lookup.equals(l.getName())).toList();
                 if (!listDefs.isEmpty())
                 {
-                    ListDefinition listDef = listDefs.get(0);
+                    ListDefinition listDef = listDefs.getFirst();
                     // Use the first one (the most recent import) as our FK to a UNION version of the table
                     LookupForeignKey fk = new LookupForeignKey()
                     {
diff --git a/src/org/labkey/targetedms/query/CDRConditionalFormattingDisplayColumnFactory.java b/src/org/labkey/targetedms/query/CDRConditionalFormattingDisplayColumnFactory.java
index c4fd26833..865414af0 100644
--- a/src/org/labkey/targetedms/query/CDRConditionalFormattingDisplayColumnFactory.java
+++ b/src/org/labkey/targetedms/query/CDRConditionalFormattingDisplayColumnFactory.java
@@ -1,6 +1,5 @@
 package org.labkey.targetedms.query;
 
-import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.CompareType;
diff --git a/src/org/labkey/targetedms/query/CrossLinkedPeptideDisplayColumn.java b/src/org/labkey/targetedms/query/CrossLinkedPeptideDisplayColumn.java
index 24f02c55c..886fe3247 100644
--- a/src/org/labkey/targetedms/query/CrossLinkedPeptideDisplayColumn.java
+++ b/src/org/labkey/targetedms/query/CrossLinkedPeptideDisplayColumn.java
@@ -16,7 +16,6 @@
 
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
diff --git a/src/org/labkey/targetedms/query/JoinedTargetedMSTable.java b/src/org/labkey/targetedms/query/JoinedTargetedMSTable.java
index cd606dab4..29d3c463d 100644
--- a/src/org/labkey/targetedms/query/JoinedTargetedMSTable.java
+++ b/src/org/labkey/targetedms/query/JoinedTargetedMSTable.java
@@ -118,9 +118,9 @@ public SQLFragment getFromSQL(String alias)
 
         // Join based on the PKs on both tables
         result.append(" ON G.");
-        result.append(getRealTable().getPkColumnNames().get(0));
+        result.append(getRealTable().getPkColumnNames().getFirst());
         result.append(" = S.");
-        result.append(_specializedTable.getPkColumnNames().get(0));
+        result.append(_specializedTable.getPkColumnNames().getFirst());
         result.append(") i ");
 
         // Re-add the clauses, but only the ones associated with a FieldKey because the others wouldn't have been removed above
diff --git a/src/org/labkey/targetedms/query/LibraryManager.java b/src/org/labkey/targetedms/query/LibraryManager.java
index 53bba6f86..561f66c36 100644
--- a/src/org/labkey/targetedms/query/LibraryManager.java
+++ b/src/org/labkey/targetedms/query/LibraryManager.java
@@ -167,13 +167,13 @@ private static String getDocumentLibFileName(Path skyFilesDir)
         }
         catch (IOException e)
         {
-            LOG.info("Failed to determine the document library file name for " + skyFilesDir + ", continuing without a library file name.", e);
+            LOG.info("Failed to determine the document library file name for {}, continuing without a library file name.", skyFilesDir, e);
         }
 
         if(!skyFiles.isEmpty())
         {
             // Documents libraries have the same name as the .sky file, with a .blib extension.
-            return skyFiles.get(0).substring(0, skyFiles.get(0).lastIndexOf('.')) + SkylineFileUtils.EXT_BLIB_W_DOT;
+            return skyFiles.getFirst().substring(0, skyFiles.getFirst().lastIndexOf('.')) + SkylineFileUtils.EXT_BLIB_W_DOT;
         }
 
         return null;
diff --git a/src/org/labkey/targetedms/query/ModifiedSequenceDisplayColumn.java b/src/org/labkey/targetedms/query/ModifiedSequenceDisplayColumn.java
index abe3d3ffc..fa7194faa 100644
--- a/src/org/labkey/targetedms/query/ModifiedSequenceDisplayColumn.java
+++ b/src/org/labkey/targetedms/query/ModifiedSequenceDisplayColumn.java
@@ -42,7 +42,6 @@
 
 import java.util.Collection;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -320,13 +319,13 @@ public void initialize(RenderContext ctx)
                                 }
                                 else
                                 {
-                                    LOG.debug("Modified residue didn't match for " + modificationSite + " at calculated index " + aaIndex + " on peptide " + sequence + " in document " + runId);
+                                    LOG.debug("Modified residue didn't match for {} at calculated index {} on peptide {} in document {}", modificationSite, aaIndex, sequence, runId);
                                 }
                             }
                         }
                         catch (NumberFormatException ignored)
                         {
-                            LOG.debug("Bad modificationSite value: " + modificationSite + " in document " + runId);
+                            LOG.debug("Bad modificationSite value: {} in document {}", modificationSite, runId);
                         }
                     }
                 }
diff --git a/src/org/labkey/targetedms/query/PeptideGroupManager.java b/src/org/labkey/targetedms/query/PeptideGroupManager.java
index b57cd0f0a..abb5effdb 100644
--- a/src/org/labkey/targetedms/query/PeptideGroupManager.java
+++ b/src/org/labkey/targetedms/query/PeptideGroupManager.java
@@ -95,7 +95,7 @@ public static List<Protein> getProteinsForRun(long runId)
     public static Protein getProteinForPeptideGroupId(long id)
     {
         List<Protein> result = getProteins(new SQLFragment("pg.Id = ?", id));
-        return result.isEmpty() ? null : result.get(0);
+        return result.isEmpty() ? null : result.getFirst();
     }
 
     public static List<Protein> getProteins(SQLFragment whereSql)
diff --git a/src/org/labkey/targetedms/query/PrecursorManager.java b/src/org/labkey/targetedms/query/PrecursorManager.java
index 3009b6f75..a5afe7651 100644
--- a/src/org/labkey/targetedms/query/PrecursorManager.java
+++ b/src/org/labkey/targetedms/query/PrecursorManager.java
@@ -176,7 +176,7 @@ public static PrecursorChromInfo getBestPrecursorChromInfo(@NotNull List<Precurs
                 return chromInfo;
             }
         }
-        return chromInfos.get(0);
+        return chromInfos.getFirst();
     }
 
     @NotNull
diff --git a/src/org/labkey/targetedms/query/QCAnnotationTable.java b/src/org/labkey/targetedms/query/QCAnnotationTable.java
index 781e19eb4..e4b2c6980 100644
--- a/src/org/labkey/targetedms/query/QCAnnotationTable.java
+++ b/src/org/labkey/targetedms/query/QCAnnotationTable.java
@@ -27,7 +27,6 @@
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.QueryUpdateServiceException;
 import org.labkey.api.query.SimpleUserSchema;
-import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSSchema;
diff --git a/src/org/labkey/targetedms/query/SampleFileTable.java b/src/org/labkey/targetedms/query/SampleFileTable.java
index d250ef4c0..ef0d52684 100644
--- a/src/org/labkey/targetedms/query/SampleFileTable.java
+++ b/src/org/labkey/targetedms/query/SampleFileTable.java
@@ -310,7 +310,7 @@ public List<FieldKey> getDefaultVisibleColumns()
                 List<Aggregate.Result> result = aggValues.get(aggregate.getFieldKey().toString());
                 if(result != null)
                 {
-                    Aggregate.Result aggResult = result.get(0);
+                    Aggregate.Result aggResult = result.getFirst();
                     if (aggResult.getValue() != null)
                     {
                         defaultCols.add(aggResult.getAggregate().getFieldKey());
diff --git a/src/org/labkey/targetedms/query/SkylineListSchema.java b/src/org/labkey/targetedms/query/SkylineListSchema.java
index b7dcce9d9..90ce5042d 100644
--- a/src/org/labkey/targetedms/query/SkylineListSchema.java
+++ b/src/org/labkey/targetedms/query/SkylineListSchema.java
@@ -61,7 +61,7 @@ private List<ListDefinition> getListDefinitions(@Nullable ContainerFilter contai
             if (!listDefs.isEmpty())
             {
                 // Use the first one as the base, as it is the most recently imported version
-                ListDefinition firstListDef = listDefs.get(0);
+                ListDefinition firstListDef = listDefs.getFirst();
                 SkylineListTable firstTable = new SkylineListTable(this, firstListDef);
                 SkylineListUnionTable result = new SkylineListUnionTable(this, firstTable);
 
diff --git a/src/org/labkey/targetedms/view/CrossLinkedPeptideInfo.java b/src/org/labkey/targetedms/view/CrossLinkedPeptideInfo.java
index c8774a0c4..242867f5e 100644
--- a/src/org/labkey/targetedms/view/CrossLinkedPeptideInfo.java
+++ b/src/org/labkey/targetedms/view/CrossLinkedPeptideInfo.java
@@ -218,8 +218,8 @@ public void testSingleCrossLink()
             Assert.assertEquals("Linker count", 1, i._linkers.size());
             Assert.assertEquals("Extra sequences", 1, i.getExtraSequences().size());
             Assert.assertEquals("Link location", Set.of(1), i.getBaseSequence().getLinkIndices());
-            Assert.assertEquals("Link location", Set.of(2), i.getExtraSequences().get(0).getLinkIndices());
-            Assert.assertEquals("Linker mass", -2.01565, i._linkers.get(0).getMass(), 0.00001);
+            Assert.assertEquals("Link location", Set.of(2), i.getExtraSequences().getFirst().getLinkIndices());
+            Assert.assertEquals("Linker mass", -2.01565, i._linkers.getFirst().getMass(), 0.00001);
         }
 
         @Test
@@ -230,7 +230,7 @@ public void testModifiedAndMultiLinked()
             Assert.assertEquals("Modified peptides", Arrays.asList("SC[+57.0]DK", "GE[-4.5]C"), i._modifiedPeptides);
             Assert.assertEquals("Linker count", 1, i._linkers.size());
             Assert.assertEquals("Link location", Set.of(1, 2), i.getBaseSequence().getLinkIndices());
-            Assert.assertEquals("Link location", Set.of(0, 1), i.getExtraSequences().get(0).getLinkIndices());
+            Assert.assertEquals("Link location", Set.of(0, 1), i.getExtraSequences().getFirst().getLinkIndices());
         }
 
         @Test
diff --git a/src/org/labkey/targetedms/view/DocumentTransitionsView.java b/src/org/labkey/targetedms/view/DocumentTransitionsView.java
index e7f6d391c..888e785f1 100644
--- a/src/org/labkey/targetedms/view/DocumentTransitionsView.java
+++ b/src/org/labkey/targetedms/view/DocumentTransitionsView.java
@@ -15,7 +15,6 @@
 
 package org.labkey.targetedms.view;
 
-import org.labkey.api.data.Sort;
 import org.labkey.api.query.QueryNestingOption;
 import org.labkey.api.view.ViewContext;
 import org.labkey.targetedms.TargetedMSSchema;
@@ -38,10 +37,4 @@ public DocumentTransitionsView(ViewContext ctx, TargetedMSSchema schema, String
         _context = ctx;
         setTitle(title);
     }
-
-    @Override
-    protected Sort getBaseSort()
-    {
-        return new Sort("Id");
-    }
 }
diff --git a/src/org/labkey/targetedms/view/IconFactory.java b/src/org/labkey/targetedms/view/IconFactory.java
index 9c0b2231b..f418a5052 100644
--- a/src/org/labkey/targetedms/view/IconFactory.java
+++ b/src/org/labkey/targetedms/view/IconFactory.java
@@ -44,19 +44,12 @@ public static String getPeptideIconPath(long peptideId, Long runId, boolean isDe
             }
             else
             {
-                switch (standardTypeEnum)
+                iconFile = switch (standardTypeEnum)
                 {
-                    case Normalization:
-                    case SurrogateStandard:
-                        iconFile = "/TargetedMS/images/PeptideStandardLib.png";
-                        break;
-                    case QC:
-                        iconFile = "/TargetedMS/images/PeptideQcLib.png";
-                        break;
-                    case iRT:
-                        iconFile = "/TargetedMS/images/PeptideIrtLib.png";
-                        break;
-                }
+                    case Normalization, SurrogateStandard -> "/TargetedMS/images/PeptideStandardLib.png";
+                    case QC -> "/TargetedMS/images/PeptideQcLib.png";
+                    case iRT -> "/TargetedMS/images/PeptideIrtLib.png";
+                };
             }
         }
         else
@@ -67,19 +60,12 @@ public static String getPeptideIconPath(long peptideId, Long runId, boolean isDe
             }
             else
             {
-                switch (standardTypeEnum)
+                iconFile = switch (standardTypeEnum)
                 {
-                    case Normalization:
-                    case SurrogateStandard:
-                        iconFile = "/TargetedMS/images/PeptideStandard.png";
-                        break;
-                    case QC:
-                        iconFile = "/TargetedMS/images/PeptideQc.png";
-                        break;
-                    case iRT:
-                        iconFile = "/TargetedMS/images/PeptideIrt.png";
-                        break;
-                }
+                    case Normalization, SurrogateStandard -> "/TargetedMS/images/PeptideStandard.png";
+                    case QC -> "/TargetedMS/images/PeptideQc.png";
+                    case iRT -> "/TargetedMS/images/PeptideIrt.png";
+                };
             }
         }
 
diff --git a/src/org/labkey/targetedms/view/moleculeListView.jsp b/src/org/labkey/targetedms/view/moleculeListView.jsp
index fadb231b0..42199bd94 100644
--- a/src/org/labkey/targetedms/view/moleculeListView.jsp
+++ b/src/org/labkey/targetedms/view/moleculeListView.jsp
@@ -52,7 +52,7 @@
         List<String> accessions = proteins.stream().map(Protein::getAccession).filter(Objects::nonNull).toList();
     %>
     <% if (accessions.size() == 1) {
-        String accession = accessions.get(0); %>
+        String accession = accessions.getFirst(); %>
         <tr>
             <td class="labkey-form-label">Accession</td>
             <td>
diff --git a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java
index 531e9f161..6ad7cfe9c 100644
--- a/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java
+++ b/src/org/labkey/targetedms/view/spectrum/LibrarySpectrumMatchGetter.java
@@ -46,7 +46,6 @@
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
diff --git a/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java b/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java
index 4db77e1b7..c5a256dd1 100644
--- a/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java
+++ b/test/src/org/labkey/test/components/targetedms/GuideSetWebPart.java
@@ -78,7 +78,7 @@ public Integer getRowId(GuideSet guideSet)
 
             if (!selResp.getRows().isEmpty())
             {
-                String rowIdStr = selResp.getRows().get(0).get("RowId").toString();
+                String rowIdStr = selResp.getRows().getFirst().get("RowId").toString();
                 return Integer.parseInt(rowIdStr);
             }
         }
diff --git a/test/src/org/labkey/test/components/targetedms/QCPlot.java b/test/src/org/labkey/test/components/targetedms/QCPlot.java
index c4c485af1..43da7429e 100644
--- a/test/src/org/labkey/test/components/targetedms/QCPlot.java
+++ b/test/src/org/labkey/test/components/targetedms/QCPlot.java
@@ -16,7 +16,6 @@
 package org.labkey.test.components.targetedms;
 
 import org.junit.Assert;
-import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.util.targetedms.QCHelper;
 import org.openqa.selenium.WebElement;
@@ -29,7 +28,6 @@
 import java.util.regex.Pattern;
 
 import static org.labkey.test.BaseWebDriverTest.getCurrentTest;
-import static org.labkey.test.util.TestLogger.log;
 
 public class QCPlot
 {
diff --git a/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java b/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java
index b4c4bcaed..bc6911cd8 100644
--- a/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java
+++ b/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java
@@ -33,14 +33,11 @@
 import org.openqa.selenium.WebElement;
 import org.openqa.selenium.interactions.Actions;
 import org.openqa.selenium.support.ui.ExpectedConditions;
-import org.openqa.selenium.support.ui.WebDriverWait;
 
-import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.NoSuchElementException;
-import java.util.Optional;
 import java.util.Set;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
@@ -78,7 +75,7 @@ private WebElement waitForPlotPanel()
                         els.addAll(elementCache().findNoRecordsMessage()) ||
                         els.addAll(elementCache().findNoDataMessage()),
                 "QC Plots Webpart load", 10_000);
-        return els.get(0);
+        return els.getFirst();
     }
 
     private void doAndWaitForUpdate(Runnable action)
@@ -556,7 +553,7 @@ public void createGuideSet(@LoggedParam GuideSet guideSet, String expectErrorMsg
         }
         else
         {
-            startPoint = elementCache().svgBackgrounds.findElements(this).get(0);
+            startPoint = elementCache().svgBackgrounds.findElements(this).getFirst();
             xStartOffset = -1 * (Integer.parseInt(startPoint.getAttribute("width")) / 2);
         }
 
@@ -568,7 +565,7 @@ public void createGuideSet(@LoggedParam GuideSet guideSet, String expectErrorMsg
         }
         else
         {
-            endPoint = elementCache().svgBackgrounds.findElements(this).get(0);
+            endPoint = elementCache().svgBackgrounds.findElements(this).getFirst();
             xEndOffset = (Integer.parseInt(endPoint.getAttribute("width")) / 2) - 1;
         }
 
@@ -579,7 +576,7 @@ public void createGuideSet(@LoggedParam GuideSet guideSet, String expectErrorMsg
         builder.moveToElement(startPoint, xStartOffset, yStartOffset).clickAndHold().moveToElement(endPoint, xEndOffset, yEndOffset).release().perform();
 
         List<WebElement> gsButtons = elementCache().guideSetSvgButton.findElements(this);
-        getWrapper().shortWait().until(ExpectedConditions.elementToBeClickable(gsButtons.get(0)));
+        getWrapper().shortWait().until(ExpectedConditions.elementToBeClickable(gsButtons.getFirst()));
 
         Integer brushPointCount = getPointElements("fill", "rgba(20, 204, 201, 1)", false).size();
         assertEquals("Unexpected number of points selected via brushing", guideSet.getBrushSelectedPoints(), brushPointCount);
@@ -587,7 +584,7 @@ public void createGuideSet(@LoggedParam GuideSet guideSet, String expectErrorMsg
         boolean expectPageReload = expectErrorMsg == null;
         if (guideSet.getBrushSelectedPoints() != null && guideSet.getBrushSelectedPoints() < 5)
         {
-            gsButtons.get(0).click(); // Create button : index 0
+            gsButtons.getFirst().click(); // Create button : index 0
             Window<?> warning = Window(getDriver()).withTitle("Create Guide Set Warning").waitFor();
             if (expectPageReload)
                 warning.clickButton("Yes");
@@ -596,12 +593,12 @@ public void createGuideSet(@LoggedParam GuideSet guideSet, String expectErrorMsg
         }
         else if (expectPageReload)
         {
-            getWrapper().clickAndWait(gsButtons.get(0)); // Create button : index 0
+            getWrapper().clickAndWait(gsButtons.getFirst()); // Create button : index 0
             waitForReady();
         }
         else
         {
-            gsButtons.get(0).click(); // Create button : index 0
+            gsButtons.getFirst().click(); // Create button : index 0
         }
 
         if (expectErrorMsg != null)
diff --git a/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java b/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java
index d258d3fb1..26d989837 100644
--- a/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java
+++ b/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java
@@ -23,6 +23,7 @@
 import java.util.List;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
@@ -126,7 +127,7 @@ public void verifyDocumentChain(List<String> latestVersions, int[] verCounts)
             assertTrue(idx != -1);
             List<String>verCount = getRowDataAsText(idx, "Versions");
             assertEquals(1, verCount.size());
-            assertEquals("Expected version count for " + latestVersions, String.valueOf(verCounts[i]), verCount.get(0));
+            assertEquals("Expected version count for " + latestVersions, String.valueOf(verCounts[i]), verCount.getFirst());
             i++;
         }
     }
@@ -134,10 +135,10 @@ public void verifyDocumentChain(List<String> latestVersions, int[] verCounts)
     public void verifyNoChain(int rowCount)
     {
         List<WebElement> buttons = getHeaderButtons();
-        assertTrue(!getWrapper().getTexts(buttons).contains(ALL_VERSIONS));
-        assertTrue(!getWrapper().getTexts(buttons).contains(LATEST_VERSIONS));
+        assertFalse(getWrapper().getTexts(buttons).contains(ALL_VERSIONS));
+        assertFalse(getWrapper().getTexts(buttons).contains(LATEST_VERSIONS));
         assertEquals(rowCount, getDataRowCount());
-        assertTrue(!getColumnLabels().contains("Versions"));
-        assertTrue(!getColumnLabels().contains("Replaced By"));
+        assertFalse(getColumnLabels().contains("Versions"));
+        assertFalse(getColumnLabels().contains("Replaced By"));
     }
 }
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
index 6dfbdff7d..d6c7a0bc1 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSIsotopologueTest.java
@@ -5,10 +5,7 @@
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.test.BaseWebDriverTest;
-import org.labkey.test.Locator;
-import org.labkey.test.components.ext4.Window;
 import org.labkey.test.components.targetedms.QCPlotsWebPart;
-import org.labkey.test.pages.panoramapremium.ConfigureMetricsUIPage;
 import org.labkey.test.pages.targetedms.PanoramaDashboard;
 
 import static org.junit.Assert.assertTrue;
diff --git a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java
index ab8e51d5c..13827b15d 100644
--- a/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java
+++ b/test/src/org/labkey/test/tests/panoramapremium/TargetedMSiRTMetricsTest.java
@@ -115,8 +115,8 @@ public void testFileWithIRTMetricValue()
 
         log("Verifying the tooltip area of QC summary web part");
         QCSummaryWebPart qcSummaryWebPart = qcDashboard.getQcSummaryWebPart();
-        QCSummaryWebPart.QcSummaryTile qcSummaryTile = qcSummaryWebPart.getQcSummaryTiles().get(0);
-        mouseOver(qcSummaryTile.getRecentSampleFiles().get(0));
+        QCSummaryWebPart.QcSummaryTile qcSummaryTile = qcSummaryWebPart.getQcSummaryTiles().getFirst();
+        mouseOver(qcSummaryTile.getRecentSampleFiles().getFirst());
         final WebElement bubble = waitForElement(qcSummaryWebPart.getBubble().withDescendant(Locator.linkWithText("sample8_R03")));
         checker().verifyTrue("iRT Correlation missing in tooltip", Locator.linkWithText("iRT Correlation").existsIn(bubble));
         checker().verifyTrue("iRT Intercept missing in tooltip", Locator.linkWithText("iRT Intercept").existsIn(bubble));
diff --git a/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java b/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java
index 50fdd277a..a9b137617 100644
--- a/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/InstrumentSchedulingTest.java
@@ -211,9 +211,9 @@ public void testSchedule() throws IOException, CommandException
         assertEquals("Wrong number of payment method dropdowns", 2, methodInputs.size());
 
         // Duplicate payment methods
-        selectOptionByText(methodInputs.get(0), PAYMENT_METHOD_2);
+        selectOptionByText(methodInputs.getFirst(), PAYMENT_METHOD_2);
         assertTextPresent("The same payment method cannot be selected more than once.");
-        selectOptionByText(methodInputs.get(0), PAYMENT_METHOD_1);
+        selectOptionByText(methodInputs.getFirst(), PAYMENT_METHOD_1);
 
         // Bogus payment percentages
         setFormElement(percentInputs.get(1), "0");
@@ -245,18 +245,18 @@ public void testSchedule() throws IOException, CommandException
         impersonate(EXTERNAL_COLLABORATOR_USER);
         List<Map<String, Object>> projects = new SelectRowsCommand("targetedms", "msProject").execute(createDefaultConnection(), getProjectName()).getRows();
         assertEquals("Wrong number of projects for " + EXTERNAL_COLLABORATOR_USER, 1, projects.size());
-        int project2Id = (Integer) projects.get(0).get("Id");
+        int project2Id = (Integer) projects.getFirst().get("Id");
         SelectRowsCommand instrumentSelect = new SelectRowsCommand("targetedms", "msInstrument");
         instrumentSelect.setFilters(Arrays.asList(new Filter("Name", INSTRUMENT_1)));
         List<Map<String, Object>> instruments = instrumentSelect.execute(createDefaultConnection(), getProjectName()).getRows();
         assertEquals("Wrong number of instruments", 1, instruments.size());
-        int instrument1Id = (Integer) instruments.get(0).get("Id");
+        int instrument1Id = (Integer) instruments.getFirst().get("Id");
 
         SelectRowsCommand paymentMethodSelect = new SelectRowsCommand("targetedms", "paymentMethod");
         paymentMethodSelect.setFilters(Arrays.asList(new Filter("Name", PAYMENT_METHOD_1)));
         List<Map<String, Object>> paymentMethods = paymentMethodSelect.execute(createDefaultConnection(), getProjectName()).getRows();
         assertEquals("Wrong number of paymentMethods", 1, paymentMethods.size());
-        int paymentMethod1Id = (Integer) paymentMethods.get(0).get("Id");
+        int paymentMethod1Id = (Integer) paymentMethods.getFirst().get("Id");
 
         int project1Id = project2Id - 1;  // Assume sequential auto-incrementing ids
         int inactiveInstrumentId = instrument1Id + 2;
@@ -343,7 +343,7 @@ public void testSetupInsertPermissions() throws IOException, CommandException
         // Insert as a lab member
         stopImpersonating();
         impersonate(LAB_MEMBER_USER);
-        Map<String, Object> project = projectInsert.execute(createDefaultConnection(), getProjectName()).getRows().get(0);
+        Map<String, Object> project = projectInsert.execute(createDefaultConnection(), getProjectName()).getRows().getFirst();
         int projectId = (Integer) project.get("Id");
 
         // Collaborator isn't part of the project, so they shouldn't be able to add a researcher
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java
index c0b5907b1..78bf30f1f 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSEarlyStagePTMReportTest.java
@@ -1,6 +1,5 @@
 package org.labkey.test.tests.targetedms;
 
-import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java
index 11aa5cd8f..50f075169 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSIrtTest.java
@@ -80,7 +80,7 @@ protected List<Map<String, Object>> getRowsForPeptide(String peptide)
 
     protected Map<String, Object> getIrtPeptide(String peptide)
     {
-        return getRowsForPeptide(peptide).get(0);
+        return getRowsForPeptide(peptide).getFirst();
     }
 
     protected double getIrtValue(String peptide)
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
index 9f6b3dacf..479640ee4 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLibraryTest.java
@@ -133,7 +133,7 @@ private void verifyLibraryProteins(List<String> proteins, List<String> files, in
             assertTrue("Expected protein " + protein + " not found in table", idx != -1);
             List<String>fileName = proteinsTable.getRowDataAsText(idx, "RunId/File");
             assertEquals(1, fileName.size());
-            assertEquals("Unexpected file name for " + protein, files.get(i), fileName.get(0));
+            assertEquals("Unexpected file name for " + protein, files.get(i), fileName.getFirst());
             i++;
         }
 
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
index c7f393179..8ec16dc28 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
@@ -19,7 +19,6 @@
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.test.Locator;
-import org.labkey.test.util.DataRegion;
 import org.labkey.test.util.DataRegionTable;
 
 import static org.junit.Assert.assertTrue;
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java
index f3f87ee71..a44542d1e 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java
@@ -30,7 +30,6 @@
 import org.labkey.test.Locator;
 import org.labkey.test.ModulePropertyValue;
 import org.labkey.test.components.targetedms.GuideSet;
-import org.labkey.test.components.targetedms.ParetoPlotsWebPart;
 import org.labkey.test.components.targetedms.QCPlotsWebPart;
 import org.labkey.test.components.targetedms.QCSummaryWebPart;
 import org.labkey.test.pages.targetedms.PanoramaDashboard;
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java
index e17395586..9916f8998 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java
@@ -26,7 +26,6 @@
 import org.labkey.test.SortDirection;
 import org.labkey.test.TestFileUtils;
 import org.labkey.test.TestTimeoutException;
-import org.labkey.test.components.ext4.RadioButton;
 import org.labkey.test.components.ext4.Window;
 import org.labkey.test.components.html.SiteNavBar;
 import org.labkey.test.components.targetedms.GuideSet;
@@ -302,7 +301,7 @@ public void testQCPlotInputs()
         // test option to "Group X-Axis values by Date"
         String initialSVGText = qcPlotsWebPart.getSVGPlotText("precursorPlot0");
         qcPlotsWebPart.setGroupXAxisValuesByDate(true);
-        assertFalse(initialSVGText.equals(qcPlotsWebPart.getSVGPlotText("precursorPlot0")));
+        assertNotEquals(initialSVGText, qcPlotsWebPart.getSVGPlotText("precursorPlot0"));
         qcPlotsWebPart.setGroupXAxisValuesByDate(false);
 
         // test that plot0 changes based on scale
@@ -314,7 +313,7 @@ public void testQCPlotInputs()
                 qcPlotsWebPart.setScale(scale);
                 String svgPlotText = qcPlotsWebPart.getSVGPlotText("precursorPlot0");
                 assertFalse(svgPlotText.isEmpty());
-                assertFalse(initialSVGText.equals(svgPlotText));
+                assertNotEquals(initialSVGText, svgPlotText);
             }
         }
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.LINEAR);
@@ -324,13 +323,13 @@ public void testQCPlotInputs()
         qcPlotsWebPart.checkPlotType(CUSUMm);
         initialSVGText = qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1");
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.LOG);
-        assertTrue(initialSVGText.equals(qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1")));
+        assertEquals(initialSVGText, qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1"));
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.PERCENT_OF_MEAN);
-        assertTrue(initialSVGText.equals(qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1")));
+        assertEquals(initialSVGText, qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1"));
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.STANDARD_DEVIATIONS);
-        assertTrue(initialSVGText.equals(qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1")));
+        assertEquals(initialSVGText, qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1"));
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.DELTA_FROM_MEAN);
-        assertTrue(initialSVGText.equals(qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1")));
+        assertEquals(initialSVGText, qcPlotsWebPart.getSVGPlotText("precursorPlot0_plotType_1"));
 
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.LINEAR);
 
@@ -845,9 +844,9 @@ public void testQCPlotExclusions()
         //confirm 3 exclusions
         DataRegionTable drt = getSchemaBrowserDataView("targetedms", "QCMetricExclusion");
         assertEquals("Wrong count", 3, drt.getDataRowCount());
-        assertEquals("Wrong metric", " ", drt.getRowDataAsText(0, "MetricId").get(0));
-        assertEquals("Wrong metric", " ", drt.getRowDataAsText(1, "MetricId").get(0));
-        assertEquals("Wrong metric", " ", drt.getRowDataAsText(2, "MetricId").get(0));
+        assertEquals("Wrong metric", " ", drt.getRowDataAsText(0, "MetricId").getFirst());
+        assertEquals("Wrong metric", " ", drt.getRowDataAsText(1, "MetricId").getFirst());
+        assertEquals("Wrong metric", " ", drt.getRowDataAsText(2, "MetricId").getFirst());
 
         importData(QC_1b_FILE, 2);
         clickFolder(subFolderName);
@@ -855,9 +854,9 @@ public void testQCPlotExclusions()
 
         drt = getSchemaBrowserDataView("targetedms", "QCMetricExclusion");
         assertEquals("Wrong count", 3, drt.getDataRowCount());
-        assertEquals("Wrong metric", " ", drt.getRowDataAsText(0, "MetricId").get(0));
-        assertEquals("Wrong metric", " ", drt.getRowDataAsText(1, "MetricId").get(0));
-        assertEquals("Wrong metric", " ", drt.getRowDataAsText(2, "MetricId").get(0));
+        assertEquals("Wrong metric", " ", drt.getRowDataAsText(0, "MetricId").getFirst());
+        assertEquals("Wrong metric", " ", drt.getRowDataAsText(1, "MetricId").getFirst());
+        assertEquals("Wrong metric", " ", drt.getRowDataAsText(2, "MetricId").getFirst());
 
         verifyUploadReport("Replicate 25fmol_Pepmix_spike_SRM_1601_03 has an ignore_in_QC=false annotation " +
                 "but there are existing exclusions that were added within Panorama or from a previous import.");
@@ -1071,7 +1070,7 @@ private void verifyQCSummarySampleFileOutliers(String acquiredDate, String outli
     {
         PanoramaDashboard qcDashboard = new PanoramaDashboard(this);
         qcDashboard.getQcSummaryWebPart().waitForRecentSampleFiles(3);
-        QCSummaryWebPart.QcSummaryTile qcSummaryTile = qcDashboard.getQcSummaryWebPart().getQcSummaryTiles().get(0);
+        QCSummaryWebPart.QcSummaryTile qcSummaryTile = qcDashboard.getQcSummaryWebPart().getQcSummaryTiles().getFirst();
         assertEquals("Unexpected outlier information for QC summary sample file for "
                 + acquiredDate, outlierInfo, qcSummaryTile.getRecentSampleFileWithOutliers(acquiredDate));
     }
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java
index 96db4eaed..7b9cbb0db 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSkydTextIdTest.java
@@ -126,8 +126,8 @@ private void verifyChromatogramReplicates(List<String> detailHrefs, String...exp
         for (String href : detailHrefs)
         {
             goToURL(new URL(href), 10000);
-            waitForElement(locators.get(0));
-            List<WebElement> firstReplicateChromatograms = locators.get(0).findElements(getDriver());
+            waitForElement(locators.getFirst());
+            List<WebElement> firstReplicateChromatograms = locators.getFirst().findElements(getDriver());
             Assert.assertNotEquals(0, firstReplicateChromatograms.size());
             for (int iReplicate = 1; iReplicate < locators.size(); iReplicate++)
             {
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java
index 1d266316e..8347a7f63 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSSmallMoleculeLightHeavyRatioTest.java
@@ -55,11 +55,11 @@ public void testLightHeavyRatio() throws IOException, CommandException
         SelectRowsCommand transitionCommand = new SelectRowsCommand("targetedms", "transitionarearatio");
         SelectRowsResponse transitionResponse = transitionCommand.execute(connection, getProjectName());
         assertEquals("Wrong number of rows", 48, transitionResponse.getRows().size());
-        assertEquals("Wrong ratio for first row", 11.234128, (Double)transitionResponse.getRows().get(0).get("arearatio"), 0.0001);
+        assertEquals("Wrong ratio for first row", 11.234128, (Double)transitionResponse.getRows().getFirst().get("arearatio"), 0.0001);
 
         SelectRowsCommand precursorCommand = new SelectRowsCommand("targetedms", "precursorarearatio");
         SelectRowsResponse precursorResponse = precursorCommand.execute(connection, getProjectName());
         assertEquals("Wrong number of rows", 24, precursorResponse.getRows().size());
-        assertEquals("Wrong ratio for first row", 12.301311, (Double)precursorResponse.getRows().get(0).get("arearatio"), 0.0001);
+        assertEquals("Wrong ratio for first row", 12.301311, (Double)precursorResponse.getRows().getFirst().get("arearatio"), 0.0001);
     }
 }
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java
index 2b1bf0650..985b32a14 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTest.java
@@ -346,7 +346,7 @@ protected void verifyQcSummary(int sampleFileCount, int precursorCount)
                 .waitForElementToDisappear(getDriver(), 15_000);
 
         QCSummaryWebPart qcSummaryWebPart = new PanoramaDashboard(this).getQcSummaryWebPart();
-        verifyQcSummary(qcSummaryWebPart.getQcSummaryTiles().get(0), null, sampleFileCount, precursorCount);
+        verifyQcSummary(qcSummaryWebPart.getQcSummaryTiles().getFirst(), null, sampleFileCount, precursorCount);
     }
 
     @LogMethod
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java
index b92e0348d..f612ecc2f 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java
@@ -6,12 +6,10 @@
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 import org.labkey.test.BaseWebDriverTest;
-import org.labkey.test.Locators;
 import org.labkey.test.components.targetedms.GuideSet;
 import org.labkey.test.components.targetedms.QCPlotsWebPart;
 import org.labkey.test.pages.targetedms.PanoramaDashboard;
 import org.labkey.test.util.PortalHelper;
-import org.openqa.selenium.support.ui.ExpectedConditions;
 
 @Category({})
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java
index 05ed29770..8792e2c5e 100644
--- a/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java
+++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSUtilizationCalendarTest.java
@@ -11,7 +11,6 @@
 import org.labkey.test.util.DataRegionTable;
 import org.openqa.selenium.NoSuchElementException;
 
-import java.sql.Timestamp;
 import java.util.Arrays;
 
 import static org.labkey.test.util.PermissionsHelper.READER_ROLE;