Auto-refactor lint cleanup (#197)

SequencedCollections: get(0) -> getFirst(), etc
Add missing @NotNull/@nullable
Simplify test assertions
Map operation simplification
Remove redundant throws clause
Switch to parameterized log message
C-style array -> Java-style array declaration
Delete overridden methods identical to parent
Switch statement -> enhanced switch statement
Remove redundant imports

Author: labkey-jeckels

OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java

@@ -60,7 +60,6 @@
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.HtmlView;
-import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.NotFoundException;
@@ -85,6 +84,7 @@ public class OConnorExperimentsController extends SpringActionController
 {
     public static final String EXPERIMENTS = "Experiments";
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(OConnorExperimentsController.class);
+    public static final org.apache.logging.log4j.Logger LOG = LogManager.getLogger(OConnorExperimentsController.class);
 
     public OConnorExperimentsController()
     {
@@ -110,7 +110,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
         {
             if (form.isFinalMigration())
             {
-                LogManager.getLogger(OConnorExperimentsController.class).info("Final migration to be performed - file move events will be performed (irreversible).");
+                LOG.info("Final migration to be performed - file move events will be performed (irreversible).");
             }
 
             // global containers
@@ -160,7 +160,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                             newType.put("Name", currentType);
                             newType.put("Enabled", true);
                             List<Map<String, Object>> newTypes = typeUpdateService.insertRows(getUser(), getContainer(), Collections.singletonList(newType), new BatchValidationException(), null, null);
-                            targetType = (Integer) newTypes.get(0).get("RowId");
+                            targetType = (Integer) newTypes.getFirst().get("RowId");
                         }
                     }
 
@@ -178,7 +178,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                         User user = UserManager.getUserByDisplayName((String) databaseMap.get("initials"));
                         if (user == null)
                         {
-                            LogManager.getLogger(OConnorExperimentsController.class).warn("User '" + databaseMap.get("initials") + "' not found for experiment " + databaseMap.get("expnumber"));
+                            LOG.warn("User '{}' not found for experiment {}", databaseMap.get("initials"), databaseMap.get("expnumber"));
                             effectiveUser = getUser();
                         }
                         else
@@ -188,7 +188,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                     }
 
                     databaseMap.put("EffectiveUser", effectiveUser);
-                    LogManager.getLogger(OConnorExperimentsController.class).info("Insert on experiment " + databaseMap.get("expnumber"));
+                    LOG.info("Insert on experiment {}", databaseMap.get("expnumber"));
                     List<Map<String, Object>> updateResult;
                     try
                     {
@@ -197,18 +197,18 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                     catch (Exception e)
                     {
                         // log the error to the logfile and continue
-                        LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber + " with exception " + e.getMessage());
+                        LOG.warn("Error inserting expNumber {} with exception {}", expNumber, e.getMessage());
                         continue;
                     }
                     if (batchErrors.hasErrors())
                     {
                         // throw batchErrors.getLastRowError();
-                        LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber);
+                        LOG.warn("Error inserting expNumber {}", expNumber);
                     }
 
-                    Container workbookContainer = ContainerManager.getForId((String)updateResult.get(0).get("EntityId"));
+                    Container workbookContainer = ContainerManager.getForId((String)updateResult.getFirst().get("EntityId"));
                     databaseMap.put("ContainerObj", workbookContainer);
-                    databaseMap.put("ContainerStr", updateResult.get(0).get("EntityId"));
+                    databaseMap.put("ContainerStr", updateResult.getFirst().get("EntityId"));
 
                     // We don't want these fields to be spoofable through the QueryUpdateService (and hence the Client API),
                     // so preserve the value from the source data manually
@@ -218,7 +218,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                     // Move files
                     File sourceFile = new File(fileContentService.getFileRoot(sourceContainer).getPath() + File.separator + "@files", databaseMap.get("expnumber").toString());
                     File targetDir = new File(fileContentService.getFileRoot(targetContainer).getPath() + File.separator + databaseMap.get("expnumber").toString() + File.separator + "@files");
-                    LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile + "' to directory '" + targetDir +"'" );
+                    LOG.info("Copy from file '{}' to directory '{}'", sourceFile, targetDir);
                     if (sourceFile.exists())
                     {
                         FileUtils.copyDirectory(sourceFile, targetDir);
@@ -260,7 +260,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                                 }
                                 else
                                 {
-                                    LogManager.getLogger(OConnorExperimentsController.class).warn("child container not found: " + parents[i] + " for experiment " + databaseMap.get("expnumber") + " with username " + databaseMap.get("initials"));
+                                    LOG.warn("child container not found: {} for experiment {} with username {}", parents[i], databaseMap.get("expnumber"), databaseMap.get("initials"));
                                 }
                             }
                         }
@@ -269,16 +269,15 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                             map.put("ParentExperiments", parentsEntityId.toArray(new String[0]));
 
                             // workaround, pass user, container - databaseMap.get("Container"), singleton list
-                            LogManager.getLogger(OConnorExperimentsController.class).info("Update rows on experiment " + databaseMap.get("expnumber"));
+                            LOG.info("Update rows on experiment {}", databaseMap.get("expnumber"));
                             try
                             {
                                 queryUpdateService.updateRows(getUser(), targetContainer, Collections.singletonList(map), null, null, null);
                             }
                             catch (Exception e)
                             {
                                 // log the error to the logfile and continue
-                                LogManager.getLogger(OConnorExperimentsController.class).warn("Error updating parent experiments for experiment number " + expNumber + " with exception " + e.getMessage());
-                                continue;
+                                LOG.warn("Error updating parent experiments for experiment number {} with exception {}", expNumber, e.getMessage());
                             }
 
                         }
@@ -304,7 +303,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                         Container workbookContainer = targetContainer.getChild(databaseMap.get("expnumber").toString());
                         if (workbookContainer == null)
                         {
-                            LogManager.getLogger(OConnorExperimentsController.class).warn("Updating wiki, container not found: " + databaseMap.get("expnumber"));
+                            LOG.warn("Updating wiki, container not found: {}", databaseMap.get("expnumber"));
                         }
                         else
                         {
@@ -320,14 +319,14 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                             catch (Exception e)
                             {
                                 // log the error to the logfile and continue
-                                LogManager.getLogger(OConnorExperimentsController.class).warn("Error wiki for experiment number " + expNumber + " with exception " + e.getMessage());
+                                LOG.warn("Error wiki for experiment number {} with exception {}", expNumber, e.getMessage());
                                 continue;
                             }
                             finally
                             {
                                 in.closeInputStream();
                             }
-                            LogManager.getLogger(OConnorExperimentsController.class).info("Inserting wiki for experiment " + databaseMap.get("expnumber"));
+                            LOG.info("Inserting wiki for experiment {}", databaseMap.get("expnumber"));
                         }
                     }
                 }
@@ -439,7 +438,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
 
             if (result != null && !result.isEmpty())
             {
-                String entityId = (String)result.get(0).get("Container");
+                String entityId = (String)result.getFirst().get("Container");
                 newExperiment = ContainerManager.getForId(entityId);
                 return true;
             }
@@ -464,7 +463,7 @@ public ApiResponse execute(Object o, BindException errors) throws Exception
             ApiSimpleResponse resp = new ApiSimpleResponse();
             if (result != null && !result.isEmpty())
             {
-                Map<String, Object> exp = result.get(0);
+                Map<String, Object> exp = result.getFirst();
 
                 resp.put("success", true);
                 resp.put("experiment", exp);

OConnorExperiments/src/org/labkey/oconnorexperiments/query/OConnorExperimentsUserSchema.java

@@ -16,6 +16,7 @@
 package org.labkey.oconnorexperiments.query;
 
 import org.jetbrains.annotations.Nullable;
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.collections.Sets;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
@@ -139,7 +140,7 @@ private TableInfo createParentExperimentsTable(String name, ContainerFilter cf)
     }
 
     @Override
-    public QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
+    public @NotNull QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
     {
         if (OConnorExperimentsController.EXPERIMENTS.equalsIgnoreCase(settings.getQueryName()))
         {

genotyping/src/org/labkey/genotyping/GenotypingController.java

@@ -125,7 +125,6 @@
 import java.math.BigInteger;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.sql.ResultSet;
 import java.sql.SQLException;
@@ -381,7 +380,7 @@ public boolean handlePost(ReturnUrlForm returnUrlForm, BindException errors)
         {
             long startTime = System.currentTimeMillis();
             SequenceManager.get().loadSequences(getContainer(), getUser());
-            LOG.info(DateUtil.formatDuration(System.currentTimeMillis() - startTime) + " to load sequences");
+            LOG.info("{} to load sequences", DateUtil.formatDuration(System.currentTimeMillis() - startTime));
 
             return true;
         }
@@ -1299,7 +1298,7 @@ public void validateForm(ImportAnalysisForm form, Errors errors)
         @Override
         public Object execute(ImportAnalysisForm form, BindException errors) throws Exception
         {
-            LOG.info("Galaxy signaled the completion of analysis " + form.getAnalysis());
+            LOG.info("Galaxy signaled the completion of analysis {}", form.getAnalysis());
             String message;
 
             // Send any exceptions back to the Galaxy task so it can log it as well.
@@ -1337,7 +1336,7 @@ public Object execute(ImportAnalysisForm form, BindException errors) throws Exce
                 message = FAILURE_PREFACE + "Analysis path doesn't match import path (see system log for more details)";
 
                 // But log more detail to the administrator so they're aware
-                LOG.error(FAILURE_PREFACE + fnf.getMessage());
+                LOG.error("{}{}", FAILURE_PREFACE, fnf.getMessage());
             }
             catch (Exception e)
             {
@@ -1657,11 +1656,6 @@ public static class RunForm extends QueryExportForm
         public enum Platforms{
 
             LS454 {
-                @Override
-                public String getTableName()
-                {
-                    return TableType.Reads.toString();
-                }
             },
             ILLUMINA {
                 @Override

genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java

@@ -17,8 +17,8 @@
 
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
-import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
+import org.jetbrains.annotations.NotNull;
 import org.labkey.api.collections.CaseInsensitiveHashSet;
 import org.labkey.api.collections.Sets;
 import org.labkey.api.data.*;
@@ -952,7 +952,7 @@ public Set<String> getTableNames()
     }
 
     @Override
-    public QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
+    public @NotNull QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
     {
         TableType type = findTableType(settings.getQueryName());
         return type == null ? super.createView(context, settings, errors) : type.createQueryView(context, settings, errors, this);

genotyping/src/org/labkey/genotyping/HaplotypeAssayProvider.java

@@ -55,7 +55,6 @@
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.ViewContext;
 
-import java.io.File;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.LinkedHashMap;

genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java

@@ -49,7 +49,6 @@
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -75,7 +74,7 @@ public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNu
     {
         if (!dataFile.exists())
         {
-            log.warn("Could not find file " + dataFile + " on disk for data with LSID " + data.getLSID());
+            log.warn("Could not find file {} on disk for data with LSID {}", dataFile, data.getLSID());
             return;
         }
         ExpRun expRun = data.getRun();
@@ -226,7 +225,7 @@ private Map<String, Integer> ensureAnimalIds(Map<String, String> ids, Map<String
                 {
                     throw new ExperimentException("Unable to insert a row into the Animal table for " + animalKey);
                 }
-                row.put("rowid", insertedRow.get(0).get("RowId"));
+                row.put("rowid", insertedRow.getFirst().get("RowId"));
             }
         }
 
@@ -299,7 +298,7 @@ private Map<HaplotypeIdentifier, Integer> ensureHaplotypeNames(List<HaplotypeIde
                 {
                     throw new ExperimentException("Unable to insert a row into the Haplotype table for " + haplotypeName);
                 }
-                row.put("rowid", insertedRow.get(0).get("RowId"));
+                row.put("rowid", insertedRow.getFirst().get("RowId"));
             }
         }
 
@@ -462,7 +461,7 @@ private void throwFirstError(BatchValidationException errors) throws ExperimentE
     {
         if (errors.hasErrors())
         {
-            throw new ExperimentException(errors.getRowErrors().get(0));
+            throw new ExperimentException(errors.getRowErrors().getFirst());
         }
     }
 

genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java

@@ -125,7 +125,7 @@ public Map<Pair<Integer, Integer>, FileInfo> parseFastqFiles(PipelineJob job) th
             long length = f.length();
             if (length == 0)
             {
-                _logger.info("File " + f.getName() + " has no content to parse.");
+                _logger.info("File {} has no content to parse.", f.getName());
                 continue;
             }
 
@@ -138,10 +138,10 @@ public Map<Pair<Integer, Integer>, FileInfo> parseFastqFiles(PipelineJob job) th
                 // good way to check if a file is truly local
                 tempFile = FileUtil.createTempFile(FileUtil.getBaseName(f) + ".", "." + FileUtil.getExtension(f));
                 tempFile.deleteOnExit();
-                _logger.debug("Copying to temp file " + tempFile + ", size is " + f.length() + " bytes");
+                _logger.debug("Copying to temp file {}, size is {} bytes", tempFile, f.length());
                 FileUtil.copyFile(f, tempFile);
 
-                _logger.info("Beginning to parse file: " + f.getName());
+                _logger.info("Beginning to parse file: {}", f.getName());
                 try (FastqReader reader = new FastqReader(tempFile))
                 {
                     File targetDir = f.getParentFile();
@@ -197,7 +197,7 @@ public Map<Pair<Integer, Integer>, FileInfo> parseFastqFiles(PipelineJob job) th
                     }
                     else if (reader.getLineNumber() == 1 && totalReads == 0 && !f.getName().contains("null"))//empty file
                     {
-                        _logger.warn("File " + fileName + " has no content to parse.");
+                        _logger.warn("File {} has no content to parse.", fileName);
                         reader.close();
                         continue;
                     }
@@ -223,7 +223,7 @@ else if (reader.getLineNumber() == 1 && totalReads == 0 && !f.getName().contains
                         Pair<Integer, Integer> key = Pair.of(sampleId, pairNumber);
                         _fileInfo.put(key, new FileInfo(newFile, totalReads));
 
-                        _logger.info("Finished parsing file: " + f.getName());
+                        _logger.info("Finished parsing file: {}", f.getName());
                     }
                 }
             }
@@ -252,7 +252,7 @@ else if (reader.getLineNumber() == 1 && totalReads == 0 && !f.getName().contains
                 File oldFile = entry.getKey();
                 File newFile = entry.getValue();
                 FileUtils.moveFile(oldFile, newFile);
-                _logger.info("Moved file " + oldFile.getName() + " to " + newFile.getName() );
+                _logger.info("Moved file {} to {}", oldFile.getName(), newFile.getName());
             }
         }
         catch (IOException e)
@@ -317,7 +317,7 @@ private void checkForDuplicateTargets(Map<File, File> filesToMove) throws Pipeli
             if (sourceFiles.size() > 1)
             {
                 error = true;
-                _logger.error("Multiple input files map to the target file " + targetFile + " - they are: " + sourceFiles);
+                _logger.error("Multiple input files map to the target file {} - they are: {}", targetFile, sourceFiles);
             }
         }
         if (error)