Fixes

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/cache/database/FileUpdater.java

@@ -50,20 +50,27 @@ public class FileUpdater {
      * tuple is not already found in the database
      */
     private final String insertFileInfoSql =
-            "INSERT INTO fileinfo (" + " collectionID, pillarID, fileID, filesize, file_timestamp, last_seen_getfileids)" +
-                    " (SELECT collectionID, ?, ?, ?, ?, ? FROM collections" + " WHERE collectionID = ? " + " AND NOT EXISTS (" +
-                    " SELECT * FROM fileinfo " + " WHERE fileID = ?" + " AND collectionID = ?" + " AND pillarID = ?))";
-
-    private final String updateFileInfoSql =
-            "UPDATE fileinfo " + "	SET filesize = ?," + " file_timestamp = ?," + " last_seen_getfileids = ?" + " WHERE fileID = ?" +
-                    "	AND collectionID = ?" + " AND pillarID = ?";
-
-    private final String insertLatestFileTime = "INSERT INTO collection_progress " + "(collectionID, pillarID, latest_file_timestamp)" +
-            " ( SELECT collectionID, ?, ? FROM collections" + " WHERE collectionID = ?" +
-            " AND NOT EXISTS ( SELECT * FROM collection_progress" + " WHERE collectionID = ?" + " AND pillarID = ?))";
+            "INSERT INTO fileinfo (collectionID, pillarID, fileID, filesize, file_timestamp, last_seen_getfileids)" +
+                    " (SELECT collectionID, ?, ?, ?, ?, ? FROM collections" +
+                    " WHERE collectionID = ? " +
+                    " AND NOT EXISTS (" +
+                    " SELECT * FROM fileinfo " +
+                    " WHERE fileID = ?" +
+                    " AND collectionID = ?" +
+                    " AND pillarID = ?))";
+
+    private final String updateFileInfoSql = "UPDATE fileinfo " +
+                    " SET filesize = ?, file_timestamp = ?, last_seen_getfileids = ?" +
+                    " WHERE fileID = ? AND collectionID = ? AND pillarID = ?";
+
+    private final String insertLatestFileTime =
+            "INSERT INTO collection_progress (collectionID, pillarID, latest_file_timestamp)" +
+                    " (SELECT collectionID, ?, ? FROM collections" +
+                    " WHERE collectionID = ? AND NOT EXISTS" +
+                    " (SELECT * FROM collection_progress WHERE collectionID = ? AND pillarID = ?))";
 
     private final String updateLatestFileTime =
-            "UPDATE collection_progress" + " SET latest_file_timestamp = ? " + " WHERE collectionID = ?" + " AND pillarID = ?";
+            "UPDATE collection_progress SET latest_file_timestamp = ? WHERE collectionID = ? AND pillarID = ?";
 
     private final Logger log = LoggerFactory.getLogger(getClass());
 

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/cache/database/StatisticsCreator.java

@@ -49,8 +49,8 @@ public class StatisticsCreator {
             + " (SELECT MAX(stat_key), ?, ?, ?, ? FROM stats WHERE collectionID = ?)";
 
     private final String insertPillarStatEntrySql = "INSERT INTO pillarstats"
-            + " (stat_key, pillarID, file_count, file_size, missing_files_count, "
-            + "checksum_errors_count, missing_checksums_count, obsolete_checksums_count, oldest_checksum_timestamp)"
+            + " (stat_key, pillarID, file_count, file_size, missing_files_count,"
+            + " checksum_errors_count, missing_checksums_count, obsolete_checksums_count, oldest_checksum_timestamp)"
             + " (SELECT MAX(stat_key), ?, ?, ?, ?, ?, ?, ?, ? FROM stats WHERE collectionID = ?)";
 
     private final Logger log = LoggerFactory.getLogger(getClass());

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/web/RestIntegrityService.java

@@ -253,8 +253,8 @@ public String getIntegrityStatus(@QueryParam("collectionID") String collectionID
         jg.writeStartArray();
         for (PillarCollectionStat stat : stats.values()) {
             writeIntegrityStatusObject(stat, jg);
-            log.debug(String.format(Locale.ROOT, "IntegrityStatus: Wrote pillar name: '%s' to pillar '%s'",
-                    stat.getPillarName(), stat.getPillarID()));
+            log.debug("IntegrityStatus: Wrote pillar name: '{}' to pillar '{}'", stat.getPillarName(),
+                    stat.getPillarID());
         }
         jg.writeEndArray();
         jg.flush();

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/workflow/CompleteIntegrityCheck.java

@@ -41,20 +41,21 @@ public CompleteIntegrityCheck() {}
 
     @Override
     public String getDescription() {
-        return "Retrieves all fileIDs and checksums from all pillars and checks for all potential integrity " + "problems.";
+        return "Retrieves all fileIDs and checksums from all pillars and checks for all potential integrity problems.";
     }
 
     @Override
     protected UpdateFileIDsStep getUpdateFileIDsStep() {
-        return new FullUpdateFileIDsStep(context.getCollector(), context.getStore(), context.getAlerter(), context.getSettings(),
-                collectionID, integrityContributors);
+        return new FullUpdateFileIDsStep(context.getCollector(), context.getStore(), context.getAlerter(),
+                context.getSettings(), collectionID, integrityContributors);
     }
 
 
     @Override
     protected UpdateChecksumsStep getUpdateChecksumsStep() {
         return new FullUpdateChecksumsStep(context.getCollector(), context.getStore(), context.getAlerter(),
-                ChecksumUtils.getDefault(context.getSettings()), context.getSettings(), collectionID, integrityContributors);
+                ChecksumUtils.getDefault(context.getSettings()), context.getSettings(), collectionID,
+                integrityContributors);
     }
 
 

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/workflow/IntegrityCheckWorkflow.java

@@ -53,15 +53,15 @@
  * And finally it is verified whether any missing or obsolete checksums can be found.
  */
 public abstract class IntegrityCheckWorkflow extends Workflow {
+    /**
+     * The default number of retries if none is set in ReferenceSettings
+     */
+    private static final int DEFAULT_MAX_RETRIES = 3;
     private final Logger log = LoggerFactory.getLogger(getClass());
     protected IntegrityWorkflowContext context;
     protected String collectionID;
     protected IntegrityContributors integrityContributors;
     protected Date workflowStart;
-    /**
-     * The default number of retries if none is set in ReferenceSettings
-     */
-    private static final int DEFAULT_MAX_RETRIES = 3;
 
     /**
      * Remember to call the initialise method needs to be called before the start method.
@@ -85,21 +85,20 @@ public void initialise(WorkflowContext context, String collectionID) {
 
     @Override
     public void start() {
-
         workflowStart = new Date();
 
         if (context == null) {
-            throw new IllegalStateException("The workflow can not be started before the initialise method has been " +
-                    "called.");
+            throw new IllegalStateException(
+                    "The workflow can not be started before the initialise method has been " + "called.");
         }
         IntegrityReporter reporter = new BasicIntegrityReporter(jobID.getCollectionID(), jobID.getWorkflowName(),
                 IntegrityServiceManager.getIntegrityReportStorageDir());
 
         super.start();
         try {
             StatisticsCollector statisticsCollector = new StatisticsCollector(collectionID);
-            Integer maxRetries
-                    = context.getSettings().getReferenceSettings().getIntegrityServiceSettings().getComponentRetries();
+            Integer maxRetries = context.getSettings().getReferenceSettings().getIntegrityServiceSettings()
+                    .getComponentRetries();
             integrityContributors = new IntegrityContributors(SettingsUtils.getPillarIDsForCollection(collectionID),
                     maxRetries == null ? DEFAULT_MAX_RETRIES : maxRetries);
 
@@ -112,35 +111,33 @@ public void start() {
             performStep(updateChecksumStep);
 
             if (cleanDeletedFiles()) {
-                HandleDeletedFilesStep handleDeletedFilesStep = new HandleDeletedFilesStep(context.getStore(),
-                        reporter, workflowStart, integrityContributors.getFinishedContributors());
+                HandleDeletedFilesStep handleDeletedFilesStep = new HandleDeletedFilesStep(context.getStore(), reporter,
+                        workflowStart, integrityContributors.getFinishedContributors());
                 performStep(handleDeletedFilesStep);
             }
 
             statisticsCollector.getCollectionStat().setStatsTime(new Date());
-            javax.xml.datatype.Duration timeBeforeMissingFileCheck =
-                    context.getSettings().getReferenceSettings().getIntegrityServiceSettings().getTimeBeforeMissingFileCheck();
+            javax.xml.datatype.Duration timeBeforeMissingFileCheck = context.getSettings().getReferenceSettings()
+                    .getIntegrityServiceSettings().getTimeBeforeMissingFileCheck();
             Duration missingFileGracePeriod = XmlUtils.xmlDurationToDuration(timeBeforeMissingFileCheck);
             HandleMissingFilesStep handleMissingFilesStep = new HandleMissingFilesStep(context.getStore(), reporter,
                     statisticsCollector, missingFileGracePeriod);
             performStep(handleMissingFilesStep);
 
-            HandleChecksumValidationStep handleChecksumValidationStep
-                    = new HandleChecksumValidationStep(context.getStore(), context.getAuditManager(), reporter,
-                    statisticsCollector);
+            HandleChecksumValidationStep handleChecksumValidationStep = new HandleChecksumValidationStep(
+                    context.getStore(), context.getAuditManager(), reporter, statisticsCollector);
             performStep(handleChecksumValidationStep);
 
             HandleMissingChecksumsStep handleMissingChecksumsStep = new HandleMissingChecksumsStep(context.getStore(),
                     reporter, statisticsCollector, getChecksumUpdateCutoffDate());
             performStep(handleMissingChecksumsStep);
 
-            HandleObsoleteChecksumsStep handleObsoleteChecksumsStep
-                    = new HandleObsoleteChecksumsStep(context.getSettings(), context.getStore(), reporter,
-                    statisticsCollector);
+            HandleObsoleteChecksumsStep handleObsoleteChecksumsStep = new HandleObsoleteChecksumsStep(
+                    context.getSettings(), context.getStore(), reporter, statisticsCollector);
             performStep(handleObsoleteChecksumsStep);
 
-            CreateStatisticsEntryStep createStatistics = new CreateStatisticsEntryStep(
-                    context.getStore(), collectionID, statisticsCollector);
+            CreateStatisticsEntryStep createStatistics = new CreateStatisticsEntryStep(context.getStore(), collectionID,
+                    statisticsCollector);
             performStep(createStatistics);
 
             if (currentState() != WorkflowState.ABORTED) {
@@ -149,7 +146,8 @@ public void start() {
                 }
                 try {
                     reporter.generateReport();
-                    IntegrityServiceManager.getIntegrityReportProvider().setLatestReport(collectionID, reporter.getReportDir());
+                    IntegrityServiceManager.getIntegrityReportProvider()
+                            .setLatestReport(collectionID, reporter.getReportDir());
                 } catch (IOException e) {
                     log.error("Failed to generate integrity report", e);
                     context.getAlerter().integrityComponentFailure("Failed to generate integrity report", collectionID);

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/workflow/step/HandleChecksumValidationStep.java

@@ -52,8 +52,8 @@ public class HandleChecksumValidationStep extends AbstractWorkFlowStep {
     private Long allPillarChecksumErrors = 0L;
     private Long collectionChecksumErrors = 0L;
 
-    public HandleChecksumValidationStep(IntegrityModel store, AuditTrailManager auditManager, IntegrityReporter reporter,
-                                        StatisticsCollector statisticsCollector) {
+    public HandleChecksumValidationStep(IntegrityModel store, AuditTrailManager auditManager,
+            IntegrityReporter reporter, StatisticsCollector statisticsCollector) {
         this.store = store;
         this.auditManager = auditManager;
         this.reporter = reporter;
@@ -71,11 +71,14 @@ public String getName() {
     }
 
     /**
-     * Queries the IntegrityModel for missing files on each pillar. Reports them if any is returned.
+     * Queries the IntegrityModel for inconsistent checksums in the collection.
+     * Checks every reported inconsistent checksum, to verify that it's actually inconsistent.
+     * Updates database model to reflect the discovered situation.
      */
     @Override
     public synchronized void performStep() throws StepFailedException {
-        try (IntegrityIssueIterator inconsistentFilesIterator = store.getFilesWithInconsistentChecksums(reporter.getCollectionID())) {
+        try (IntegrityIssueIterator inconsistentFilesIterator = store.getFilesWithInconsistentChecksums(
+                reporter.getCollectionID())) {
             String fileID;
             while ((fileID = inconsistentFilesIterator.getNextIntegrityIssue()) != null) {
                 handleChecksumInconsistency(store.getFileInfos(fileID, reporter.getCollectionID()), fileID);
@@ -120,7 +123,7 @@ private void handleChecksumInconsistency(Collection<FileInfo> infos, String file
     }
 
     /**
-     * Creates a audit-trail for inconsistency between checksums.
+     * Creates an audit-trail for inconsistency between checksums.
      * If only one pillar is alone with a checksum compared to all the others, then it is pointed out at the possible
      * cause.
      *

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/workflow/step/HandleMissingChecksumsStep.java

@@ -41,14 +41,14 @@ public class HandleMissingChecksumsStep extends AbstractWorkFlowStep {
     private final IntegrityModel store;
     private final IntegrityReporter reporter;
     private final StatisticsCollector sc;
-    private final Date cutoff;
+    private final Date cutoffDate;
 
     public HandleMissingChecksumsStep(IntegrityModel store, IntegrityReporter reporter, StatisticsCollector statisticsCollector,
                                       Date latestChecksumUpdate) {
         this.store = store;
         this.reporter = reporter;
         this.sc = statisticsCollector;
-        this.cutoff = latestChecksumUpdate;
+        this.cutoffDate = latestChecksumUpdate;
     }
 
     @Override
@@ -72,7 +72,7 @@ public synchronized void performStep() throws StepFailedException {
 
             String missingFile;
             try (IntegrityIssueIterator missingChecksumsIterator = store.findFilesWithMissingChecksum(reporter.getCollectionID(), pillar,
-                    cutoff)) {
+                    cutoffDate)) {
                 while ((missingFile = missingChecksumsIterator.getNextIntegrityIssue()) != null) {
                     try {
                         reporter.reportMissingChecksum(missingFile, pillar);

bitrepository-integrity-service/src/main/java/org/bitrepository/integrityservice/workflow/step/HandleMissingFilesStep.java

@@ -55,8 +55,8 @@ public class HandleMissingFilesStep extends AbstractWorkFlowStep {
     private final StatisticsCollector sc;
     private final Duration gracePeriod;
 
-    public HandleMissingFilesStep(IntegrityModel store, IntegrityReporter reporter, StatisticsCollector statisticsCollector,
-                                  Duration missingFileGracePeriod) {
+    public HandleMissingFilesStep(IntegrityModel store, IntegrityReporter reporter,
+            StatisticsCollector statisticsCollector, Duration missingFileGracePeriod) {
         this.store = store;
         this.reporter = reporter;
         this.sc = statisticsCollector;
@@ -69,9 +69,7 @@ public String getName() {
     }
 
     /**
-     * Queries the IntegrityModel for inconsistent checksums in the collection.
-     * Checks every reported inconsistent checksum, to verify that it's actually inconsistent.
-     * Updates database model to reflect the discovered situation.
+     * Queries the IntegrityModel for missing files on each pillar. Reports them if any is returned.
      */
     @Override
     public synchronized void performStep() throws StepFailedException {
@@ -82,10 +80,11 @@ public synchronized void performStep() throws StepFailedException {
         }
         Instant missingAfterInstant = Instant.now().minus(gracePeriod);
         Date missingAfterDate = Date.from(missingAfterInstant);
-        log.info("Looking for missing files, files need to be older than {} to be considered missing.", missingAfterDate);
+        log.info("Looking for missing files, files need to be older than {} to be considered missing.",
+                missingAfterDate);
 
-        try (IntegrityIssueIterator issueIterator = store.findFilesWithMissingCopies(reporter.getCollectionID(), pillars.size(), 0L,
-                Long.MAX_VALUE)) {
+        try (IntegrityIssueIterator issueIterator = store.findFilesWithMissingCopies(reporter.getCollectionID(),
+                pillars.size(), 0L, Long.MAX_VALUE)) {
 
             String missingFile;
             while ((missingFile = issueIterator.getNextIntegrityIssue()) != null) {