Various bug fixes and improvements to the checker code, from Grace Carpenter, Jim Downing and Nathan Sarr

git-svn-id: http://scm.dspace.org/svn/repo/trunk@1412 9c30dcfa-912a-0410-8fc2-9e0234be79fd

dspace/config/templates/log4j.properties

@@ -73,3 +73,12 @@ log4j.appender.A1.MaxBackupIndex=500
 # A1 uses PatternLayout.
 log4j.appender.A1.layout=org.apache.log4j.PatternLayout
 log4j.appender.A1.layout.ConversionPattern=%d %-5p %c @ %m%n
+
+# A2 is the log for the Checker
+log4j.category.org.dspace.checker=INFO, A2
+log4j.appender.A2=org.apache.log4j.RollingFileAppender
+log4j.appender.A2.File=@@log.dir@@/checker.log
+log4j.appender.A2.layout=org.apache.log4j.PatternLayout
+log4j.appender.A2.layout.ConversionPattern=%m%n
+log4j.appender.A2.MaxFileSize=1048576
+log4j.appender.A2.MaxBackupIndex=500

dspace/src/org/dspace/app/checker/ChecksumChecker.java

@@ -49,6 +49,7 @@ import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
 import org.apache.log4j.Logger;
 import org.dspace.checker.BitstreamDispatcher;
+import org.dspace.checker.BitstreamInfoDAO;
 import org.dspace.checker.CheckerCommand;
 import org.dspace.checker.HandleDispatcher;
 import org.dspace.checker.LimitedCountDispatcher;
@@ -113,14 +114,14 @@ public class ChecksumChecker
         // create an options object and populate it
         Options options = new Options();
 
-        options.addOption("l", "looping", false, "Loop through bitstreams");
+        options.addOption("l", "looping", false, "Loop once through bitstreams");
         options.addOption("L", "continuous", false,
-                "Continuously loop through bitstreams");
+                "Loop continuously through bitstreams");
         options.addOption("h", "help", false, "Help");
         options.addOption("d", "duration", true, "Checking duration");
         options.addOption("c", "count", true, "Check count");
         options.addOption("a", "handle", true, "Specify a handle to check");
-        options.addOption("e", "errors", false, "Report Errors Only");
+        options.addOption("v", "verbose", false, "Report all processing");
 
         OptionBuilder.withArgName("bitstream-ids").hasArgs().withDescription(
                 "Space separated list of bitstream ids");
@@ -176,88 +177,81 @@ public class ChecksumChecker
         Date processStart = Calendar.getInstance().getTime();
 
         BitstreamDispatcher dispatcher = null;
-        if (line.getOptions().length == 0)
+        
+        // process should loop infinitely through
+        // most_recent_checksum table
+        if (line.hasOption('l'))
         {
-            dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
+            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, false); 
-                    processStart, false), 1);
         }
-        else
+        else if (line.hasOption('L'))
         {
-            // process should loop infinitely through
+            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, true);
-            // most_recent_checksum table
+        }
-            if (line.hasOption('l'))
+        else if (line.hasOption('b'))
-            {
+        {
-                dispatcher = new SimpleDispatcher(processStart, false); 
+            // check only specified bitstream(s)
-            }
+            String[] ids = line.getOptionValues('b');
-            else if (line.hasOption('L'))
+            List idList = new ArrayList(ids.length);
-            {
-                dispatcher = new SimpleDispatcher(processStart, true);
-            }
-            else if (line.hasOption('b'))
-            {
-                // check only specified bitstream(s)
-                String[] ids = line.getOptionValues('b');
-                List idList = new ArrayList(ids.length);
 
-                for (int i = 0; i < ids.length; i++)
+            for (int i = 0; i < ids.length; i++)
-                {
-                    try
-                    {
-                        idList.add(new Integer(ids[i]));
-                    }
-                    catch (NumberFormatException nfe)
-                    {
-                        System.err.println("The following argument: " + ids[i]
-                                + " is not an integer");
-                        System.exit(0);
-                    }
-                }
-                dispatcher = new ListDispatcher(idList);
-            }
-
-            else if (line.hasOption('a'))
             {
-                dispatcher = new HandleDispatcher(line.getOptionValue('a'));
-            }
-            else if (line.hasOption('d'))
-            {
-                // run checker process for specified duration
                 try
                 {
-                    dispatcher = new LimitedDurationDispatcher(
+                    idList.add(new Integer(ids[i]));
-                            new SimpleDispatcher(processStart, true), new Date(
-                                    System.currentTimeMillis()
-                                            + Utils.parseDuration(line
-                                                    .getOptionValue('d'))));
                 }
-                catch (Exception e)
+                catch (NumberFormatException nfe)
                 {
-                    LOG.fatal("Couldn't parse " + line.getOptionValue('d')
+                    System.err.println("The following argument: " + ids[i]
-                            + " as a duration: ", e);
+                            + " is not an integer");
                     System.exit(0);
                 }
             }
-            else if (line.hasOption('c'))
+            dispatcher = new ListDispatcher(idList);
+        }
+
+        else if (line.hasOption('a'))
+        {
+            dispatcher = new HandleDispatcher(new BitstreamInfoDAO(), line.getOptionValue('a'));
+        }
+        else if (line.hasOption('d'))
+        {
+            // run checker process for specified duration
+            try
             {
-                // run checker process for specified number of bitstreams
+                dispatcher = new LimitedDurationDispatcher(
-                dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
+                        new SimpleDispatcher(new BitstreamInfoDAO(), processStart, true), new Date(
-                        processStart, false));
+                                System.currentTimeMillis()
+                                        + Utils.parseDuration(line
+                                                .getOptionValue('d'))));
+            }
+            catch (Exception e)
+            {
+                LOG.fatal("Couldn't parse " + line.getOptionValue('d')
+                        + " as a duration: ", e);
+                System.exit(0);
             }
         }
-
+        else if (line.hasOption('c'))
-        if (dispatcher == null)
         {
-            System.out
+        	int count = new Integer(line.getOptionValue('c')).intValue();
-                    .println("Error: insufficient option commands to run checker.");
+            
-            printHelp(options);
+        	// run checker process for specified number of bitstreams
+            dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
+                    new BitstreamInfoDAO(), processStart, false), count);
         }
-
+        else
+        {
+            dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
+                    new BitstreamInfoDAO(), processStart, false), 1);
+        }
+        
         ResultsLogger logger = new ResultsLogger(processStart);
         CheckerCommand checker = new CheckerCommand();
-        // report errors only
+        // verbose reporting
-        if (line.hasOption('e'))
+        if (line.hasOption('v'))
         {
-            checker.setReportErrorsOnly(true);
+            checker.setReportVerbose(true);
         }
         checker.configureLog();
         checker.setProcessStartDate(processStart);
@@ -283,14 +277,14 @@ public class ChecksumChecker
                         + " OR ChecksumChecker -d 2h");
         System.out
                 .println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
-        System.out.println("\nLoop through all bitstreams: "
+        System.out.println("\nLoop once through all bitstreams: "
                 + "ChecksumChecker -l");
         System.out
-                .println("\nLoop through all bitstreams continuously: ChecksumChecker -L");
+                .println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
         System.out
                 .println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
-        System.out.println("Default (no arguments) is '-c 1'");
+        System.out.println("\nReport all processing (verbose)(default reports only errors): ChecksumChecker -v");
-        System.out.println("\nReport errors only in logs: ChecksumChecker -e");
+        System.out.println("\nDefault (no arguments) is equivalent to '-c 1'");
         System.exit(0);
     }
 

dspace/src/org/dspace/checker/BitstreamDAO.java

@@ -46,6 +46,9 @@ import org.dspace.storage.bitstore.BitstreamStorageManager;
  * </p>
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public class BitstreamDAO
 {

dspace/src/org/dspace/checker/BitstreamDispatcher.java

@@ -33,7 +33,6 @@
  */
 package org.dspace.checker;
 
-import java.sql.SQLException;
 
 /**
  * <p>
@@ -54,8 +53,10 @@ import java.sql.SQLException;
  * </ol>
  * 
  * 
- * @author Nate Sarr
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public interface BitstreamDispatcher
 {
@@ -72,10 +73,6 @@ public interface BitstreamDispatcher
      * @return the next bitstream id, or BitstreamDispatcher.SENTINEL if there
      *         isn't another value
      * 
-     * @throws SQLException
-     *             if there is some problem querying a database
-     * 
-     * @todo This should probably wrap the SQL exception
      */
-    public int next() throws SQLException;
+    public int next();
 }

dspace/src/org/dspace/checker/BitstreamInfo.java

@@ -42,7 +42,9 @@ import java.util.Date;
  * </p>
  * 
  * @author Jim Downing
- * @author Nate Sarr
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public final class BitstreamInfo
 {

dspace/src/org/dspace/checker/BitstreamInfoDAO.java

@@ -38,7 +38,9 @@ import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Timestamp;
+import java.util.ArrayList;
 import java.util.Date;
+import java.util.List;
 
 import org.apache.log4j.Logger;
 import org.dspace.storage.rdbms.DatabaseManager;
@@ -50,11 +52,19 @@ import org.dspace.storage.rdbms.DatabaseManager;
  * checker.
  * </p>
  * 
- * @author Nate Sarr
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public final class BitstreamInfoDAO extends DAOSupport
 {
+    /**
+     * This value should be returned by <code>next()</code> to indicate that
+     * there are no more values.
+     */
+    public static int SENTINEL = -1;
+
     /** Query that gets bitstream information for a specified ID. */
     private static final String FIND_BY_BITSTREAM_ID = "select bitstream.deleted, bitstream.store_number, bitstream.size_bytes, "
             + "bitstreamformatregistry.short_description, bitstream.bitstream_id,  "
@@ -88,27 +98,6 @@ public final class BitstreamInfoDAO extends DAOSupport
             + "select 'x' from most_recent_checksum "
             + "where most_recent_checksum.bitstream_id = bitstream.bitstream_id );";
 
-    /**
-     * Query that select a specified bitstream from bitstream table and inserts
-     * it into the most_recent_checksum table if it does not already exist.
-     */
-    private static final String INSERT_MISSING_CHECKSUM_BITSTREAM = "insert into most_recent_checksum ( "
-            + "bitstream_id, to_be_processed, expected_checksum, current_checksum, "
-            + "last_process_start_date, last_process_end_date, "
-            + "checksum_algorithm, matched_prev_checksum, result ) "
-            + "select bitstream.bitstream_id, "
-            + "true, "
-            + "CASE WHEN bitstream.checksum IS NULL THEN '' ELSE bitstream.checksum END, "
-            + "?, "
-            + "?, "
-            + "CASE WHEN bitstream.checksum_algorithm IS NULL "
-            + "THEN 'MD5' ELSE bitstream.checksum_algorithm END, true, "
-            + "CASE WHEN bitstream.deleted = true THEN 'BITSTREAM_MARKED_DELETED' else 'CHECKSUM_MATCH' END "
-            + "from bitstream where bitstream.bitstream_id = ? "
-            + "and not exists( "
-            + "select 'x' from most_recent_checksum "
-            + "where most_recent_checksum.bitstream_id = ? );";
-
     /**
      * Query that updates most_recent_checksum table with checksum result for
      * specified bitstream ID.
@@ -123,6 +112,42 @@ public final class BitstreamInfoDAO extends DAOSupport
     private static final String DELETE_BITSTREAM_INFO = "Delete from most_recent_checksum "
             + "where bitstream_id = ?";
 
+    /**
+     * This selects the next bitstream in order of last processing end date. The
+     * timestamp is truncated to milliseconds this is because the Date for java
+     * does not support nanoseconds and milliseconds were considered accurate
+     * enough
+     */
+    public static final String GET_OLDEST_BITSTREAM = "select bitstream_id  "
+            + "from most_recent_checksum " + "where to_be_processed = true "
+            + "order by date_trunc('milliseconds', last_process_end_date), "
+            + "bitstream_id " + "ASC LIMIT 1";
+
+    /**
+     * Selects the next bitstream in order of last processing end date, ensuring
+     * that no bitstream is checked more than once since the date parameter
+     * used.
+     */
+    public static final String GET_OLDEST_BITSTREAM_DATE = "select bitstream_id  "
+            + "from most_recent_checksum "
+            + "where to_be_processed = true "
+            + "and last_process_start_date < ? "
+            + "order by date_trunc('milliseconds', last_process_end_date), "
+            + "bitstream_id " + "ASC LIMIT 1";
+
+    /** SQL query to retrieve bitstreams for a given item. */
+    private static final String ITEM_BITSTREAMS = "SELECT b2b.bitstream_id "
+            + "FROM bundle2bitstream b2b, item2bundle i2b WHERE "
+            + "b2b.bundle_id=i2b.bundle_id AND i2b.item_id=?";
+
+    /** SQL query to retrieve bitstreams for a given collection. */
+    private static final String COLLECTION_BITSTREAMS = "SELECT b2b.bitstream_id "
+            + "FROM bundle2bitstream b2b, item2bundle i2b, collection2item c2i WHERE "
+            + "b2b.bundle_id=i2b.bundle_id AND c2i.item_id=i2b.item_id AND c2i.collection_id=?";
+
+    /** SQL query to retrieve bitstreams for a given community. */
+    private static final String COMMUNITY_BITSTREAMS = "SELECT b2b.bitstream_id FROM bundle2bitstream b2b, item2bundle i2b, collection2item c2i, community2collection c2c WHERE b2b.bundle_id=i2b.bundle_id AND c2i.item_id=i2b.item_id AND c2c.collection_id=c2i.collection_id AND c2c.community_id=?";
+
     /** Standard Log4J logger. */
     private static final Logger LOG = Logger.getLogger(BitstreamInfoDAO.class);
 
@@ -257,13 +282,12 @@ public final class BitstreamInfoDAO extends DAOSupport
 
         try
         {
-            LOG.debug("updateing missing bitstreams");
+            LOG.debug("updating missing bitstreams");
             conn = DatabaseManager.getConnection();
             stmt = conn.prepareStatement(INSERT_MISSING_CHECKSUM_BITSTREAMS);
             stmt.setTimestamp(1, new java.sql.Timestamp(new Date().getTime()));
             stmt.setTimestamp(2, new java.sql.Timestamp(new Date().getTime()));
             stmt.executeUpdate();
-            LOG.debug("Committing update");
 
             checksumHistoryDAO.updateMissingBitstreams(conn);
             conn.commit();
@@ -327,64 +351,6 @@ public final class BitstreamInfoDAO extends DAOSupport
         return numDeleted;
     }
 
-    /**
-     * Queries the bitstream table for the specified bitstream ID and inserts it
-     * into the most_recent_checksum table if it does not already exist.
-     * 
-     * @param id
-     *            the bitstream id.
-     * 
-     * @return true if the bitstream was found and updated
-     */
-    public boolean updateMissingBitstream(int id)
-    {
-        Connection conn = null;
-        PreparedStatement stmt = null;
-
-        boolean bitstreamFound = false;
-
-        try
-        {
-            conn = DatabaseManager.getConnection();
-            stmt = conn.prepareStatement(INSERT_MISSING_CHECKSUM_BITSTREAM);
-            stmt.setTimestamp(1, new java.sql.Timestamp(new Date().getTime()));
-            stmt.setTimestamp(2, new java.sql.Timestamp(new Date().getTime()));
-            stmt.setInt(3, id);
-            stmt.setInt(4, id);
-
-            int rowsUpdated = stmt.executeUpdate();
-
-            if (rowsUpdated == 1)
-            {
-                bitstreamFound = true;
-            }
-
-            if (rowsUpdated > 1)
-            {
-                conn.rollback();
-                throw new IllegalStateException(
-                        "Too many rows updated! Number of rows updated: "
-                                + rowsUpdated
-                                + " only one row should be updated for bitstream id "
-                                + id);
-            }
-            conn.commit();
-        }
-        catch (SQLException e)
-        {
-            LOG.error("Problem with inserting missing bitstream. "
-                    + e.getMessage(), e);
-            throw new RuntimeException("Problem inserting missing bitstream. "
-                    + e.getMessage(), e);
-        }
-        finally
-        {
-            cleanup(stmt, conn);
-        }
-
-        return bitstreamFound;
-    }
-
     public int deleteBitstreamInfoWithHistory(int id)
     {
         Connection conn = null;
@@ -411,4 +377,219 @@ public final class BitstreamInfoDAO extends DAOSupport
         return numDeleted;
 
     }
+
+    /**
+     * Get the oldest bitstream in the most recent checksum table. If more than
+     * one found the first one in the result set is returned.
+     * 
+     * @return the bitstream id or -1 if the no bitstreams are found
+     * 
+     */
+    public int getOldestBitstream()
+    {
+        Connection conn = null;
+        PreparedStatement prepStmt = null;
+        ResultSet rs = null;
+
+        try
+        {
+
+            conn = DatabaseManager.getConnection();
+            prepStmt = conn.prepareStatement(GET_OLDEST_BITSTREAM);
+            rs = prepStmt.executeQuery();
+            if (rs.next())
+            {
+                return rs.getInt(1);
+            }
+            else
+            {
+                return SENTINEL;
+            }
+        }
+        catch (SQLException e)
+        {
+            LOG.error("Problem with get oldest bitstream " + e.getMessage(), e);
+            throw new RuntimeException("Oldest bitstream error. "
+                    + e.getMessage(), e);
+
+        }
+        finally
+        {
+            cleanup(prepStmt, conn);
+
+        }
+    }
+
+    /**
+     * Returns the oldest bistream that in the set of bitstreams that are less
+     * than the specified date. If no bitstreams are found -1 is returned.
+     * 
+     * @param lessThanDate
+     * @return id of olded bitstream or -1 if not bistreams are found
+     */
+    public int getOldestBitstream(Timestamp lessThanDate)
+    {
+        Connection conn = null;
+        PreparedStatement prepStmt = null;
+        ResultSet rs = null;
+
+        try
+        {
+            conn = DatabaseManager.getConnection();
+            prepStmt = conn.prepareStatement(GET_OLDEST_BITSTREAM_DATE);
+            prepStmt.setTimestamp(1, lessThanDate);
+            rs = prepStmt.executeQuery();
+            if (rs.next())
+            {
+                return rs.getInt(1);
+            }
+            else
+            {
+                return SENTINEL;
+            }
+        }
+        catch (SQLException e)
+        {
+            LOG.error("get oldest bitstream less than date " + e.getMessage(),
+                    e);
+            throw new RuntimeException("get oldest bitstream less than date. "
+                    + e.getMessage(), e);
+
+        }
+        finally
+        {
+            cleanup(prepStmt, conn);
+
+        }
+    }
+
+    /**
+     * Get the bitstream ids for a given Item
+     * 
+     * @param itemId
+     * @return the list of bitstream ids for this item
+     */
+    public List getItemBitstreams(int itemId)
+    {
+        List ids = new ArrayList();
+
+        Connection conn = null;
+        PreparedStatement ps = null;
+        ResultSet rs = null;
+
+        try
+        {
+            conn = DatabaseManager.getConnection();
+            ps = conn.prepareStatement(ITEM_BITSTREAMS);
+            ps.setInt(1, itemId);
+
+            rs = ps.executeQuery();
+
+            while (rs.next())
+            {
+                ids.add(new Integer(rs.getInt(1)));
+            }
+
+        }
+        catch (SQLException e)
+        {
+            LOG.error("get item bitstreams " + e.getMessage(), e);
+            throw new RuntimeException(
+                    "get item bitstreams. " + e.getMessage(), e);
+
+        }
+        finally
+        {
+            cleanup(ps, conn, rs);
+        }
+
+        return ids;
+    }
+
+    /**
+     * Get the bitstream ids for a given collection
+     * 
+     * @param itemId
+     * @return the list of bitstream ids for this item
+     */
+    public List getCollectionBitstreams(int collectionId)
+    {
+        List ids = new ArrayList();
+
+        Connection conn = null;
+        PreparedStatement ps = null;
+        ResultSet rs = null;
+
+        try
+        {
+            conn = DatabaseManager.getConnection();
+            ps = conn.prepareStatement(COLLECTION_BITSTREAMS);
+            ps.setInt(1, collectionId);
+
+            rs = ps.executeQuery();
+
+            while (rs.next())
+            {
+                ids.add(new Integer(rs.getInt(1)));
+            }
+
+        }
+        catch (SQLException e)
+        {
+            LOG.error("get item bitstreams " + e.getMessage(), e);
+            throw new RuntimeException(
+                    "get item bitstreams. " + e.getMessage(), e);
+
+        }
+        finally
+        {
+            cleanup(ps, conn, rs);
+        }
+
+        return ids;
+    }
+
+    /**
+     * Get the bitstream ids for a given community
+     * 
+     * @param itemId
+     * @return the list of bitstream ids for this item
+     */
+    public List getCommunityBitstreams(int communityId)
+    {
+        List ids = new ArrayList();
+
+        Connection conn = null;
+        PreparedStatement ps = null;
+        ResultSet rs = null;
+
+        try
+        {
+            conn = DatabaseManager.getConnection();
+            ps = conn.prepareStatement(COMMUNITY_BITSTREAMS);
+            ps.setInt(1, communityId);
+
+            rs = ps.executeQuery();
+
+            while (rs.next())
+            {
+                ids.add(new Integer(rs.getInt(1)));
+            }
+
+        }
+        catch (SQLException e)
+        {
+            LOG.error("get item bitstreams " + e.getMessage(), e);
+            throw new RuntimeException(
+                    "get item bitstreams. " + e.getMessage(), e);
+
+        }
+        finally
+        {
+            cleanup(ps, conn, rs);
+        }
+
+        return ids;
+    }
+
 }

dspace/src/org/dspace/checker/CheckerCommand.java

@@ -54,9 +54,10 @@ import org.dspace.core.Utils;
  * against the last calculated checksum for that bitstream.
  * </p>
  * 
- * @author Nate Sarr
- * @author Grace Carpenter
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  * 
  * @todo the accessor methods are currently unused - are they useful?
  * @todo check for any existing resource problems
@@ -96,8 +97,8 @@ public final class CheckerCommand
      */
     private ChecksumResultsCollector collector = null;
 
-    /** Report only errors */
+    /** Report all processing */
-    private boolean reportErrorsOnly = false;
+    private boolean reportVerbose = false;
 
     /**
      * Default constructor uses DSpace plugin manager to construct dependencies.
@@ -135,37 +136,25 @@ public final class CheckerCommand
             collector = new ResultsLogger(processStartDate);
         }
 
-        // loop through bitstreams and check
-        try
-        {
-            bitstreamInfoDAO.updateMissingBitstreams();
-            int id = dispatcher.next();
-            LOG.debug("Processing bitstream id = " + id);
-            while (id != BitstreamDispatcher.SENTINEL)
-            {
-                BitstreamInfo info = checkBitstream(id);
-
-                if (reportErrorsOnly
-                        && (info.getChecksumCheckResult() == ChecksumCheckResults.CHECKSUM_MATCH))
-                {
-                    // NO-OP do not report good checksums
-                }
-                else
-                {
-                    collector.collect(info);
-                }
-
-                id = dispatcher.next();
-            }
-        }
-        catch (SQLException e)
-        {
-            LOG.error("Next bitstream metadata could not be retrieved. ", e);
-        }
-
         // update missing bitstreams that were entered into the
         // bitstream table - this always done.
         bitstreamInfoDAO.updateMissingBitstreams();
+
+        int id = dispatcher.next();
+
+        while (id != BitstreamDispatcher.SENTINEL)
+        {
+            LOG.debug("Processing bitstream id = " + id);
+            BitstreamInfo info = checkBitstream(id);
+
+            if (reportVerbose
+                    || (info.getChecksumCheckResult() != ChecksumCheckResults.CHECKSUM_MATCH))
+            {
+                collector.collect(info);
+            }
+
+            id = dispatcher.next();
+        }
     }
 
     /**
@@ -181,15 +170,6 @@ public final class CheckerCommand
         // get bitstream info from bitstream table
         BitstreamInfo info = bitstreamInfoDAO.findByBitstreamId(id);
 
-        // make sure bitstream and most_recent_checksum in sync for the id
-        if (info == null)
-        {
-            if (bitstreamInfoDAO.updateMissingBitstream(id))
-            {
-                info = bitstreamInfoDAO.findByBitstreamId(id);
-            }
-        }
-
         // requested id was not found in bitstream
         // or most_recent_checksum table
         if (info == null)
@@ -480,9 +460,9 @@ public final class CheckerCommand
      * 
      * @return true if only errors reported
      */
-    public boolean isReportErrorsOnly()
+    public boolean isReportVerbose()
     {
-        return reportErrorsOnly;
+        return reportVerbose;
     }
 
     /**
@@ -491,8 +471,8 @@ public final class CheckerCommand
      * @param reportErrorsOnly
      *            true to report only errors in the logs.
      */
-    public void setReportErrorsOnly(boolean reportErrorsOnly)
+    public void setReportVerbose(boolean reportVerbose)
     {
-        this.reportErrorsOnly = reportErrorsOnly;
+        this.reportVerbose = reportVerbose;
     }
 }

dspace/src/org/dspace/checker/ChecksumCheckResults.java

@@ -37,8 +37,10 @@ package org.dspace.checker;
  * Enumeration of ChecksumCheckResults containing constants for checksum
  * comparison result that must correspond to values in checksum_result table.
  * 
- * @author Grace Carpenter
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  * 
  * @todo Refactor these as properties of ChecksumChecker?
  */

dspace/src/org/dspace/checker/ChecksumHistory.java

@@ -40,7 +40,10 @@ import java.util.Date;
  * Represents a history record for the bitstream.
  * </p>
  * 
- * @author Nate Sarr
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public class ChecksumHistory
 {

dspace/src/org/dspace/checker/ChecksumHistoryDAO.java

@@ -19,8 +19,10 @@ import org.dspace.storage.rdbms.DatabaseManager;
  * </p>
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
  * @author Nathan Sarr
  * 
+ * 
  */
 public class ChecksumHistoryDAO extends DAOSupport
 {
@@ -149,7 +151,7 @@ public class ChecksumHistoryDAO extends DAOSupport
     /**
      * @param conn
      */
-    protected void updateMissingBitstreams(Connection conn)
+    protected void updateMissingBitstreams(Connection conn) throws SQLException
     {
         PreparedStatement stmt = null;
         try
@@ -163,10 +165,9 @@ public class ChecksumHistoryDAO extends DAOSupport
             throw new RuntimeException("Problem updating missing history. "
                     + e.getMessage(), e);
         }
-
         finally
         {
-            cleanup(stmt, conn);
+            cleanup(stmt);
         }
     }
 

dspace/src/org/dspace/checker/ChecksumResultDAO.java

@@ -49,7 +49,10 @@ import org.dspace.storage.rdbms.DatabaseManager;
  * Database Access for the checksum results information.
  * </p>
  * 
- * @author Nate Sarr
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public final class ChecksumResultDAO extends DAOSupport
 {

dspace/src/org/dspace/checker/ChecksumResultsCollector.java

@@ -37,6 +37,9 @@ package org.dspace.checker;
  * Component that receives BitstreamInfo results from a checker.
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public interface ChecksumResultsCollector
 {

dspace/src/org/dspace/checker/DAOSupport.java

@@ -8,6 +8,14 @@ import java.sql.Statement;
 import org.apache.log4j.Logger;
 import org.dspace.storage.rdbms.DatabaseManager;
 
+/**
+ * Database Helper Class to cleanup database resources
+ * 
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
+ */
 public class DAOSupport
 {
 

dspace/src/org/dspace/checker/DSpaceBitstreamInfo.java

@@ -37,7 +37,10 @@ package org.dspace.checker;
  * Value Object that holds bitstream information that will be used for dspace
  * bitstream.
  * 
- * @author Nate Sarr
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public final class DSpaceBitstreamInfo
 {

dspace/src/org/dspace/checker/DailyReportEmailer.java

@@ -69,7 +69,10 @@ import org.dspace.core.ConfigurationManager;
  * after the checksum checker has been run.
  * </p>
  * 
- * @author Nate Sarr
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  * 
  */
 public class DailyReportEmailer

dspace/src/org/dspace/checker/HandleDispatcher.java

@@ -33,9 +33,6 @@
  */
 package org.dspace.checker;
 
-import java.sql.Connection;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
@@ -51,21 +48,12 @@ import org.dspace.handle.HandleManager;
  * item, collection or community referred to by Handle.
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public class HandleDispatcher implements BitstreamDispatcher
 {
-    /** SQL query to retrieve bitstreams for a given item. */
-    private static final String ITEM_BITSTREAMS = "SELECT b2b.bitstream_id "
-            + "FROM bundle2bitstream b2b, item2bundle i2b WHERE "
-            + "b2b.bundle_id=i2b.bundle_id AND i2b.item_id=?";
-
-    /** SQL query to retrieve bitstreams for a given collection. */
-    private static final String COLLECTION_BITSTREAMS = "SELECT b2b.bitstream_id "
-            + "FROM bundle2bitstream b2b, item2bundle i2b, collection2item c2i WHERE "
-            + "b2b.bundle_id=i2b.bundle_id AND c2i.item_id=i2b.item_id AND c2i.collection_id=?";
-
-    /** SQL query to retrieve bitstreams for a given community. */
-    private static final String COMMUNITY_BITSTREAMS = "SELECT b2b.bitstream_id FROM bundle2bitstream b2b, item2bundle i2b, collection2item c2i, community2collection c2c WHERE b2b.bundle_id=i2b.bundle_id AND c2i.item_id=i2b.item_id AND c2c.collection_id=c2i.collection_id AND c2c.community_id=?";
 
     /** Log 4j logger. */
     private static final Logger LOG = Logger.getLogger(HandleDispatcher.class);
@@ -79,6 +67,11 @@ public class HandleDispatcher implements BitstreamDispatcher
     /** the delegate to dispatch to. */
     ListDispatcher delegate = null;
 
+    /**
+     * Database access for retrieving bitstreams
+     */
+    BitstreamInfoDAO bitstreamInfoDAO;
+
     /**
      * Blanked off, no-op constructor.
      */
@@ -93,8 +86,9 @@ public class HandleDispatcher implements BitstreamDispatcher
      * @param hdl
      *            the handle to get bitstreams from.
      */
-    public HandleDispatcher(String hdl)
+    public HandleDispatcher(BitstreamInfoDAO bitInfoDAO, String hdl)
     {
+        bitstreamInfoDAO = bitInfoDAO;
         handle = hdl;
     }
 
@@ -104,41 +98,26 @@ public class HandleDispatcher implements BitstreamDispatcher
      * @throws SQLException
      *             if database access fails.
      */
-    private void init() throws SQLException
+    private void init()
     {
         Context context = null;
+        int dsoType = -1;
 
+        int id = -1;
         try
         {
             context = new Context();
             DSpaceObject dso = HandleManager.resolveToObject(context, handle);
+            id = dso.getID();
+            dsoType = dso.getType();
             context.abort();
 
-            List ids = new ArrayList();
+        }
+        catch (SQLException e)
+        {
+            LOG.error("init error " + e.getMessage(), e);
+            throw new RuntimeException("init error" + e.getMessage(), e);
 
-            switch (dso.getType())
-            {
-            case Constants.BITSTREAM:
-                ids.add(new Integer(dso.getID()));
-
-                break;
-
-            case Constants.ITEM:
-                ids = getItemIds(dso.getID());
-
-                break;
-
-            case Constants.COLLECTION:
-                ids = getCollectionIds(dso.getID());
-
-                break;
-
-            case Constants.COMMUNITY:
-                ids = getCommunityIds(dso.getID());
-            }
-
-            delegate = new ListDispatcher(ids);
-            init = Boolean.TRUE;
         }
         finally
         {
@@ -148,6 +127,30 @@ public class HandleDispatcher implements BitstreamDispatcher
                 context.abort();
             }
         }
+
+        List ids = new ArrayList();
+
+        switch (dsoType)
+        {
+        case Constants.BITSTREAM:
+            ids.add(new Integer(id));
+            break;
+
+        case Constants.ITEM:
+            ids = bitstreamInfoDAO.getItemBitstreams(id);
+            break;
+
+        case Constants.COLLECTION:
+            ids = bitstreamInfoDAO.getCollectionBitstreams(id);
+            break;
+
+        case Constants.COMMUNITY:
+            ids = bitstreamInfoDAO.getCommunityBitstreams(id);
+            break;
+        }
+
+        delegate = new ListDispatcher(ids);
+        init = Boolean.TRUE;
     }
 
     /**
@@ -155,7 +158,7 @@ public class HandleDispatcher implements BitstreamDispatcher
      * 
      * @see org.dspace.checker.BitstreamDispatcher#next()
      */
-    public int next() throws SQLException
+    public int next()
     {
         synchronized (init)
         {
@@ -167,100 +170,4 @@ public class HandleDispatcher implements BitstreamDispatcher
 
         return delegate.next();
     }
-
-    /**
-     * Utility query method to get item ids.
-     * 
-     * @param id
-     *            the item id
-     * @return a list of bitstream ids for items.
-     * @throws SQLException
-     *             if database access fails
-     */
-    private List getItemIds(int id) throws SQLException
-    {
-        return getIdList(id, ITEM_BITSTREAMS);
-    }
-
-    /**
-     * Utility query method.
-     * 
-     * @param id
-     *            Collection id
-     * @return a list of bitstream ids for collection
-     * @throws SQLException
-     *             if database access error occurs.
-     */
-    private List getCollectionIds(int id) throws SQLException
-    {
-        return getIdList(id, COLLECTION_BITSTREAMS);
-    }
-
-    /**
-     * Utility query method.
-     * 
-     * @param id
-     *            the community id
-     * @return the bitstream ids.
-     * @throws SQLException
-     *             if a database access error occurs.
-     */
-    private List getCommunityIds(int id) throws SQLException
-    {
-        return getIdList(id, COMMUNITY_BITSTREAMS);
-    }
-
-    /**
-     * Utility query method.
-     * 
-     * @param arg
-     *            community/collection/item id.
-     * @param query
-     *            query to be excuted
-     * @return list of bitstream ids.
-     * @throws SQLException
-     *             if database access occurs.
-     */
-    private List getIdList(int arg, String query) throws SQLException
-    {
-        List ids = new ArrayList();
-
-        Connection conn = null;
-        PreparedStatement ps = null;
-        ResultSet rs = null;
-
-        Context ctx = new Context();
-
-        try
-        {
-            conn = ctx.getDBConnection();
-            ps = conn.prepareStatement(query);
-            ps.setInt(1, arg);
-
-            rs = ps.executeQuery();
-
-            while (rs.next())
-            {
-                ids.add(new Integer(rs.getInt(1)));
-            }
-
-            LOG.debug("Returned " + ids.size() + " ids for handle " + handle);
-        }
-        finally
-        {
-            if (rs != null)
-            {
-                rs.close();
-            }
-
-            if (ps != null)
-            {
-                ps.close();
-            }
-
-            ctx.complete();
-        }
-
-        return ids;
-    }
 }

dspace/src/org/dspace/checker/LimitedCountDispatcher.java

@@ -42,6 +42,9 @@ import org.dspace.core.PluginManager;
  * dispatcher.
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public class LimitedCountDispatcher implements BitstreamDispatcher
 {
@@ -92,7 +95,7 @@ public class LimitedCountDispatcher implements BitstreamDispatcher
      * @throws SQLException
      *             if database error occurs.
      */
-    public int next() throws SQLException
+    public int next()
     {
         if (remaining > 0)
         {

dspace/src/org/dspace/checker/LimitedDurationDispatcher.java

@@ -33,7 +33,6 @@
  */
 package org.dspace.checker;
 
-import java.sql.SQLException;
 import java.util.Date;
 
 /**
@@ -48,6 +47,9 @@ import java.util.Date;
  * </p>
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public class LimitedDurationDispatcher implements BitstreamDispatcher
 {
@@ -90,7 +92,7 @@ public class LimitedDurationDispatcher implements BitstreamDispatcher
     /**
      * @see org.dspace.checker.BitstreamDispatcher#next()
      */
-    public int next() throws SQLException
+    public int next()
     {
         return (System.currentTimeMillis() > end) ? SENTINEL : delegate.next();
     }

dspace/src/org/dspace/checker/ListDispatcher.java

@@ -33,7 +33,6 @@
  */
 package org.dspace.checker;
 
-import java.sql.SQLException;
 import java.util.Collections;
 import java.util.EmptyStackException;
 import java.util.List;
@@ -43,6 +42,9 @@ import java.util.Stack;
  * Really simple dispatcher that just iterates over a pre-defined list of ids.
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public class ListDispatcher implements BitstreamDispatcher
 {
@@ -74,7 +76,7 @@ public class ListDispatcher implements BitstreamDispatcher
     /**
      * @see org.dspace.checker.BitstreamDispatcher#next()
      */
-    public synchronized int next() throws SQLException
+    public synchronized int next()
     {
         try
         {

dspace/src/org/dspace/checker/ReporterDAO.java

@@ -47,7 +47,10 @@ import org.dspace.storage.rdbms.DatabaseManager;
 /**
  * This class will report information on the checksum checker process.
  * 
- * @author Nate Sarr
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  * 
  */
 public class ReporterDAO extends DAOSupport

dspace/src/org/dspace/checker/ResultsLogger.java

@@ -45,7 +45,10 @@ import org.dspace.core.I18N;
  * </p>
  * 
  * 
+ * @author Jim Downing
  * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  * 
  */
 public class ResultsLogger implements ChecksumResultsCollector
@@ -131,7 +134,7 @@ public class ResultsLogger implements ChecksumResultsCollector
                 .info(msg("checksum-algorithm") + ": "
                         + info.getChecksumAlgorithm());
         LOG.info(msg("previous-checksum") + ": " + info.getStoredChecksum());
-        LOG.info(msg("previous-checksum-data")
+        LOG.info(msg("previous-checksum-date")
                 + ": "
                 + ((info.getProcessEndDate() != null) ? DATE_FORMAT.format(info
                         .getProcessEndDate()) : "unknown"));

dspace/src/org/dspace/checker/ResultsPruner.java

@@ -57,6 +57,9 @@ import org.dspace.core.Utils;
  * and can use a different configuration file if it is passed in.
  * 
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  * 
  */
 public final class ResultsPruner

dspace/src/org/dspace/checker/SimpleDispatcher.java

@@ -33,45 +33,19 @@
  */
 package org.dspace.checker;
 
-import java.sql.Connection;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
 import java.util.Date;
 
-import org.dspace.storage.rdbms.DatabaseManager;
-
 /**
  * An implementation of the selection strategy that selects bitstreams in the
  * order that they were last checked, looping endlessly.
  * 
- * @author Nate Sarr
  * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public class SimpleDispatcher implements BitstreamDispatcher
 {
-    /**
-     * This selects the next bitstream that is to be processed, in order of last
-     * processing end date. The timestamp is truncated to milliseconds this is
-     * because the Date for java does not support nanoseconds and milliseconds
-     * were considered accurate enough
-     */
-    public static final String FIND_BITSTREAMS_LOOP = "select bitstream_id  "
-            + "from most_recent_checksum " + "where to_be_processed = true "
-            + "order by date_trunc('milliseconds', last_process_end_date), "
-            + "bitstream_id " + "ASC LIMIT 1";
-
-    /**
-     * Selects the next bitstream in order of last processing end date, ensuring
-     * that no bitstream is checked more than once since the date parameter
-     * used.
-     */
-    public static final String FIND_BITSTREAMS_NO_LOOP = "select bitstream_id  "
-            + "from most_recent_checksum "
-            + "where to_be_processed = true "
-            + "and last_process_start_date < ? "
-            + "order by date_trunc('milliseconds', last_process_end_date), "
-            + "bitstream_id " + "ASC LIMIT 1";
 
     /**
      * Should this dispatcher keep on dispatching around the collection?
@@ -89,6 +63,11 @@ public class SimpleDispatcher implements BitstreamDispatcher
      */
     private int bitstreamId = -1;
 
+    /**
+     * Access for bitstream information
+     */
+    private BitstreamInfoDAO bitstreamInfoDAO;
+
     /**
      * Creates a new SimpleDispatcher.
      * 
@@ -98,8 +77,10 @@ public class SimpleDispatcher implements BitstreamDispatcher
      *            indicates whether checker should loop infinitely through
      *            most_recent_checksum table
      */
-    public SimpleDispatcher(Date startTime, boolean looping)
+    public SimpleDispatcher(BitstreamInfoDAO bitstreamInfoDAO, Date startTime,
+            boolean looping)
     {
+        this.bitstreamInfoDAO = bitstreamInfoDAO;
         this.processStartTime = startTime;
         this.loopContinuously = looping;
     }
@@ -117,57 +98,19 @@ public class SimpleDispatcher implements BitstreamDispatcher
      * 
      * @see org.dspace.checker.BitstreamDispatcher#next()
      */
-    public synchronized int next() throws SQLException
+    public synchronized int next()
     {
-        Connection conn = null;
+        // should process loop infinitely through the
-        PreparedStatement prepStmt = null;
+        // bitstreams in most_recent_checksum table?
-        ResultSet rs = null;
+        if (!loopContinuously && (processStartTime != null))
-
-        try
         {
-            // create the connection and execute the statement
+            return bitstreamInfoDAO.getOldestBitstream(new java.sql.Timestamp(
-            conn = DatabaseManager.getConnection();
+                    processStartTime.getTime()));
-
-            // should process loop infinitely through the
-            // bitstreams in most_recent_checksum table?
-            if (!loopContinuously && (processStartTime != null))
-            {
-                prepStmt = conn.prepareStatement(FIND_BITSTREAMS_NO_LOOP);
-                prepStmt.setTimestamp(1, new java.sql.Timestamp(
-                        processStartTime.getTime()));
-            }
-            else
-            {
-                prepStmt = conn.prepareStatement(FIND_BITSTREAMS_LOOP);
-            }
-
-            rs = prepStmt.executeQuery();
-
-            if (rs.next())
-            {
-                return rs.getInt(1);
-            }
-            else
-            {
-                return SENTINEL;
-            }
         }
-        finally
+        else
         {
-            if (rs != null)
+            return bitstreamInfoDAO.getOldestBitstream();
-            {
-                rs.close();
-            }
-
-            if (prepStmt != null)
-            {
-                prepStmt.close();
-            }
-
-            if (conn != null)
-            {
-                DatabaseManager.freeConnection(conn);
-            }
         }
+
     }
 }

dspace/src/org/dspace/checker/SimpleReporter.java

@@ -41,7 +41,10 @@ import java.util.Date;
  * 
  * Simple Reporting Class which can return several different reports.
  * 
- * @author Nate Sarr
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  */
 public interface SimpleReporter
 {

dspace/src/org/dspace/checker/SimpleReporterImpl.java

@@ -47,7 +47,10 @@ import org.dspace.core.I18N;
  * 
  * Simple Reporter implementation.
  * 
- * @author Nate Sarr
+ * @author Jim Downing
+ * @author Grace Carpenter
+ * @author Nathan Sarr
+ * 
  * @todo estimate string buffer sizes.
  */
 public class SimpleReporterImpl implements SimpleReporter

dspace/src/org/dspace/core/I18N.java

@@ -135,7 +135,9 @@ public class I18N {
 	 * @return Localized message 
 	 */
 	public String getMessage(String msg, Class clazz) {
-		return getMessage(msg, clazz.getName());
+		String className = clazz.getName();
+		return messages.getString(new StringBuilder(50).append(className)
+				.append(".").append(msg).toString());
 	}
 
 	/**