Merge pull request #822 from KevinVdV/DS-2396

[DS-2396] Checksum checker and bitstream.user_format_description

dspace-api/src/main/java/org/dspace/app/checker/ChecksumChecker.java

@@ -8,6 +8,7 @@
 package org.dspace.app.checker;
 
 import java.io.FileNotFoundException;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Date;
@@ -32,6 +33,7 @@ import org.dspace.checker.ListDispatcher;
 import org.dspace.checker.ResultsLogger;
 import org.dspace.checker.ResultsPruner;
 import org.dspace.checker.SimpleDispatcher;
+import org.dspace.core.Context;
 import org.dspace.core.Utils;
 
 /**
@@ -78,8 +80,7 @@ public final class ChecksumChecker
      *            <dd>Don't prune results before running checker</dd>
      *            </dl>
      */
-    public static void main(String[] args)
+    public static void main(String[] args) throws SQLException {
-    {
         // set up command line parser
         CommandLineParser parser = new PosixParser();
         CommandLine line = null;
@@ -230,7 +231,13 @@ public final class ChecksumChecker
         checker.setProcessStartDate(processStart);
         checker.setDispatcher(dispatcher);
         checker.setCollector(logger);
-        checker.process();
+        Context context = new Context();
+        try {
+            checker.process(context);
+        } finally {
+            context.commit();
+            context.complete();
+        }
         System.exit(0);
     }
 

dspace-api/src/main/java/org/dspace/checker/BitstreamInfoDAO.java

@@ -17,7 +17,9 @@ import java.util.Date;
 import java.util.List;
 
 import org.apache.log4j.Logger;
+import org.dspace.content.Bitstream;
 import org.dspace.core.ConfigurationManager;
+import org.dspace.core.Context;
 import org.dspace.storage.rdbms.DatabaseManager;
 
 /**
@@ -43,9 +45,9 @@ public final class BitstreamInfoDAO extends DAOSupport
     /** 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,  "
-            + "bitstream.user_format_description, bitstream.internal_id, "
+            + "bitstream.internal_id, "
-            + "bitstream.source, bitstream.checksum_algorithm, bitstream.checksum, "
+            + "bitstream.checksum_algorithm, bitstream.checksum, "
-            + "bitstream.name, most_recent_checksum.last_process_end_date,"
+            + "most_recent_checksum.last_process_end_date,"
             + "most_recent_checksum.to_be_processed "
             + "from bitstream left outer join bitstreamformatregistry on "
             + "bitstream.bitstream_format_id = bitstreamformatregistry.bitstream_format_id, "
@@ -226,7 +228,7 @@ public final class BitstreamInfoDAO extends DAOSupport
      * @return the bitstream information needed for checksum validation. Returns
      *         null if bitstream info isn't found.
      */
-    public BitstreamInfo findByBitstreamId(int id)
+    public BitstreamInfo findByBitstreamId(Context context, int id)
     {
         Connection conn = null;
         BitstreamInfo info = null;
@@ -246,14 +248,14 @@ public final class BitstreamInfoDAO extends DAOSupport
             // if the bitstream is found return it
             if (rs.next())
             {
+                Bitstream bitstream = Bitstream.find(context, rs.getInt("bitstream_id"));
                 info = new BitstreamInfo(rs.getBoolean("deleted"), rs
                         .getInt("store_number"), rs.getLong("size_bytes"), rs
                         .getString("short_description"), rs
-                        .getInt("bitstream_id"), rs
+                        .getInt("bitstream_id"), bitstream.getUserFormatDescription(), rs
-                        .getString("user_format_description"), rs
+                        .getString("internal_id"), bitstream.getSource(), rs
-                        .getString("internal_id"), rs.getString("source"), rs
                         .getString("checksum_algorithm"), rs
-                        .getString("checksum"), rs.getString("name"), rs
+                        .getString("checksum"), bitstream.getName(), rs
                         .getTimestamp("last_process_end_date"), rs
                         .getBoolean("to_be_processed"), new Date());
             }

dspace-api/src/main/java/org/dspace/checker/CheckerCommand.java

@@ -16,6 +16,7 @@ import java.sql.SQLException;
 import java.util.Date;
 
 import org.apache.log4j.Logger;
+import org.dspace.core.Context;
 import org.dspace.core.Utils;
 
 /**
@@ -93,7 +94,7 @@ public final class CheckerCommand
      * setBitstreamDispatcher before calling this method
      * </p>
      */
-    public void process()
+    public void process(Context context)
     {
         LOG.debug("Begin Checker Processing");
 
@@ -116,7 +117,7 @@ public final class CheckerCommand
         while (id != BitstreamDispatcher.SENTINEL)
         {
             LOG.debug("Processing bitstream id = " + id);
-            BitstreamInfo info = checkBitstream(id);
+            BitstreamInfo info = checkBitstream(context, id);
 
             if (reportVerbose
                     || !ChecksumCheckResults.CHECKSUM_MATCH.equals(info.getChecksumCheckResult()))
@@ -136,10 +137,10 @@ public final class CheckerCommand
      * 
      * @return the information about the bitstream and its checksum data
      */
-    private BitstreamInfo checkBitstream(final int id)
+    private BitstreamInfo checkBitstream(Context context, final int id)
     {
         // get bitstream info from bitstream table
-        BitstreamInfo info = bitstreamInfoDAO.findByBitstreamId(id);
+        BitstreamInfo info = bitstreamInfoDAO.findByBitstreamId(context, id);
 
         // requested id was not found in bitstream
         // or most_recent_checksum table

dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java

@@ -10,6 +10,7 @@ package org.dspace.checker;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.sql.SQLException;
 import java.util.Date;
 import java.util.GregorianCalendar;
 import javax.mail.MessagingException;
@@ -22,6 +23,7 @@ import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
 import org.apache.log4j.Logger;
 import org.dspace.core.ConfigurationManager;
+import org.dspace.core.Context;
 import org.dspace.core.Email;
 
 /**
@@ -178,9 +180,11 @@ public class DailyReportEmailer
 
         File report = null;
         FileWriter writer = null;
+        Context context = null;
 
         try
         {
+            context = new Context();
             // the number of bitstreams in report
             int numBitstreams = 0;
 
@@ -221,7 +225,7 @@ public class DailyReportEmailer
                         tomorrow, writer);
                 writer
                         .write("\n--------------------------------- Report Spacer ---------------------------\n\n");
-                numBitstreams += reporter.getUncheckedBitstreamsReport(writer);
+                numBitstreams += reporter.getUncheckedBitstreamsReport(context, writer);
                 writer
                         .write("\n--------------------------------- End Report ---------------------------\n\n");
                 writer.flush();
@@ -279,7 +283,7 @@ public class DailyReportEmailer
                     writer
                             .write("\n--------------------------------- Begin Reporting ------------------------\n\n");
                     numBitstreams += reporter
-                            .getUncheckedBitstreamsReport(writer);
+                            .getUncheckedBitstreamsReport(context, writer);
                     writer.flush();
                     writer.close();
                     emailer.sendReport(report, numBitstreams);
@@ -293,9 +297,14 @@ public class DailyReportEmailer
         catch (IOException e)
         {
             log.fatal(e);
-        }
+        } catch (SQLException e) {
-        finally
+            log.fatal(e);
+        } finally
         {
+            if(context != null && context.isValid())
+            {
+                context.abort();
+            }
             if (writer != null)
             {
                 try

dspace-api/src/main/java/org/dspace/checker/ReporterDAO.java

@@ -16,7 +16,9 @@ import java.util.LinkedList;
 import java.util.List;
 
 import org.apache.log4j.Logger;
+import org.dspace.content.Bitstream;
 import org.dspace.core.ConfigurationManager;
+import org.dspace.core.Context;
 import org.dspace.storage.rdbms.DatabaseManager;
 
 /**
@@ -77,9 +79,8 @@ public class ReporterDAO extends DAOSupport
      */
     public static final String FIND_UNKNOWN_BITSTREAMS = "select bitstream.deleted, bitstream.store_number, bitstream.size_bytes, "
             + "bitstreamformatregistry.short_description, bitstream.bitstream_id,  "
-            + "bitstream.user_format_description, bitstream.internal_id, "
+            + "bitstream.internal_id, "
-            + "bitstream.source, bitstream.checksum_algorithm, bitstream.checksum, "
+            + "bitstream.checksum_algorithm, bitstream.checksum "
-            + "bitstream.name, bitstream.description "
             + "from bitstream left outer join bitstreamformatregistry on "
             + "bitstream.bitstream_format_id = bitstreamformatregistry.bitstream_format_id "
             + "where not exists( select 'x' from most_recent_checksum "
@@ -224,7 +225,7 @@ public class ReporterDAO extends DAOSupport
      * 
      * @return a List of DSpaceBitstreamInfo objects
      */
-    public List<DSpaceBitstreamInfo> getUnknownBitstreams()
+    public List<DSpaceBitstreamInfo> getUnknownBitstreams(Context context)
     {
         List<DSpaceBitstreamInfo> unknownBitstreams = new LinkedList<DSpaceBitstreamInfo>();
 
@@ -244,16 +245,15 @@ public class ReporterDAO extends DAOSupport
             // add the bitstream history objects
             while (rs.next())
             {
+                Bitstream bitstream = Bitstream.find(context, rs.getInt("bitstream_id"));
                 unknownBitstreams.add(new DSpaceBitstreamInfo(rs
                         .getBoolean("deleted"), rs.getInt("store_number"), rs
                         .getInt("size_bytes"), rs
                         .getString("short_description"), rs
-                        .getInt("bitstream_id"), rs
+                        .getInt("bitstream_id"), bitstream.getFormatDescription(), rs
-                        .getString("user_format_description"), rs
+                        .getString("internal_id"), bitstream.getSource(), rs
-                        .getString("internal_id"), rs.getString("source"), rs
                         .getString("checksum_algorithm"), rs
-                        .getString("checksum"), rs.getString("name"), rs
+                        .getString("checksum"), bitstream.getName(), bitstream.getDescription()));
-                        .getString("description")));
             }
         }
         catch (SQLException e)

dspace-api/src/main/java/org/dspace/checker/SimpleReporter.java

@@ -7,6 +7,8 @@
  */
 package org.dspace.checker;
 
+import org.dspace.core.Context;
+
 import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.util.Date;
@@ -110,6 +112,6 @@ public interface SimpleReporter
      *             if io error occurs
      * 
      */
-    public int getUncheckedBitstreamsReport(OutputStreamWriter osw)
+    public int getUncheckedBitstreamsReport(Context context, OutputStreamWriter osw)
             throws IOException;
 }

dspace-api/src/main/java/org/dspace/checker/SimpleReporterImpl.java

@@ -14,6 +14,7 @@ import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
 
+import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
 
 /**
@@ -240,11 +241,11 @@ public class SimpleReporterImpl implements SimpleReporter
      * @throws IOException
      *             if io error occurs
      */
-    public int getUncheckedBitstreamsReport(OutputStreamWriter osw)
+    public int getUncheckedBitstreamsReport(Context context, OutputStreamWriter osw)
             throws IOException
     {
         // get all the bitstreams marked deleted for today
-        List<DSpaceBitstreamInfo> bitstreams = reporter.getUnknownBitstreams();
+        List<DSpaceBitstreamInfo> bitstreams = reporter.getUnknownBitstreams(context);
 
         osw.write("\n");
         osw.write(msg("unchecked-bitstream-report"));