version 1.6beta checkin

git-svn-id: https://subversion.umiacs.umd.edu/ace/trunk@33 f1b3a171-7291-4a19-a512-95ad0ad9394a

ace-am/src/java/edu/umiacs/ace/driver/FileBean.java

@@ -30,6 +30,8 @@
 // $Id$
 package edu.umiacs.ace.driver;
 
+import java.util.Arrays;
+
 /**
  *
  * @author toaster
@@ -84,7 +86,11 @@ public class FileBean {
      * @param parentPathList
      */
     public void setPathList( String[] pathList ) {
-        this.pathList = pathList;
+        if ( pathList != null ) {
+            this.pathList = Arrays.copyOf(pathList, pathList.length);
+        } else {
+            this.pathList = null;
+        }
     }
 
     public String[] getPathList() {

ace-am/src/java/edu/umiacs/ace/driver/QueryThrottle.java

@@ -51,6 +51,18 @@ public class QueryThrottle implements ServletContextListener {
     private static final String PARAM_BPS = "throttle.bps";
     private static final Logger LOG = Logger.getLogger(QueryThrottle.class);
 
+    private static void setMinWait( long minWait ) {
+        QueryThrottle.minWait = minWait;
+    }
+
+    private static void setMaxBps( long maxBps ) {
+        QueryThrottle.maxBps = maxBps;
+    }
+
+    public static long getMaxBps() {
+        return maxBps;
+    }
+
     public static void waitToRun() throws InterruptedException {
         if ( minWait <= 0 ) {
             return;
@@ -68,9 +80,6 @@ public class QueryThrottle implements ServletContextListener {
 
     }
 
-    public static long getMaxBps() {
-        return maxBps;
-    }
 
     private static synchronized void workCheck() {
         synchronized ( PARAM_TIME ) {
@@ -84,13 +93,13 @@ public class QueryThrottle implements ServletContextListener {
 
 
         if ( Strings.isValidInt(time) ) {
-            minWait = Integer.parseInt(time);
+            setMinWait(Integer.parseInt(time));
             LOG.info("Setting query throttle minwait to " + minWait);
         }
 
         String maxBpsString = sce.getServletContext().getInitParameter(PARAM_BPS);
         if ( Strings.isValidLong(maxBpsString) ) {
-            maxBps = Long.parseLong(maxBpsString);
+           setMaxBps(Long.parseLong(maxBpsString));
         }
 
 

ace-am/src/java/edu/umiacs/ace/driver/RetrieveItemServlet.java

@@ -112,7 +112,7 @@ public final class RetrieveItemServlet extends EntityManagerServlet {
             writeItemToResponse(response, collectionPath, coll, em);
 
         }
-        LOG.debug("Collection: " + collection + " item: " + (item != null ? item.getPath() : ""));
+        LOG.debug("Retrieved item, Collection: " + collection + " item: " + item.getPath());
 
     }
 

ace-am/src/java/edu/umiacs/ace/driver/benchmark/BenchmarkAccess.java

@@ -240,10 +240,11 @@ public class BenchmarkAccess extends StorageDriver {
         private String[] createPathList() {
             String[] retString = new String[arrayCounter.length + 1];
 
-            String path = "";
+            StringBuilder path = new StringBuilder();
             for ( int idx = 0; idx < arrayCounter.length; idx++ ) {
-                path = path + "/dir-" + arrayCounter[idx];
-                retString[arrayCounter.length - idx] = path;
+                path.append("/dir-");
+                path.append(arrayCounter[idx]);
+                retString[arrayCounter.length - idx] = path.toString();
             }
             retString[0] = path + "/file-" + currFile;
 

ace-am/src/java/edu/umiacs/ace/driver/filter/FilterServlet.java

@@ -137,11 +137,11 @@ public class FilterServlet extends EntityManagerServlet {
         Map paramMap = request.getParameterMap();
 
         if ( !Strings.isEmpty(paramMap.get(PARAM_MODIFY)) ) {
-            for ( Object param : paramMap.keySet() ) {
-                String name = (String) param;
-                if ( name.startsWith(PARAM_REGEX_PREFIX) && !Strings.isEmpty(paramMap.get(
-                        param)) ) {
-                    String[] regex = (String[]) paramMap.get(param);
+            for ( Object o : paramMap.entrySet() ) {
+                Map.Entry entry = (Map.Entry) o;
+                String name = (String) entry.getKey();
+                if ( name.startsWith(PARAM_REGEX_PREFIX) && !Strings.isEmpty(entry.getValue()) ) {
+                    String[] regex = (String[]) entry.getValue();
                     String count = name.substring(PARAM_REGEX_PREFIX.length());
                     int type = Integer.parseInt(((String[]) paramMap.get(
                             PARAM_TYPE_PREFIX + count))[0]);
@@ -179,11 +179,11 @@ public class FilterServlet extends EntityManagerServlet {
         }
     }
 
-    public class ErrorList<T> extends ArrayList<T> {
+    public static class ErrorList<T> extends ArrayList<T> {
 
         private boolean error = false;
 
-        public ErrorList() {
+        private ErrorList() {
         }
 
         public ErrorList( List l ) {
@@ -195,12 +195,12 @@ public class FilterServlet extends EntityManagerServlet {
         }
     }
 
-    public class MyFilterEntry extends FilterEntry {
+    public static class MyFilterEntry extends FilterEntry {
 
         private String error = null;
         private boolean matchesTest = false;
 
-        public MyFilterEntry() {
+        private MyFilterEntry() {
         }
 
         public MyFilterEntry( FilterEntry fe ) {

ace-am/src/java/edu/umiacs/ace/driver/srb/SrbAccess.java

@@ -60,7 +60,7 @@ import org.apache.log4j.Logger;
  *
  * @author toaster
  */
-public class SrbAccess extends StorageDriver {
+public final class SrbAccess extends StorageDriver {
 
     private static final Logger LOG = Logger.getLogger(SrbAccess.class);
     private static final String PARAM_SERVER = "server";
@@ -254,7 +254,7 @@ public class SrbAccess extends StorageDriver {
         return new WrappedInputStream(sfis, sfs, cp);
     }
 
-    class WrappedInputStream extends FilterInputStream {
+    static class WrappedInputStream extends FilterInputStream {
 
         private ConnectionPool cp;
         private SRBFileSystem sfs;

ace-am/src/java/edu/umiacs/ace/driver/srb/SrbDirectoryIterator.java

@@ -64,14 +64,14 @@ import org.apache.log4j.NDC;
  *
  * @author toaster
  */
-public class SrbDirectoryIterator implements Iterator<FileBean> {
+public final class SrbDirectoryIterator implements Iterator<FileBean> {
 
     private DriverStateBean[] statebeans;
     private static final int MAX_THREADS = 5;
     private static final int RETRY = 5;
     private static final Logger LOG = Logger.getLogger(
             SrbDirectoryIterator.class);
-    private Collection collection;
+//    private Collection collection;
     private ConnectionPool pool;
     private boolean finished = false;
     private LinkedBlockingQueue<FileBean> readyList = new LinkedBlockingQueue<FileBean>();
@@ -86,7 +86,7 @@ public class SrbDirectoryIterator implements Iterator<FileBean> {
 
     public SrbDirectoryIterator( Collection c, SrbSettings settings,
             MonitoredItem[] basePath, PathFilter filter, String digestAlgorithm ) {
-        this.collection = c;
+//        this.collection = c;
         this.pool = settings.createPool();
         this.root = c.getDirectory();
         this.filter = filter;

ace-am/src/java/edu/umiacs/ace/driver/swap/SwapFileAccess.java

@@ -192,28 +192,6 @@ public class SwapFileAccess extends StorageDriver {
         return null;
     }
 
-    private class MyConnectListener implements ConnectionListener {
-
-        Operation result = null;
-
-        @Override
-        public synchronized void connectionEvent( InetSocketAddress isa, Operation oprtn ) {
-            if ( result == null && oprtn != Operation.DISCONNECT ) {
-                result = oprtn;
-                notifyAll();
-            }
-
-        }
-        // block till result
-
-        public synchronized Operation getResult() throws InterruptedException {
-            while ( result == null ) {
-                wait();
-            }
-            return result;
-        }
-    }
-
     private String getSingleParam( Map m, String paramName ) {
         Object o = m.get(paramName);
 
@@ -356,4 +334,28 @@ public class SwapFileAccess extends StorageDriver {
         return connection.getInputStream();
 
     }
+
+
+    private static class MyConnectListener implements ConnectionListener {
+
+        Operation result = null;
+
+        @Override
+        public synchronized void connectionEvent( InetSocketAddress isa, Operation oprtn ) {
+            if ( result == null && oprtn != Operation.DISCONNECT ) {
+                result = oprtn;
+                notifyAll();
+            }
+
+        }
+        // block till result
+
+        public synchronized Operation getResult() throws InterruptedException {
+            while ( result == null ) {
+                wait();
+            }
+            return result;
+        }
+    }
+
 }

ace-am/src/java/edu/umiacs/ace/driver/swap/SwapIterator.java

@@ -64,7 +64,7 @@ import org.swap.client.SwapFile;
  *
  * @author toaster
  */
-public class SwapIterator implements Iterator<FileBean> {
+public final class SwapIterator implements Iterator<FileBean> {
 
     private Queue<SwapFile> dirsToProcess = new LinkedList<SwapFile>();
     private LinkedBlockingQueue<SwapFile> filesToProcess = new LinkedBlockingQueue<SwapFile>();

ace-am/src/java/edu/umiacs/ace/monitor/access/CollectionCountContext.java

@@ -82,7 +82,6 @@ public class CollectionCountContext implements ServletContextListener {
                 Thread.currentThread().setName("Startup Count Thread");
                 NDC.push("[Count]");
                 lock.lock();
-//                {
                 LOG.debug("Starting count for all collections");
                 try {
                     EntityManager em = PersistUtil.getEntityManager();
@@ -91,6 +90,7 @@ public class CollectionCountContext implements ServletContextListener {
 
                     for ( Object o : collQuery.getResultList() ) {
                         if ( abort ) {
+                            LOG.info("Collection count aborting, tomcat probably shutting down");
                             return;
                         }
                         queryCollection((Collection) o);
@@ -211,6 +211,8 @@ public class CollectionCountContext implements ServletContextListener {
             long totalErrors = 0;
 
             while ( rs.next() ) {
+                if (abort)
+                    return;
                 char state = rs.getString(1).charAt(0);
                 long count = rs.getLong(2);
 
@@ -271,7 +273,7 @@ public class CollectionCountContext implements ServletContextListener {
             SQL.release(rs);
             SQL.release(ps);
             SQL.release(connection);
-            LOG.debug("Finished count on " + c.getName());
+            LOG.trace("Finished count on " + c.getName());
 
         }
     }

ace-am/src/java/edu/umiacs/ace/monitor/access/StatusServlet.java

@@ -101,7 +101,7 @@ public class StatusServlet extends EntityManagerServlet {
                 request.getSession().setAttribute(SESSION_WORKINGCOLLECTION, csb);
             } else if ( request.getSession().getAttribute(
                     SESSION_WORKINGCOLLECTION) != null && ((CollectionSummaryBean) request.getSession().getAttribute(
-                    SESSION_WORKINGCOLLECTION)).getCollection().getId() == col.getId() ) {
+                    SESSION_WORKINGCOLLECTION)).getCollection().getId().equals(col.getId()) ) {
                 request.getSession().setAttribute(SESSION_WORKINGCOLLECTION, csb);
 
             }

ace-am/src/java/edu/umiacs/ace/monitor/access/browse/BrowseServlet.java

@@ -160,12 +160,15 @@ public class BrowseServlet extends EntityManagerServlet {
 
     }
 
-    public class FileBean {
+    public static class FileBean {
 
         MonitoredItem root;
         String name;
         String itemProof;
 
+        private FileBean() {
+        }
+
         public String getItemProof() {
             return itemProof;
         }

ace-am/src/java/edu/umiacs/ace/monitor/access/browse/DirectoryTree.java

@@ -150,7 +150,7 @@ public class DirectoryTree {
 
     }
 
-    public class DirectoryNode implements Comparable {
+    public static class DirectoryNode implements Comparable {
 
         private boolean expanded = false;
         private boolean directory = false;
@@ -159,6 +159,9 @@ public class DirectoryTree {
         List<DirectoryNode> children = new ArrayList<DirectoryNode>();
         private char status;
 
+        private DirectoryNode() {
+        }
+
         public boolean isExpanded() {
             return expanded;
         }
@@ -187,6 +190,52 @@ public class DirectoryTree {
             return String.valueOf(status);
         }
 
+
+
+        @Override
+        public int hashCode() {
+            int hash = 5;
+            hash = 11 * hash + (this.expanded ? 1 : 0);
+            hash = 11 * hash + (this.directory ? 1 : 0);
+            hash = 11 * hash + (this.path != null ? this.path.hashCode() : 0);
+            hash = 11 * hash + (int) (this.id ^ (this.id >>> 32));
+            hash = 11 * hash + (this.children != null ? this.children.hashCode() : 0);
+            hash = 11 * hash + this.status;
+            return hash;
+        }
+
+        @Override
+        public boolean equals( Object obj ) {
+            if ( obj == null ) {
+                return false;
+            }
+            if ( getClass() != obj.getClass() ) {
+                return false;
+            }
+            final DirectoryNode other = (DirectoryNode) obj;
+            if ( this.expanded != other.expanded ) {
+                return false;
+            }
+            if ( this.directory != other.directory ) {
+                return false;
+            }
+            if ( (this.path == null) ? (other.path != null) : !this.path.equals(other.path) ) {
+                return false;
+            }
+            if ( this.id != other.id ) {
+                return false;
+            }
+            if ( this.children != other.children &&
+                    (this.children == null || !this.children.equals(other.children)) ) {
+                return false;
+            }
+            if ( this.status != other.status ) {
+                return false;
+            }
+            return true;
+        }
+
+        @Override
         public int compareTo( Object o ) {
             if ( o instanceof DirectoryNode ) {
                 DirectoryNode n = (DirectoryNode) o;

ace-am/src/java/edu/umiacs/ace/monitor/audit/AuditConfigurationContext.java

@@ -34,6 +34,7 @@ import edu.umiacs.ace.driver.StorageDriver;
 import edu.umiacs.ace.driver.StorageDriverFactory;
 import edu.umiacs.ace.util.PersistUtil;
 import edu.umiacs.ace.monitor.core.Collection;
+import edu.umiacs.ace.monitor.core.MonitoredItem;
 import edu.umiacs.util.Strings;
 import java.util.List;
 import java.util.Timer;
@@ -119,10 +120,13 @@ public final class AuditConfigurationContext implements ServletContextListener {
         AuditTokens.cancellAll();
     }
 
-    public class PauseBean {
+    public static class PauseBean {
 
         private boolean paused = false;
 
+        private PauseBean() {
+        }
+
         public void setPaused( boolean paused ) {
             this.paused = paused;
         }
@@ -137,11 +141,11 @@ public final class AuditConfigurationContext implements ServletContextListener {
         }
     }
 
-    class MyTimerTask extends TimerTask {
+    static class MyTimerTask extends TimerTask {
 
         private PauseBean pb;
 
-        public MyTimerTask( PauseBean pb ) {
+        private MyTimerTask( PauseBean pb ) {
             this.pb = pb;
         }
 
@@ -174,7 +178,7 @@ public final class AuditConfigurationContext implements ServletContextListener {
                         LOG.debug("No last sync for " + c.getName() + " running");
                         sa = StorageDriverFactory.createStorageAccess(c,
                                 em);
-                        AuditThreadFactory.createThread(c, sa, null);
+                        AuditThreadFactory.createThread(c, sa, (MonitoredItem[])null);
                     } else {
                         long syncTime = c.getLastSync().getTime();
                         long currTime = System.currentTimeMillis();
@@ -184,7 +188,7 @@ public final class AuditConfigurationContext implements ServletContextListener {
                                     + " greater than " + (c.getCheckPeriod() * HOUR * 24));
                             sa = StorageDriverFactory.createStorageAccess(c,
                                     em);
-                            AuditThreadFactory.createThread(c, sa, null);
+                            AuditThreadFactory.createThread(c, sa, (MonitoredItem[]) null);
                         } else {
                             LOG.trace("No Sync on " + c.getName());
                         }

ace-am/src/java/edu/umiacs/ace/monitor/audit/AuditTokens.java

@@ -32,7 +32,6 @@ package edu.umiacs.ace.monitor.audit;
 
 import edu.umiacs.ace.ims.api.IMSService;
 import edu.umiacs.ace.ims.api.TokenValidator;
-import edu.umiacs.ace.ims.ws.TokenResponse;
 import edu.umiacs.ace.util.PersistUtil;
 import edu.umiacs.ace.monitor.core.MonitoredItem;
 import edu.umiacs.ace.monitor.core.MonitoredItemManager;
@@ -43,7 +42,6 @@ import edu.umiacs.ace.token.AceToken;
 import edu.umiacs.ace.util.TokenUtil;
 import edu.umiacs.util.Strings;
 import java.security.MessageDigest;
-import java.util.Date;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
@@ -56,7 +54,7 @@ import org.apache.log4j.Logger;
  * 
  * @author toaster
  */
-public class AuditTokens extends Thread implements CancelCallback {
+public final class AuditTokens extends Thread implements CancelCallback {
 
     private static final Map<Collection, AuditTokens> runningThreads =
             new HashMap<Collection, AuditTokens>();
@@ -78,7 +76,7 @@ public class AuditTokens extends Thread implements CancelCallback {
 
     private AuditTokens( Collection collection ) {
         this.collection = collection;
-        session = new Date().getTime();
+        session = System.currentTimeMillis();
         logManager = new LogEventManager(session, collection);
         this.start();
     }

ace-am/src/java/edu/umiacs/ace/monitor/audit/FileAuditCallback.java

@@ -42,10 +42,7 @@ import edu.umiacs.ace.ims.ws.TokenRequest;
 import edu.umiacs.ace.ims.ws.TokenResponse;
 import edu.umiacs.ace.monitor.core.Collection;
 import edu.umiacs.ace.monitor.log.LogEnum;
-import edu.umiacs.ace.token.AceToken;
 import edu.umiacs.util.Strings;
-import java.io.Serializable;
-import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;

ace-am/src/java/edu/umiacs/ace/monitor/compare/CollectionCompare.java

@@ -533,13 +533,13 @@ public class CollectionCompare {
         };
     }
 
-    class ReadIterator implements Iterator<SourceFile> {
+    static class ReadIterator implements Iterator<SourceFile> {
 
         private BufferedReader input;
         private SourceFile next = null;
         private String prefix = null;
 
-        public ReadIterator( InputStream input, String prefix ) {
+        private ReadIterator( InputStream input, String prefix ) {
             this.prefix = prefix;
             this.input = new BufferedReader(new InputStreamReader(input));
             next = readNext();
@@ -595,12 +595,12 @@ public class CollectionCompare {
         }
     }
 
-    class SourceFile {
+    static class SourceFile {
 
         private String name;
         private String digest;
 
-        public SourceFile( String name, String digest ) {
+        private SourceFile( String name, String digest ) {
             this.name = name;
             this.digest = digest;
         }
@@ -622,14 +622,14 @@ public class CollectionCompare {
         }
     }
 
-    public class DifferingName implements Comparable<DifferingName> {
+    public static class DifferingName implements Comparable<DifferingName> {
 
         private String compString;
         private String sourceName;
         private String destinationName;
         private String digest;
 
-        public DifferingName( String sourceName, String destinationName,
+        private DifferingName( String sourceName, String destinationName,
                 String digest ) {
             this.sourceName = sourceName;
             this.destinationName = destinationName;
@@ -681,14 +681,14 @@ public class CollectionCompare {
         }
     }
 
-    public class DifferingDigest implements Comparable<DifferingDigest> {
+    public static class DifferingDigest implements Comparable<DifferingDigest> {
 
         private String name;
         private String sourceDigest;
         private String targetDigest;
         private String compString;
 
-        public DifferingDigest( String name, String sourceDigest,
+        private DifferingDigest( String name, String sourceDigest,
                 String targetDigest ) {
             this.name = name;
             this.sourceDigest = sourceDigest;
@@ -720,6 +720,7 @@ public class CollectionCompare {
             this.sourceDigest = sourceDigest;
         }
 
+        @Override
         public int compareTo( DifferingDigest o ) {
             return compString.compareTo(o.compString);
         }

ace-am/src/java/edu/umiacs/ace/monitor/compare/CompareServlet.java

@@ -186,13 +186,13 @@ public class CompareServlet extends EntityManagerServlet {
 
     }
 
-    class TableCompareRunnable implements Runnable {
+    static class TableCompareRunnable implements Runnable {
 
         private CollectionCompare cc;
         private Collection c;
         private MonitoredItem baseItem;
 
-        public TableCompareRunnable( CollectionCompare cc, Collection c,
+        private TableCompareRunnable( CollectionCompare cc, Collection c,
                 MonitoredItem baseItem ) {
             this.cc = cc;
             this.c = c;

ace-am/src/java/edu/umiacs/ace/monitor/compare/DuplicateReportServlet.java

@@ -109,6 +109,8 @@ public class DuplicateReportServlet extends EntityManagerServlet {
 
                 rs.close();
                 pst.close();
+                LOG.info("Duplicate report on " + collection.getName() + " time "
+                + (System.currentTimeMillis() - startTime) + " total dups " + totalDups);
 
             } catch ( SQLException e ) {
                 throw new