report jsp fix, corrected missing newfile log entry, pom cleanup, irods 1.1 update

git-svn-id: https://subversion.umiacs.umd.edu/ace/trunk@68 f1b3a171-7291-4a19-a512-95ad0ad9394a

ace-am/pom.xml

@@ -6,10 +6,10 @@
     <artifactId>ace</artifactId>
     <groupId>edu.umiacs.ace</groupId>
     <version>1.6-SNAPSHOT</version>
+    <relativePath>../pom.xml</relativePath>
   </parent>
   <groupId>edu.umiacs.ace</groupId>
   <artifactId>ace-am</artifactId>
-  <version>1.6-SNAPSHOT</version>
   <name>ace-am</name>
   <packaging>war</packaging>
   <url>http://maven.apache.org</url>
@@ -18,35 +18,13 @@
     <netbeans.hint.deploy.server>Tomcat60</netbeans.hint.deploy.server>
   </properties>
 
-<repositories>
-  <repository>
-     <id>EclipseLink Repo</id>
-     <url>http://www.eclipse.org/downloads/download.php?r=1&amp;nf=1&amp;file=/rt/eclipselink/maven.repo</url>
-     <!-- use this for javax.persistence
-     <snapshots>
-        <enabled>true</enabled>
-     </snapshots> -->
-  </repository>
-  <repository>
-    <url>http://www.umiacs.umd.edu/~toaster/mavenrepo</url>
-    <id>local</id>
-    <layout>default</layout>
-    <name>Local scratch repo</name>
-  </repository>
-  <repository>
-    <url>http://ftp.ing.umu.se/mirror/eclipse/rt/eclipselink/maven.repo</url>
-    <id>eclipselink</id>
-    <layout>default</layout>
-    <name>Repository for library Library[eclipselink]</name>
-  </repository>
-</repositories>
 
   <dependencies>
     <!-- local ace deps -->
     <dependency>
       <groupId>edu.umiacs.ace</groupId>
       <artifactId>ace-ims-api</artifactId>
-      <version>1.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
 
 
@@ -162,7 +140,7 @@
     <dependency>
       <groupId>edu.umiacs</groupId>
       <artifactId>irods-api</artifactId>
-      <version>1.0</version>
+      <version>1.1</version>
     </dependency>
   </dependencies>
 </project>

ace-am/src/main/java/edu/umiacs/ace/driver/irods/IrodsHandler.java

@@ -51,15 +51,23 @@ public class IrodsHandler implements BulkFileHandler {
     private LinkedBlockingQueue<FileBean> readyList;
     private PathFilter filter;
     private MessageDigest digest;
-//    private boolean ignore = false;
     private String workingFile;
     private long fileSize;
     private static final Logger LOG = Logger.getLogger(IrodsHandler.class);
+    private String root;
 
+    /**
+     *
+     * @param readyList
+     * @param filter
+     * @param digestAlgorithm
+     * @param base prefix to add to returned files (no trailing /)
+     */
     public IrodsHandler( LinkedBlockingQueue<FileBean> readyList,
             PathFilter filter, String digestAlgorithm ) {
         this.readyList = readyList;
         this.filter = filter;
+        this.root = "";
         try {
             digest = MessageDigest.getInstance(digestAlgorithm);
         } catch ( NoSuchAlgorithmException ex ) {
@@ -67,6 +75,10 @@ public class IrodsHandler implements BulkFileHandler {
         }
     }
 
+    public void setRoot(String root) {
+        this.root = root;
+    }
+
     @Override
     public void openFile( String path, long length ) throws IOException {
         LOG.trace("Opening file for digesting: " + path);
@@ -130,7 +142,8 @@ public class IrodsHandler implements BulkFileHandler {
      * @return
      */
     private String[] extractPathList( String file ) {
-        String[] tmpPathList = file.split("/");
+        String completefile = root + file;
+        String[] tmpPathList = completefile.split("/");
 
         if ( tmpPathList.length == 1 ) {
             return tmpPathList;

ace-am/src/main/java/edu/umiacs/ace/driver/irods/IrodsIterator.java

@@ -60,11 +60,11 @@ public class IrodsIterator implements Iterator<FileBean> {
     private ConnectOperation co;
     private String root;
     private BulkFileSaver bfs;
-    private Queue<BulkFileSaver> saverList = new LinkedList<BulkFileSaver>();
+    private Queue<MonitoredItem> saverList = new LinkedList<MonitoredItem>();
 
-    public IrodsIterator( Collection c, IrodsSetting ic,
+    public IrodsIterator(Collection c, IrodsSetting ic,
             MonitoredItem[] startPathList, PathFilter filter,
-            String digestAlgorithm ) {
+            String digestAlgorithm) {
         this.co = new ConnectOperation(ic.getServer(), ic.getPort(),
                 ic.getUsername(), ic.getPassword(), ic.getZone());
         this.stateBean = new DriverStateBean();
@@ -75,31 +75,50 @@ public class IrodsIterator implements Iterator<FileBean> {
 
             handler = new IrodsHandler(readyList, filter, digestAlgorithm);
 
-            MyListener listener = new MyListener();
-            if ( startPathList != null ) {
-                String startPath;
 
-                for ( MonitoredItem mi : startPathList ) {
-                    startPath = root + mi.getPath();
-                    bfs = new BulkFileSaver(co, handler, startPath);
-                    bfs.addListener(listener);
-                    saverList.add(bfs);
+            if (startPathList != null) {
+//                String startPath;
+
+                for (MonitoredItem mi : startPathList) {
+                    saverList.offer(mi);
                 }
+                runNextItem();
+//                saverList.poll();
             } else {
+                MyListener listener = new MyListener();
                 bfs = new BulkFileSaver(co, handler, root);
                 bfs.addListener(listener);
-                saverList.add(bfs);
+//                saverList.add(bfs);
+                handler.setRoot("");
+                bfs.execute(true);
+
             }
 
-            saverList.poll().execute(true);
 
-        } catch ( IOException ioe ) {
+        } catch (IOException ioe) {
             LOG.error("Could not connect to irods", ioe);
             throw new RuntimeException("Could not connect to irods", ioe);
         }
     }
 
+    private void runNextItem() {
+        String startPath;
+        MonitoredItem mi = saverList.poll();
+        if (mi == null) {
+            bfs = null;
+            return;
+        }
+        MyListener listener = new MyListener();
+        startPath = root + mi.getPath();
+        handler.setRoot(mi.getPath());
+        bfs = new BulkFileSaver(co, handler, startPath);
+        bfs.addListener(listener);
+        bfs.execute(true);
+//                    saverList.add(bfs);
+    }
+
     public void cancel() {
+        saverList.clear();
         bfs.cancel();
     }
 
@@ -117,10 +136,10 @@ public class IrodsIterator implements Iterator<FileBean> {
         takingThread = Thread.currentThread();
         try {
             return readyList.take();
-        } catch ( InterruptedException ie ) {
+        } catch (InterruptedException ie) {
 
 
-            if ( readyList.isEmpty() ) {
+            if (readyList.isEmpty()) {
                 LOG.error("Interrupted Exception in next, return null");
                 return null;
             }
@@ -147,14 +166,14 @@ public class IrodsIterator implements Iterator<FileBean> {
         }
 
         @Override
-        public void startFile( String fullPath ) {
+        public void startFile(String fullPath) {
             bytes = 0;
             stateBean.setStateAndReset(State.READING);
             stateBean.setFile(fullPath);
         }
 
         @Override
-        public void bytesWritten( int bytesWritten ) {
+        public void bytesWritten(int bytesWritten) {
 
             bytes += bytesWritten;
             stateBean.setRead(bytes);
@@ -162,7 +181,7 @@ public class IrodsIterator implements Iterator<FileBean> {
         }
 
         @Override
-        public void endFile( String fullPath ) {
+        public void endFile(String fullPath) {
             stateBean.setStateAndReset(State.LISTING);
 
         }
@@ -171,22 +190,23 @@ public class IrodsIterator implements Iterator<FileBean> {
         public void endTransfer() {
             stateBean.setRunningThread(null);
             LOG.debug("endTransfer called on irods iterator");
-            if ( !saverList.isEmpty() ) {
-                saverList.poll().execute(true);
+            if (!saverList.isEmpty()) {
+                runNextItem();
+//                saverList.poll().execute(true);
                 return;
             } else {
                 handler = null;
-                if ( takingThread != null && readyList.isEmpty() ) {
+                if (takingThread != null && readyList.isEmpty()) {
                     takingThread.interrupt();
                 }
             }
         }
 
         @Override
-        public void handleException( Throwable t ) {
+        public void handleException(Throwable t) {
             cancel();
             handler = null;
-            if ( takingThread != null && readyList.isEmpty() ) {
+            if (takingThread != null && readyList.isEmpty()) {
                 takingThread.interrupt();
             }
             LOG.error("Error in bulk saver", t);

ace-am/src/main/java/edu/umiacs/ace/monitor/audit/AuditThread.java

@@ -486,12 +486,20 @@ public final class AuditThread extends Thread implements CancelCallback {
                 trans.commit();
             } else {
                 // OK, no registered item, do the registration
-                LogEvent event = addNewFile(currentFile, fileName,
+                LogEvent[] event = addNewFile(currentFile, fileName,
                         parentName, mim);
-                EntityTransaction trans = em.getTransaction();
-                trans.begin();
-                em.persist(event);
-                trans.commit();
+
+                // transaction inside loop to ensure order of commits
+                // default, jpa ignores order of persist calls
+                for (LogEvent le : event) {
+                    if (le != null) {
+                        EntityTransaction trans = em.getTransaction();
+                        trans.begin();
+                        em.persist(le);
+                        trans.commit();
+                    }
+                }
+
             }
         } finally {
             em.close();
@@ -587,25 +595,27 @@ public final class AuditThread extends Thread implements CancelCallback {
         return event;
     }
 
-    private LogEvent addNewFile(FileBean currentFile, String fileName,
+    private LogEvent[] addNewFile(FileBean currentFile, String fileName,
             final String parentName, final MonitoredItemManager mim) {
 
         newFilesFound++;
-        LogEvent event;
+        LogEvent[] event = new LogEvent[2];
+
         LOG.trace("Registering new item " + fileName);
+        event[0] = logManager.createItemEvent(LogEnum.FILE_NEW, fileName,
+                coll.getDirectory() + fileName);
         if (currentFile.isError()) {
             mim.addItem(fileName, parentName, false, coll, 'M', 0);
 //            lem.errorReading(fileName, coll,
 //                    currentFile.getErrorMessage());
-            event = logManager.createItemEvent(LogEnum.ERROR_READING, fileName,
+            event[1] = logManager.createItemEvent(LogEnum.ERROR_READING, fileName,
                     currentFile.getErrorMessage());
             totalErrors++;
         } else {
             // create new item with state of missing token
             mim.addItem(fileName, parentName, false, coll, 'T',
                     currentFile.getFileSize());
-            event = logManager.createItemEvent(LogEnum.FILE_NEW, fileName,
-                    coll.getDirectory() + fileName);
+            event[1] = null;
 //            lem.foundNewFile(fileName, coll);
             TokenRequest request = new TokenRequest();
             request.setName(fileName);

ace-am/src/main/webapp/META-INF/context.xml

@@ -50,7 +50,7 @@
   <Parameter name="log4j.rootLogger" value="FATAL, A1"/>
   <Parameter name="log4j.appender.A1.layout" value="org.apache.log4j.PatternLayout"/>
   <Parameter name="log4j.appender.A1.layout.ConversionPattern" value="%d{[dd/MMM/yyyy:HH:mm:ss]} %x%m%n"/>
-  <Parameter name="log4j.logger.edu.umiacs.irods" value="TRACE"/>
+  <Parameter name="log4j.logger.edu.umiacs.irods" value="INFO"/>
   <Parameter name="log4j.logger.edu.umiacs" value="TRACE"/>
   <!--<Parameter name="log4j.logger.edu.umiacs.irods.api.IRodsConnection" value="TRACE"/>-->
 </Context>

ace-am/src/main/webapp/footer.jsp

@@ -5,5 +5,5 @@
    "http://www.w3.org/TR/html4/loose.dtd">
 
 <div class="footer">
-    Version 1.6beta &copy; 2010, University of Maryland Institute for Advanced Computer Studies.  All Rights Reserved. <a href="http://adapt.umiacs.umd.edu/ace">ACE Website</a>
+    Version 1.6beta2 &copy; 2010, University of Maryland Institute for Advanced Computer Studies.  All Rights Reserved. <a href="http://adapt.umiacs.umd.edu/ace">ACE Website</a>
 </div>

ace-am/src/main/webapp/report.jsp

@@ -134,7 +134,7 @@ on Libraries node in Projects view can be used to add the JSTL 1.1 library.
                         </c:choose>
                     </td>
                     <td class="datecol"><span>${fn:replace(item.lastSeen, " ", "&nbsp;")}</span></td>
-                    <td><a href="EventLog?logpath=${item.path}">log</a> <a href="RemoveItem?itemid=${item.id}&amp;redirect=Report">remove</a> </td>
+                    <td><a href="EventLog?logpath=${item.path}">log</a> <a href="RemoveItem?itemid=${item.id}&amp;redirect=Report%3Fcollectionid=${collection.collection.id}">remove</a> </td>
                 </tr>
             </c:forEach>
             <tr><td colspan="5">

ace-common/pom.xml

@@ -9,7 +9,6 @@
   </parent>
   <groupId>edu.umiacs.ace</groupId>
   <artifactId>ace-common</artifactId>
-  <version>1.6-SNAPSHOT</version>
   <name>ace-common</name>
   <url>http://maven.apache.org</url>
     <properties>

ace-ims-api/pom.xml

@@ -6,10 +6,10 @@
     <artifactId>ace</artifactId>
     <groupId>edu.umiacs.ace</groupId>
     <version>1.6-SNAPSHOT</version>
+    <relativePath>../pom.xml</relativePath>
   </parent>
   <groupId>edu.umiacs.ace</groupId>
   <artifactId>ace-ims-api</artifactId>
-  <version>1.0-SNAPSHOT</version>
   <name>ace-ims-api</name>
   <url>http://maven.apache.org</url>
     <properties>
@@ -26,12 +26,12 @@
     <dependency>
       <groupId>edu.umiacs.ace</groupId>
       <artifactId>ace-ims-ws</artifactId>
-      <version>1.0-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
     <dependency>
       <groupId>edu.umiacs.ace</groupId>
       <artifactId>ace-common</artifactId>
-      <version>1.6-SNAPSHOT</version>
+      <version>${project.version}</version>
     </dependency>
 
     <dependency>

ace-ims-ws/pom.xml

@@ -9,7 +9,6 @@
   </parent>
   <groupId>edu.umiacs.ace</groupId>
   <artifactId>ace-ims-ws</artifactId>
-  <version>1.0-SNAPSHOT</version>
   <name>ace-ims-ws</name>
   <url>http://maven.apache.org</url>
   <build>