- removed the 'thirdparty' directory (now the 'gridworks' script will download and install needed tools if they are not present in the system already)

- added 'findbugs' command that uses the findbugs static analyzer to look for problems in the code
- fixed a bunch of issues that findbugs found (a few methods would go a little faster, and a few NPE will be avoided... nothing major but good to have)


git-svn-id: http://google-refine.googlecode.com/svn/trunk@382 7d457c2a-affb-35e4-300a-418c747d4874

build.xml

@@ -26,7 +26,6 @@
     <property name="graphics.dir" value="${basedir}/src/graphics" />
     <property name="conf.dir" value="${basedir}/src/conf" />
     <property name="lib.dir" value="${basedir}/lib" />
-    <property name="tools.dir" value="${basedir}/thirdparty" />
     <property name="tests.dir" value="${basedir}/tests" />
     
     <property name="server_classes.dir" value="${build.dir}/classes" />
@@ -100,7 +99,7 @@
         <taskdef 
             name="jarbundler" 
             classname="net.sourceforge.jarbundler.JarBundler" 
-            classpath="${tools.dir}/jarbundler-2.1.0.jar" 
+            classpath="${jarbundler.dir}/jarbundler-2.1.0.jar" 
         />
         
         <mkdir dir="${mac.dir}"/>
@@ -138,7 +137,7 @@
         <taskdef 
             name="launch4j" 
             classname="net.sf.launch4j.ant.Launch4jTask" 
-            classpath="${tools.dir}/launch4j/launch4j.jar:${tools.dir}/launch4j/lib/xstream.jar" 
+            classpath="${launch4j.dir}/launch4j.jar:${launch4j.dir}/lib/xstream.jar" 
         />
         <launch4j>
           <config 
@@ -224,8 +223,6 @@
         <copy file="${basedir}/README.txt" tofile="${linux.dir}/README.txt"/>
         <copy file="${basedir}/gridworks" tofile="${linux.dir}/gridworks"/>
         
-        <echo file="${linux.dir}/.revision" append="false">${revision}</echo>
-        
         <tar longfile="gnu" compression="gzip" destfile="${dist.dir}/gridworks-${version}-${revision}.tar.gz">
            <tarfileset dir="${linux.dir}/.." filemode="755">
                <include name="${linux.name}/gridworks"/>
@@ -237,6 +234,19 @@
         </tar>
     </target>
 
+    <target name="findbugs" depends="build">
+        <taskdef 
+            name="findbugs" 
+            classname="edu.umd.cs.findbugs.anttask.FindBugsTask"
+            classpath="${findbugs.dir}/lib/findbugs-ant.jar" 
+        />
+        <findbugs jvmargs="-Xmx1024m" home="${findbugs.dir}" output="html" outputFile="${build.dir}/gridworks-findbugs.html" >
+          <auxClasspath refid="class.path" />
+          <sourcePath path="${src.dir}" />
+          <class location="${webapp_classes.dir}" />
+        </findbugs>        
+    </target>
+
     <target name="clean">
         <delete file="${build.dir}/gridworks.jar" />
         <delete dir="${server_classes.dir}" />

gridworks

@@ -4,7 +4,7 @@
 #               Gridworks Control System                 #
 ##########################################################
 
-# -------------- functions ------------------------------------
+# -------------- utility functions ----------------------
 
 fail () {
    cat <<EOF
@@ -50,7 +50,8 @@ and <action> is one of
    build ..................... Build Gridworks      
    run ....................... Run Gridworks
 
-   test ...................... Test Gridworks      
+   test ...................... Test Gridworks 
+   findbugs .................. Run Findbugs against Gridworks     
    
    mac_dist <version> ........ Make MacOSX binary distribution
    windows_dist <version> .... Make Windows binary distribution
@@ -66,7 +67,7 @@ EOF
 }
                 
 add_option() {
-  OPTS="$OPTS $1"
+    OPTS="$OPTS $1"
 }
                 
 load_configs() {
@@ -80,45 +81,6 @@ check_macosx() {
         error "This action can only run on MacOSX"
     fi
 }
-    
-ant_prepare() {
-    if [ ! -d $GRIDWORKS_BUILD_DIR ] ; then 
-        mkdir $GRIDWORKS_BUILD_DIR || exit 1
-    fi
-    
-    ANT=`which ant`
-    if [ "$ANT" = "" ] ; then
-        cd thirdparty
-        ANT_TAR=`ls | grep apache-ant | grep tar.gz | grep -v svn`
-        ANT_DIR=`echo $ANT_TAR | sed 's/.tar.gz//'`
-        if [ ! -d $ANT_DIR ] ; then
-            tar xzf $ANT_TAR -C . || exit 1
-        fi
-        ANT="`pwd`/$ANT_DIR/bin/ant"
-        cd ..
-    fi
-}
-
-ant() {
-    ant_prepare   
-    $ANT -f build.xml -Dbuild.dir="$GRIDWORKS_BUILD_DIR" -Ddist.dir="$GRIDWORKS_DIST_DIR" -Dversion="$VERSION" -Dnum_version="$NUM_VERSION" -Drevision="$REVISION" $1 || exit 1
-}
-
-dist_prepare() {
-    if [ ! -d $GRIDWORKS_DIST_DIR ] ; then 
-        mkdir $GRIDWORKS_DIST_DIR || exit 1
-    fi
-}
-       
-launch4j_prepare() {
-    cd thirdparty
-    LAUNCH4J_TAR=`ls | grep launch4j | grep tar.gz | grep -v svn`
-    LAUNCH4J_DIR="launch4j"
-    if [ ! -d "$LAUNCH4J_DIR" ] ; then
-        tar xzf $LAUNCH4J_TAR || exit 1
-    fi
-    cd ..
-}
 
 get_version() {
     VERSION=$1        
@@ -135,8 +97,6 @@ get_revision() {
         INFO=`svn info`
     elif [ -d ".git" ]; then
         INFO=`git svn info`
-    elif [ -f ".revision" ]; then
-        REVISION=`cat .revision`
     else
         error "cannot obtain revision, exiting!"
     fi
@@ -144,6 +104,124 @@ get_revision() {
     REVISION=`echo $INFO | sed 's/.*Revision: /r/' | sed 's/ .*//'`
 }
 
+get_url_file() {
+    return `echo $1 | sed 's|.*/||'`
+}
+    
+download() {
+    URL=$1
+    DEST=$2
+    
+    if [ `which curl` == "" ] && [ `which wget` == "" ]; then
+        error "We need either 'curl' or 'wget' present in PATH to download external dependencies."
+    fi
+    
+    if [ `which curl` != "" ] ; then
+        curl -o $DEST $URL || exit 1
+    fi
+    
+    if [ `which wget` != "" ] ; then
+        wget -O $DEST $URL || exit 1
+    fi
+}
+
+# ----------------------------------------------------------------------------------------------
+
+build_prepare() {
+    if [ ! -d $GRIDWORKS_BUILD_DIR ] ; then 
+        mkdir $GRIDWORKS_BUILD_DIR || exit 1
+    fi
+}
+
+dist_prepare() {
+    if [ ! -d $GRIDWORKS_DIST_DIR ] ; then 
+        mkdir $GRIDWORKS_DIST_DIR || exit 1
+    fi
+}
+
+tools_prepare() {
+    if [ ! -d $GRIDWORKS_TOOLS_DIR ] ; then 
+        mkdir $GRIDWORKS_TOOLS_DIR || exit 1
+    fi
+}
+            
+ant_prepare() {
+    ANT_URL="http://www.apache.org/dist/ant/binaries/apache-ant-1.8.0-bin.tar.gz"
+    ANT_FILE=`echo $ANT_URL | sed 's|.*/||'`
+    ANT_DIR="apache-ant-1.8.0"
+    
+    ANT=`which ant`
+    if [ $ANT == "" ] ; then
+        if [ $ANT_HOME == "" ] ; then
+            cd $GRIDWORKS_TOOLS_DIR
+            if [ ! -f $ANT_FILE ] ; then
+                download $ANT_URL $ANT_FILE
+            fi
+            if [ ! -d $ANT_DIR ] ; then
+                tar xzf $ANT_FILE -C . || exit 1
+            fi
+            export ANT_HOME="`pwd`/$ANT_DIR"
+            cd ..
+        fi
+        ANT="$ANT_HOME/bin/ant"
+    fi
+}
+
+launch4j_prepare() {
+    LAUNCH4J_URL="http://downloads.sourceforge.net/project/launch4j/launch4j-3/3.0.1/launch4j-3.0.1-macosx.tgz"
+    LAUNCH4J_FILE=`echo $LAUNCH4J_URL | sed 's|.*/||'`
+    LAUNCH4J_DIR="launch4j"
+    
+    cd $GRIDWORKS_TOOLS_DIR
+    if [ ! -f "$LAUNCH4J_FILE" ] ; then
+        download $LAUNCH4J_URL $LAUNCH4J_FILE
+    fi
+    if [ ! -d "$LAUNCH4J_DIR" ] ; then
+        tar xzf $LAUNCH4J_FILE || exit 1
+    fi
+    cd ..
+}
+    
+jarbundler_prepare() {
+    JARBUNDLER_URL="http://www.informagen.com/JarBundler/dist/jarbundler.tar.gz"
+    JARBUNDLER_FILE=`echo $JARBUNDLER_URL | sed 's|.*/||'`
+    JARBUNDLER_DIR="jarbundler-2.1.0"
+
+    cd $GRIDWORKS_TOOLS_DIR
+    if [ ! -f "$JARBUNDLER_FILE" ] ; then
+        download $JARBUNDLER_URL $JARBUNDLER_FILE
+    fi
+    if [ ! -d "$JARBUNDLER_DIR" ] ; then
+        tar xzf $JARBUNDLER_FILE || exit 1
+    fi
+    cd ..
+}
+   
+findbugs_prepare() {
+    FINDBUGS_URL="http://downloads.sourceforge.net/project/findbugs/findbugs/1.3.9/findbugs-1.3.9.tar.gz"
+    FINDBUGS_FILE=`echo $FINDBUGS_URL | sed 's|.*/||'`
+    FINDBUGS_DIR="findbugs-1.3.9"
+
+    cd $GRIDWORKS_TOOLS_DIR
+    if [ ! -f "$FINDBUGS_FILE" ] ; then
+        download $FINDBUGS_URL $FINDBUGS_FILE
+    fi
+    if [ ! -d "$FINDBUGS_DIR" ] ; then
+        tar xzf $FINDBUGS_FILE || exit 1
+    fi
+    cd ..
+}
+   
+# ----------------------------------------------------------------------------------------------
+
+ant() {
+    ant_prepare   
+    #export ANT_OPTS="-Xmx1024M"
+    $ANT -f build.xml $ANT_PARAMS -Dbuild.dir="$GRIDWORKS_BUILD_DIR" -Ddist.dir="$GRIDWORKS_DIST_DIR" -Dversion="$VERSION" -Dnum_version="$NUM_VERSION" -Drevision="$REVISION" $1 || exit 1
+}
+
+# ----------------------------------------------------------------------------------------------
+
 dist() {
     mac_dist $1
     windows_dist $1
@@ -172,6 +250,7 @@ windows_dist() {
     get_version $1
     get_revision
     
+    ANT_PARAMS="-Dlaunch4j.dir=${GRIDWORKS_TOOLS_DIR}/${LAUNCH4J_DIR}"
     ant windows
 }
 
@@ -186,9 +265,11 @@ linux_dist() {
 mac_dist() {
     check_macosx
     dist_prepare
+    jarbundler_prepare
     get_version $1
     get_revision
     
+    ANT_PARAMS="-Djarbundler.dir=${GRIDWORKS_TOOLS_DIR}/${JARBUNDLER_DIR}"
     ant mac
 
     mkdir -p "$GRIDWORKS_BUILD_DIR/mac/.background"
@@ -276,11 +357,7 @@ run() {
     if [ "$GRIDWORKS_DATA_DIR" != "" ] ; then
         add_option "-Dgridworks.data_dir=$GRIDWORKS_DATA_DIR"
     fi
-    
+        
-    get_revision
-    
-    add_option "-Dgridworks.version=$REVISION"
-    
     CLASSPATH="$GRIDWORKS_BUILD_DIR/classes:$GRIDWORKS_LIB_DIR/*"
 
     RUN_CMD="$JAVA -cp $CLASSPATH $OPTS com.metaweb.gridworks.Gridworks"
@@ -309,6 +386,13 @@ execute() {
     exec $RUN_CMD $*
 }
     
+findbugs() {
+    findbugs_prepare
+    
+    ANT_PARAMS="-Dfindbugs.dir=${GRIDWORKS_TOOLS_DIR}/${FINDBUGS_DIR}"
+    ant findbugs
+}    
+
 # -------------------------- script -----------------------------
     
 # ----- Normalize the current directory -------------------------
@@ -336,7 +420,7 @@ if [ ! -z "$JAVA_HOME" ] ; then
 else 
     JAVA=`which java`
     if [ -z "$JAVA" ] ; then
-        if [ "$SYSTEM" = 'Darwin' ] ; then
+        if [ "$SYSTEM" == 'Darwin' ] ; then
             JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Home
         else
             error "The 'java' command should be in your path or the 'JAVA_HOME' environment variable should be set"
@@ -411,6 +495,10 @@ if [ "$GRIDWORKS_LIB_DIR" == "" ] ; then
     GRIDWORKS_LIB_DIR="lib"
 fi
 
+if [ "$GRIDWORKS_TOOLS_DIR" == "" ] ; then
+    GRIDWORKS_TOOLS_DIR="tools"
+fi
+
 if [ "$GRIDWORKS_DIST_DIR" == "" ] ; then
     GRIDWORKS_DIST_DIR="dist"
 fi
@@ -418,38 +506,16 @@ fi
 # ----- Respond to the action given --------------------------------------------
 
 case "$ACTION" in
-
+  build) build_prepare; ant build;;
-  build)
+  clean) ant clean;;
-    ant build;;
+  distclean) ant distclean;;
-
+  test) test $1;;  
-  clean)
+  findbugs) findbugs;;  
-    ant clean;;
+  run) run;;  
-
+  execute) execute $*;;  
-  distclean)
+  mac_dist) mac_dist $1;;
-    ant distclean;;
+  windows_dist) windows_dist $1;;
-
+  linux_dist) linux_dist $1;;
-  test) 
+  dist) dist $1;;
-    test $1;;  
+  *) usage; ;;
-
-  run) 
-    run;;  
-
-  execute) 
-    execute $*;;  
-    
-  mac_dist)
-    mac_dist $1;;
-
-  windows_dist)
-    windows_dist $1;;
-    
-  linux_dist)
-    linux_dist $1;;
-    
-  dist)
-    dist $1;;
-      
-  *)
-    usage; ;;
-    
 esac

src/main/java/com/metaweb/gridworks/GridworksServlet.java

@@ -59,7 +59,7 @@ public class GridworksServlet extends HttpServlet {
     
     private static final long serialVersionUID = 2386057901503517403L;
     
-    static protected Map<String, Command> _commands = new HashMap<String, Command>();
+    static final protected Map<String, Command> _commands = new HashMap<String, Command>();
     
     // timer for periodically saving projects
     static protected Timer _timer;

src/main/java/com/metaweb/gridworks/ProjectManager.java

@@ -43,7 +43,7 @@ public class ProjectManager {
     
     static public ProjectManager singleton;
     
-    static public void initialize() {
+    static public synchronized void initialize() {
         if (singleton == null) {
             File dir = getProjectLocation();
             Gridworks.log("Using workspace directory: " + dir.getAbsolutePath());
@@ -325,8 +325,6 @@ public class ProjectManager {
         List<SaveRecord> records = new ArrayList<SaveRecord>();
         Date now = new Date();
         
-        boolean gc = false;
-        
         synchronized (this) {
             for (long id : _projectsMetadata.keySet()) {
                 ProjectMetadata metadata = _projectsMetadata.get(id);
@@ -347,8 +345,6 @@ public class ProjectManager {
                          *  modified. We can safely remove it from the cache to save some memory.
                          */
                         _projects.remove(id);
-                        
-                        gc = true;
                     }
                 }
             }
@@ -384,10 +380,6 @@ public class ProjectManager {
                 }
             }
         }
-        
-        if (gc) {
-            System.gc();
-        }
     }
     
     public void deleteProject(Project project) {

src/main/java/com/metaweb/gridworks/browsing/facets/NumericBinIndex.java

@@ -87,10 +87,10 @@ public class NumericBinIndex {
         _min = (Math.floor(_min / _step) * _step);
         _max = (Math.ceil(_max / _step) * _step);
         
-        int binCount = (int) ((_max - _min) / _step);
+        double binCount = (_max - _min) / _step;
         if (binCount > 100) {
             _step *= 2;
-            binCount = Math.round((1 + binCount) / 2);
+            binCount = (binCount + 1) / 2;
         }
         
         if (_max <= originalMax) {
@@ -98,7 +98,7 @@ public class NumericBinIndex {
         	binCount++;
         }
         
-        _bins = new int[binCount];
+        _bins = new int[(int) Math.round(binCount)];
         for (double d : allValues) {
             int bin = (int) Math.floor((d - _min) / _step);
             _bins[bin]++;

src/main/java/com/metaweb/gridworks/clustering/binning/BinningClusterer.java

@@ -1,5 +1,6 @@
 package com.metaweb.gridworks.clustering.binning;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
@@ -27,7 +28,7 @@ public class BinningClusterer extends Clusterer {
 
     private Keyer _keyer;
     
-    static protected Map<String, Keyer> _keyers = new HashMap<String, Keyer>();
+    static final protected Map<String, Keyer> _keyers = new HashMap<String, Keyer>();
 
     List<Map<String,Integer>> _clusters;
      
@@ -65,19 +66,19 @@ public class BinningClusterer extends Clusterer {
         public boolean visit(Project project, int rowIndex, Row row, boolean includeContextual, boolean includeDependent) {
             Cell cell = row.getCell(_colindex);
             if (cell != null && cell.value != null) {
-                String v = cell.value.toString();
+                Object v = cell.value;
                 String s = (v instanceof String) ? ((String) v) : v.toString();
                 String key = _keyer.key(s,_params);
                 if (_map.containsKey(key)) {
                     Map<String,Integer> m = _map.get(key);
-                    if (m.containsKey(v)) {
+                    if (m.containsKey(s)) {
-                        m.put(v, m.get(v) + 1);
+                        m.put(s, m.get(s) + 1);
                     } else {
-                        m.put(v,1);
+                        m.put(s,1);
                     }
                 } else {
                     Map<String,Integer> m = new TreeMap<String,Integer>();
-                    m.put(v,1);
+                    m.put(s,1);
                     _map.put(key, m);
                 }
             }
@@ -89,7 +90,8 @@ public class BinningClusterer extends Clusterer {
         }
     }
             
-    public class SizeComparator implements Comparator<Map<String,Integer>> {
+    public static class SizeComparator implements Comparator<Map<String,Integer>>, Serializable {
+        private static final long serialVersionUID = -1390696157208674054L;
         public int compare(Map<String,Integer> o1, Map<String,Integer> o2) {
             int s1 = o1.size();
             int s2 = o2.size();
@@ -109,7 +111,8 @@ public class BinningClusterer extends Clusterer {
         }
     }
 
-    public class EntriesComparator implements Comparator<Entry<String,Integer>> {
+    public static class EntriesComparator implements Comparator<Entry<String,Integer>>, Serializable {
+        private static final long serialVersionUID = 2763378036791777964L;
         public int compare(Entry<String,Integer> o1, Entry<String,Integer> o2) {
             return o2.getValue() - o1.getValue();
         }

src/main/java/com/metaweb/gridworks/clustering/knn/kNNClusterer.java

@@ -41,7 +41,7 @@ public class kNNClusterer extends Clusterer {
 
     private Distance _distance;
     
-    static protected Map<String, Distance> _distances = new HashMap<String, Distance>();
+    static final protected Map<String, Distance> _distances = new HashMap<String, Distance>();
 
     List<Set<Serializable>> _clusters;
 
@@ -148,7 +148,8 @@ public class kNNClusterer extends Clusterer {
         _clusters = visitor.getClusters();
     }
 
-    public class ValuesComparator implements Comparator<Entry<Serializable,Integer>> {
+    public static class ValuesComparator implements Comparator<Entry<Serializable,Integer>>, Serializable {
+        private static final long serialVersionUID = 204469656070583155L;
         public int compare(Entry<Serializable,Integer> o1, Entry<Serializable,Integer> o2) {
             return o2.getValue() - o1.getValue();
         }

src/main/java/com/metaweb/gridworks/commands/edit/AnnotateOneRowCommand.java

@@ -46,7 +46,7 @@ public class AnnotateOneRowCommand extends Command {
         }
     }
     
-    protected class StarOneRowProcess extends QuickHistoryEntryProcess {
+    protected static class StarOneRowProcess extends QuickHistoryEntryProcess {
         final int rowIndex;
         final boolean starred;
         

src/main/java/com/metaweb/gridworks/commands/edit/CreateProjectCommand.java

@@ -9,6 +9,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.Reader;
+import java.io.Serializable;
 import java.io.StringReader;
 import java.io.UnsupportedEncodingException;
 import java.net.URL;
@@ -145,7 +146,7 @@ public class CreateProjectCommand extends Command {
         }
     }
         
-    class SafeInputStream extends FilterInputStream {
+    static class SafeInputStream extends FilterInputStream {
         public SafeInputStream(InputStream stream) {
             super(stream);
         }
@@ -191,24 +192,29 @@ public class CreateProjectCommand extends Command {
             // behave precisely the same, there is no polymorphic behavior so we have
             // to treat each instance explicitly... one of those times you wish you had
             // closures
-            if (is instanceof TarInputStream) {
+            try {
-                TarInputStream tis = (TarInputStream) is;
+                if (is instanceof TarInputStream) {
-                TarEntry te;
+                    TarInputStream tis = (TarInputStream) is;
-                while ((te = tis.getNextEntry()) != null) {
+                    TarEntry te;
-                    if (!te.isDirectory()) {
+                    while ((te = tis.getNextEntry()) != null) {
-                        mapExtension(te.getName(),ext_map);
+                        if (!te.isDirectory()) {
-                    }
+                            mapExtension(te.getName(),ext_map);
-                }
+                        }
-            } else if (is instanceof ZipInputStream) {
+                    }
-                ZipInputStream zis = (ZipInputStream) is;
+                } else if (is instanceof ZipInputStream) {
-                ZipEntry ze;
+                    ZipInputStream zis = (ZipInputStream) is;
-                while ((ze = zis.getNextEntry()) != null) {
+                    ZipEntry ze;
-                    if (!ze.isDirectory()) {
+                    while ((ze = zis.getNextEntry()) != null) {
-                        mapExtension(ze.getName(),ext_map);
+                        if (!ze.isDirectory()) {
+                            mapExtension(ze.getName(),ext_map);
+                        }
                     }
                 }
+            } finally {
+                try {
+                    is.close();
+                } catch (IOException e) {}
             }
-            is.close();
 
             // sort extensions by how often they appear
             List<Entry<String,Integer>> values = new ArrayList<Entry<String,Integer>>(ext_map.entrySet());
@@ -239,32 +245,37 @@ public class CreateProjectCommand extends Command {
             // second pass, load the data for real
             is = getStream(fileName, new FileInputStream(file));
             SafeInputStream sis = new SafeInputStream(is);
-            if (is instanceof TarInputStream) {
+            try {
-                TarInputStream tis = (TarInputStream) is;
+                if (is instanceof TarInputStream) {
-                TarEntry te;
+                    TarInputStream tis = (TarInputStream) is;
-                while ((te = tis.getNextEntry()) != null) {
+                    TarEntry te;
-                    if (!te.isDirectory()) {
+                    while ((te = tis.getNextEntry()) != null) {
-                        String name = te.getName();
+                        if (!te.isDirectory()) {
-                        String ext = getExtension(name)[1];
+                            String name = te.getName();
-                        if (exts.contains(ext)) {
+                            String ext = getExtension(name)[1];
-                            internalImportFile(project, options, name, sis);
+                            if (exts.contains(ext)) {
-                        }
+                                internalImportFile(project, options, name, sis);
-                    }
+                            }
-                }
+                        }
-            } else if (is instanceof ZipInputStream) {
+                    }
-                ZipInputStream zis = (ZipInputStream) is;
+                } else if (is instanceof ZipInputStream) {
-                ZipEntry ze;
+                    ZipInputStream zis = (ZipInputStream) is;
-                while ((ze = zis.getNextEntry()) != null) {
+                    ZipEntry ze;
-                    if (!ze.isDirectory()) {
+                    while ((ze = zis.getNextEntry()) != null) {
-                        String name = ze.getName();
+                        if (!ze.isDirectory()) {
-                        String ext = getExtension(name)[1];
+                            String name = ze.getName();
-                        if (exts.contains(ext)) {
+                            String ext = getExtension(name)[1];
-                            internalImportFile(project, options, name, sis);
+                            if (exts.contains(ext)) {
+                                internalImportFile(project, options, name, sis);
+                            }
                         }
                     }
                 }
+            } finally {
+                try {
+                    sis.reallyClose();
+                } catch (IOException e) {}
             }
-            sis.reallyClose();
 
         } else if (fileName.endsWith(".gz")) {
             internalImportFile(project, options, getExtension(fileName)[0], new GZIPInputStream(inputStream));
@@ -275,7 +286,9 @@ public class CreateProjectCommand extends Command {
         }
     }
 
-    public class ValuesComparator implements Comparator<Entry<String,Integer>> {
+    public static class ValuesComparator implements Comparator<Entry<String,Integer>>, Serializable {
+        private static final long serialVersionUID = 8845863616149837657L;
+
         public int compare(Entry<String,Integer> o1, Entry<String,Integer> o2) {
             return o2.getValue() - o1.getValue();
         }
@@ -308,10 +321,8 @@ public class CreateProjectCommand extends Command {
             return new TarInputStream(new GZIPInputStream(is));
         } else if (fileName.endsWith(".tar.bz2")) {
             return new TarInputStream(new CBZip2InputStream(is));
-        } else if (fileName.endsWith(".zip")) {
-            return new ZipInputStream(is);
         } else {
-            return null;
+            return new ZipInputStream(is);
         }
     }
     
@@ -328,12 +339,19 @@ public class CreateProjectCommand extends Command {
         byte[] buffer = new byte[4 * 1024];
         long count = 0;
         int n = 0;
-        while (-1 != (n = input.read(buffer))) {
+        try {
-            output.write(buffer, 0, n);
+            while (-1 != (n = input.read(buffer))) {
-            count += n;
+                output.write(buffer, 0, n);
+                count += n;
+            }
+        } finally {
+            try {
+                output.close();
+            } catch (IOException e) {}
+            try {
+                input.close();
+            } catch (IOException e) {}
         }
-        output.close();
-        input.close();
         return count;
     }
     

src/main/java/com/metaweb/gridworks/commands/edit/EditOneCellCommand.java

@@ -75,7 +75,7 @@ public class EditOneCellCommand extends Command {
         }
     }
     
-    protected class EditOneCellProcess extends QuickHistoryEntryProcess {
+    protected static class EditOneCellProcess extends QuickHistoryEntryProcess {
         final int rowIndex;
         final int cellIndex;
         final Serializable value;

src/main/java/com/metaweb/gridworks/commands/info/ExportRowsCommand.java

@@ -20,7 +20,9 @@ import com.metaweb.gridworks.exporters.XlsExporter;
 import com.metaweb.gridworks.model.Project;
 
 public class ExportRowsCommand extends Command {
-    static protected Map<String, Exporter> s_formatToExporter = new HashMap<String, Exporter>();
+    
+    static final protected Map<String, Exporter> s_formatToExporter = new HashMap<String, Exporter>();
+    
     static {
         s_formatToExporter.put("tripleloader", new TripleloaderExporter());
         s_formatToExporter.put("html", new HtmlTableExporter());

src/main/java/com/metaweb/gridworks/commands/info/GetAllProjectMetadataCommand.java

@@ -3,6 +3,7 @@ package com.metaweb.gridworks.commands.info;
 import java.io.IOException;
 import java.util.Map;
 import java.util.Properties;
+import java.util.Map.Entry;
 
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
@@ -32,9 +33,9 @@ public class GetAllProjectMetadataCommand extends Command {
             writer.key("projects");
                 writer.object();
                 Map<Long, ProjectMetadata> m = ProjectManager.singleton.getAllProjectMetadata();
-                for (Long id : m.keySet()) {
+                for (Entry<Long,ProjectMetadata> e : m.entrySet()) {
-                    writer.key(id.toString());
+                    writer.key(e.getKey().toString());
-                    m.get(id).write(writer, options);
+                    e.getValue().write(writer, options);
                 }
                 writer.endObject();
                 

src/main/java/com/metaweb/gridworks/commands/recon/ReconJudgeOneCellCommand.java

@@ -81,14 +81,14 @@ public class ReconJudgeOneCellCommand extends Command {
         }
     }
     
-    protected class JudgeOneCellProcess extends QuickHistoryEntryProcess {
+    protected static class JudgeOneCellProcess extends QuickHistoryEntryProcess {
+
         final int rowIndex;
         final int cellIndex;
         final Judgment judgment;
         final ReconCandidate match;
         Cell newCell;
         
-        
         JudgeOneCellProcess(
             Project project, 
             String briefDescription, 

src/main/java/com/metaweb/gridworks/expr/functions/Get.java

@@ -16,7 +16,7 @@ public class Get implements Function {
         if (args.length > 1 && args.length <= 3) {
             Object v = args[0];
             Object from = args[1];
-            Object to = args.length == 3 ? args[2] : null;
+            Object to = (args.length == 3) ? args[2] : null;
             
             if (v != null && from != null) {
                 if (v instanceof HasFields) {
@@ -42,8 +42,7 @@ public class Get implements Function {
                                         ((Object[]) v)[start] :
                                         ExpressionUtils.toObjectList(v).get(start));
                             } else {
-                                int end = to != null && to instanceof Number ? 
+                                int end = (to != null && to instanceof Number) ? ((Number) to).intValue() : length;
-                                        ((Number) to).intValue() : length;
                                             
                                 if (end < 0) {
                                     end = length + end;
@@ -63,7 +62,7 @@ public class Get implements Function {
                                 }
                             }
                         } else {
-                            String s = (v instanceof String ? (String) v : v.toString());
+                            String s = (v instanceof String) ? (String) v : v.toString();
                             
                             int start = ((Number) from).intValue();
                             if (start < 0) {

src/main/java/com/metaweb/gridworks/expr/functions/Slice.java

@@ -15,7 +15,7 @@ public class Slice implements Function {
         if (args.length > 1 && args.length <= 3) {
             Object v = args[0];
             Object from = args[1];
-            Object to = args.length == 3 ? args[2] : null;
+            Object to = (args.length == 3) ? args[2] : null;
             
             if (v != null && from != null && from instanceof Number && (to == null || to instanceof Number)) {
                 if (v.getClass().isArray() || v instanceof List<?>) {
@@ -24,8 +24,7 @@ public class Slice implements Function {
                             ExpressionUtils.toObjectList(v).size();
                     
                     int start = ((Number) from).intValue();
-                    int end = to != null && to instanceof Number ? 
+                    int end = (to != null && to instanceof Number) ? ((Number) to).intValue() : length;
-                            ((Number) to).intValue() : length;
                                 
                     if (start < 0) {
                         start = length + start;
@@ -47,7 +46,7 @@ public class Slice implements Function {
                         return ExpressionUtils.toObjectList(v).subList(start, end);
                     }
                 } else {
-                    String s = (v instanceof String ? (String) v : v.toString());
+                    String s = (v instanceof String) ? (String) v : v.toString();
                     
                     int start = ((Number) from).intValue();
                     if (start < 0) {

src/main/java/com/metaweb/gridworks/history/ChangeSequence.java

@@ -44,6 +44,7 @@ public class ChangeSequence implements Change {
     
     static public Change load(LineNumberReader reader) throws Exception {
         String line = reader.readLine();
+        if (line == null) line = "";
         int equal = line.indexOf('=');
         
         assert "count".equals(line.substring(0, equal));

src/main/java/com/metaweb/gridworks/model/Project.java

@@ -196,10 +196,12 @@ public class Project {
                 int count = Integer.parseInt(value);
                 
                 for (int i = 0; i < count; i++) {
-                	Row row = Row.load(reader.readLine());
+                    line = reader.readLine();
-                    project.rows.add(row);
+                    if (line != null) {
-                    
+                    	Row row = Row.load(line);
-                    maxCellCount = Math.max(maxCellCount, row.cells.size());
+                        project.rows.add(row);
+                        maxCellCount = Math.max(maxCellCount, row.cells.size());
+                    }
                 }
             }
         }

src/main/java/com/metaweb/gridworks/model/Recon.java

@@ -15,6 +15,7 @@ import com.metaweb.gridworks.Jsonizable;
 import com.metaweb.gridworks.expr.HasFields;
  
 public class Recon implements HasFields, Jsonizable {
+    
     static public enum Judgment {
         None,
         Matched,
@@ -41,16 +42,14 @@ public class Recon implements HasFields, Jsonizable {
         }
     }
     
-    
+    static final public int Feature_typeMatch = 0;
-    static public int Feature_typeMatch = 0;
+    static final public int Feature_nameMatch = 1;
-    static public int Feature_nameMatch = 1;
+    static final public int Feature_nameLevenshtein = 2;
-    static public int Feature_nameLevenshtein = 2;
+    static final public int Feature_nameWordDistance = 3;
-    static public int Feature_nameWordDistance = 3;
+    static final public int Feature_max = 4;
-    static public int Feature_max = 4;
 
-    static protected Map<String, Integer> s_featureMap;
+    static final protected Map<String, Integer> s_featureMap = new HashMap<String, Integer>();
     static {
-        s_featureMap = new HashMap<String, Integer>();
         s_featureMap.put("typeMatch", Feature_typeMatch);
         s_featureMap.put("nameMatch", Feature_nameMatch);
         s_featureMap.put("nameLevenshtein", Feature_nameLevenshtein);

src/main/java/com/metaweb/gridworks/model/Row.java

@@ -4,6 +4,7 @@ import java.io.Writer;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Properties;
+import java.util.Map.Entry;
 
 import org.json.JSONArray;
 import org.json.JSONException;
@@ -134,9 +135,9 @@ public class Row implements HasFields, Jsonizable {
             if (options.containsKey("extra")) {
                 Properties extra = (Properties) options.get("extra");
                 if (extra != null) {
-                    for (Object key : extra.keySet()) {
+                    for (Entry<Object,Object> e : extra.entrySet()) {
-                        writer.key((String) key);
+                        writer.key((String) e.getKey());
-                        writer.value(extra.get(key));
+                        writer.value(e.getValue());
                     }
                 }
             }
@@ -194,7 +195,7 @@ public class Row implements HasFields, Jsonizable {
         
     }
     
-    protected class Record implements HasFields {
+    protected static class Record implements HasFields {
     	final int _recordRowIndex;
     	final int _currentRowIndex;
     	
@@ -211,7 +212,7 @@ public class Row implements HasFields, Jsonizable {
 		}
     }
     
-    protected class RecordCells implements HasFields {
+    protected static class RecordCells implements HasFields {
     	final int _recordRowIndex;
     	
     	protected RecordCells(int recordRowIndex) {
@@ -247,8 +248,9 @@ public class Row implements HasFields, Jsonizable {
 		}
     }
     
-    protected class CellTuple extends ArrayList<Cell> implements HasFields {
+    protected static class CellTuple extends ArrayList<Cell> implements HasFields {
-		private static final long serialVersionUID = -651032866647686293L;
+
+        private static final long serialVersionUID = -651032866647686293L;
 
 		public Object getField(String name, Properties bindings) {
 			Object[] r = new Object[this.size()];

src/main/java/com/metaweb/gridworks/model/changes/ColumnAdditionChange.java

@@ -94,7 +94,10 @@ public class ColumnAdditionChange extends ColumnChange {
                 
                 newCells = new ArrayList<CellAtRow>(newCellCount);
                 for (int i = 0; i < newCellCount; i++) {
-                    newCells.add(CellAtRow.load(line = reader.readLine()));
+                    line = reader.readLine();
+                    if (line != null) {
+                        newCells.add(CellAtRow.load(line));
+                    }
                 }
             }
         }

src/main/java/com/metaweb/gridworks/model/changes/ColumnRemovalChange.java

@@ -87,7 +87,10 @@ public class ColumnRemovalChange extends ColumnChange {
                 
                 oldCells = new CellAtRow[oldCellCount];
                 for (int i = 0; i < oldCellCount; i++) {
-                    oldCells[i] = CellAtRow.load(line = reader.readLine());
+                    line = reader.readLine();
+                    if (line != null) {
+                        oldCells[i] = CellAtRow.load(line);
+                    }
                 }
             }
         }

src/main/java/com/metaweb/gridworks/model/changes/DataExtensionChange.java

@@ -302,7 +302,9 @@ public class DataExtensionChange implements Change {
                 rowIndices = new ArrayList<Integer>(count);
                 for (int i = 0; i < count; i++) {
                     line = reader.readLine();
-                    rowIndices.add(Integer.parseInt(line));
+                    if (line != null) {
+                        rowIndices.add(Integer.parseInt(line));
+                    }
                 }
             } else if ("columnNameCount".equals(field)) {
                 int count = Integer.parseInt(value);
@@ -310,7 +312,9 @@ public class DataExtensionChange implements Change {
                 columnNames = new ArrayList<String>(count);
                 for (int i = 0; i < count; i++) {
                     line = reader.readLine();
-                    columnNames.add(line);
+                    if (line != null) {
+                        columnNames.add(line);
+                    }
                 }
             } else if ("columnTypeCount".equals(field)) {
                 int count = Integer.parseInt(value);
@@ -327,6 +331,8 @@ public class DataExtensionChange implements Change {
                 for (int i = 0; i < count; i++) {
                     line = reader.readLine();
                     
+                    if (line == null) continue;
+                    
                     int rowCount = Integer.parseInt(line);
                     Object[][] data = new Object[rowCount][];
                     
@@ -358,7 +364,9 @@ public class DataExtensionChange implements Change {
                 oldRows = new ArrayList<Row>(count);
                 for (int i = 0; i < count; i++) {
                     line = reader.readLine();
-                    oldRows.add(Row.load(line));
+                    if (line != null) {
+                        oldRows.add(Row.load(line));
+                    }
                 }
             } else if ("newRowCount".equals(field)) {
                 int count = Integer.parseInt(value);
@@ -366,7 +374,9 @@ public class DataExtensionChange implements Change {
                 newRows = new ArrayList<Row>(count);
                 for (int i = 0; i < count; i++) {
                     line = reader.readLine();
-                    newRows.add(Row.load(line));
+                    if (line != null) {
+                        newRows.add(Row.load(line));
+                    }
                 }
             }
 

src/main/java/com/metaweb/gridworks/model/changes/MassRowChange.java

@@ -67,7 +67,9 @@ public class MassRowChange implements Change {
                 oldRows = new ArrayList<Row>(count);
                 for (int i = 0; i < count; i++) {
                     line = reader.readLine();
-                    oldRows.add(Row.load(line));
+                    if (line != null) {
+                        oldRows.add(Row.load(line));
+                    }
                 }
             } else if ("newRowCount".equals(field)) {
                 int count = Integer.parseInt(line.substring(equal + 1));
@@ -75,10 +77,11 @@ public class MassRowChange implements Change {
                 newRows = new ArrayList<Row>(count);
                 for (int i = 0; i < count; i++) {
                     line = reader.readLine();
-                    newRows.add(Row.load(line));
+                    if (line != null) {
+                        newRows.add(Row.load(line));
+                    }
                 }
             }
-
         }
         
         MassRowChange change = new MassRowChange(newRows);

src/main/java/com/metaweb/gridworks/model/recon/HeuristicReconConfig.java

@@ -265,8 +265,6 @@ public class HeuristicReconConfig extends ReconConfig {
             e.printStackTrace();
         }
         
-        System.gc();
-        
         return recons;
     }
 
@@ -361,8 +359,6 @@ public class HeuristicReconConfig extends ReconConfig {
             recons.add(recon);
         }
         
-        System.gc();
-        
         return recons;
     }
 
@@ -441,9 +437,8 @@ public class HeuristicReconConfig extends ReconConfig {
         return common / longWords.size();
     }
     
-    static protected Set<String> s_stopWords;
+    static final protected Set<String> s_stopWords = new HashSet<String>();
     static {
-        s_stopWords = new HashSet<String>();
         s_stopWords.add("the");
         s_stopWords.add("a");
         s_stopWords.add("and");

src/main/java/com/metaweb/gridworks/operations/MultiValuedCellJoinOperation.java

@@ -64,7 +64,7 @@ public class MultiValuedCellJoinOperation extends AbstractOperation {
         int cellIndex = column.getCellIndex();
         
         Column keyColumn = project.columnModel.getColumnByName(_keyColumnName);
-        if (column == null) {
+        if (keyColumn == null) {
             throw new Exception("No key column named " + _keyColumnName);
         }
         int keyCellIndex = keyColumn.getCellIndex();

src/main/java/com/metaweb/gridworks/operations/MultiValuedCellSplitOperation.java

@@ -70,7 +70,7 @@ public class MultiValuedCellSplitOperation extends AbstractOperation {
         int cellIndex = column.getCellIndex();
         
         Column keyColumn = project.columnModel.getColumnByName(_keyColumnName);
-        if (column == null) {
+        if (keyColumn == null) {
             throw new Exception("No key column named " + _keyColumnName);
         }
         int keyCellIndex = keyColumn.getCellIndex();

src/main/java/com/metaweb/gridworks/operations/OperationRegistry.java

@@ -10,8 +10,9 @@ import com.metaweb.gridworks.model.AbstractOperation;
 import com.metaweb.gridworks.model.Project;
 
 public abstract class OperationRegistry {
-    static public Map<String, Class<? extends AbstractOperation>> s_opNameToClass;
+
-    static public Map<Class<? extends AbstractOperation>, String> s_opClassToName;
+    static final public Map<String, Class<? extends AbstractOperation>> s_opNameToClass = new HashMap<String, Class<? extends AbstractOperation>>();
+    static final public Map<Class<? extends AbstractOperation>, String> s_opClassToName = new HashMap<Class<? extends AbstractOperation>, String>();
     
     static protected void register(String name, Class<? extends AbstractOperation> klass) {
         s_opNameToClass.put(name, klass);
@@ -19,9 +20,6 @@ public abstract class OperationRegistry {
     }
     
     static {
-        s_opNameToClass = new HashMap<String, Class<? extends AbstractOperation>>();
-        s_opClassToName = new HashMap<Class<? extends AbstractOperation>, String>();
-        
         register("recon", ReconOperation.class);
         register("recon-mark-new-topics", ReconMarkNewTopicsOperation.class);
         register("recon-match-best-candidates", ReconMatchBestCandidatesOperation.class);

src/main/java/com/metaweb/gridworks/protograph/transpose/TripleLoaderTransposedNodeFactory.java

@@ -90,13 +90,8 @@ public class TripleLoaderTransposedNodeFactory implements TransposedNodeFactory
     }
     
     protected class AnonymousTransposedNode extends TransposedNodeWithChildren {
-        AnonymousNode node;
         
-        protected AnonymousTransposedNode(
+        protected AnonymousTransposedNode(AnonymousNode node) { }
-            AnonymousNode node
-        ) {
-            this.node = node;
-        }
         
         public String write(String subject, String predicate) {
             if (children.size() == 0 || subject == null) {
@@ -116,7 +111,7 @@ public class TripleLoaderTransposedNodeFactory implements TransposedNodeFactory
                         sb.append(", ");
                     }
                     sb.append("\"" + properties.get(i).id + "\": ");
-                    sb.append(s instanceof String ? JSONObject.quote(s) : s.toString());
+                    sb.append(JSONObject.quote(s));
                 }
             }
             sb.append(" }");

src/main/java/com/metaweb/gridworks/util/ParsingUtilities.java

@@ -20,7 +20,8 @@ import org.json.JSONObject;
 import org.json.JSONTokener;
 
 public class ParsingUtilities {
-    static public SimpleDateFormat s_sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
+
+    static final public SimpleDateFormat s_sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
     
     static public Properties parseUrlParameters(HttpServletRequest request) {
         Properties options = new Properties();

src/server/java/com/metaweb/util/signal/SignalHandler.java

@@ -8,7 +8,7 @@ public abstract class SignalHandler {
         try {
             _wrapper = new SignalHandlerWrapper(signalName, this);
         } catch (Throwable e) {
-            new java.lang.RuntimeException("Signal handling facilities are not available in this JVM.");
+            throw new java.lang.RuntimeException("Signal handling facilities are not available in this JVM.");
         }
     }