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

Browse Source 
- 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
This commit is contained in:
Stefano Mazzocchi 2010-04-05 07:15:16 +00:00
parent 798b2a36ca
commit 2efbf0031f
33 changed files with 328 additions and 225 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
build.xml
View File

@ -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}" />

234
gridworks
View File

@ -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)
ant build;;
clean)
ant clean;;
distclean)
ant distclean;;
test)
test $1;;
run)
run;;
execute)
execute $*;;
mac_dist)
mac_dist $1;;
windows_dist)
windows_dist $1;;
linux_dist)
linux_dist $1;;
dist)
dist $1;;
*)
usage; ;;
build) build_prepare; ant build;;
clean) ant clean;;
distclean) ant distclean;;
test) test $1;;
findbugs) findbugs;;
run) run;;
execute) execute $*;;
mac_dist) mac_dist $1;;
windows_dist) windows_dist $1;;
linux_dist) linux_dist $1;;
dist) dist $1;;
*) usage; ;;
esac

2
src/main/java/com/metaweb/gridworks/GridworksServlet.java
View File

@ -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;

10
src/main/java/com/metaweb/gridworks/ProjectManager.java
View File

@ -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) {

6
src/main/java/com/metaweb/gridworks/browsing/facets/NumericBinIndex.java
View File

@ -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]++;

19
src/main/java/com/metaweb/gridworks/clustering/binning/BinningClusterer.java
View File

@ -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)) {
m.put(v, m.get(v) + 1);
if (m.containsKey(s)) {
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();
}

5
src/main/java/com/metaweb/gridworks/clustering/knn/kNNClusterer.java
View File

@ -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();
}

2
src/main/java/com/metaweb/gridworks/commands/edit/AnnotateOneRowCommand.java
View File

@ -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;

112
src/main/java/com/metaweb/gridworks/commands/edit/CreateProjectCommand.java
View File

@ -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) {
TarInputStream tis = (TarInputStream) is;
TarEntry te;
while ((te = tis.getNextEntry()) != null) {
if (!te.isDirectory()) {
mapExtension(te.getName(),ext_map);
}
}
} else if (is instanceof ZipInputStream) {
ZipInputStream zis = (ZipInputStream) is;
ZipEntry ze;
while ((ze = zis.getNextEntry()) != null) {
if (!ze.isDirectory()) {
mapExtension(ze.getName(),ext_map);
try {
if (is instanceof TarInputStream) {
TarInputStream tis = (TarInputStream) is;
TarEntry te;
while ((te = tis.getNextEntry()) != null) {
if (!te.isDirectory()) {
mapExtension(te.getName(),ext_map);
}
}
} else if (is instanceof ZipInputStream) {
ZipInputStream zis = (ZipInputStream) is;
ZipEntry ze;
while ((ze = zis.getNextEntry()) != null) {
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) {
TarInputStream tis = (TarInputStream) is;
TarEntry te;
while ((te = tis.getNextEntry()) != null) {
if (!te.isDirectory()) {
String name = te.getName();
String ext = getExtension(name)[1];
if (exts.contains(ext)) {
internalImportFile(project, options, name, sis);
}
}
}
} else if (is instanceof ZipInputStream) {
ZipInputStream zis = (ZipInputStream) is;
ZipEntry ze;
while ((ze = zis.getNextEntry()) != null) {
if (!ze.isDirectory()) {
String name = ze.getName();
String ext = getExtension(name)[1];
if (exts.contains(ext)) {
internalImportFile(project, options, name, sis);
try {
if (is instanceof TarInputStream) {
TarInputStream tis = (TarInputStream) is;
TarEntry te;
while ((te = tis.getNextEntry()) != null) {
if (!te.isDirectory()) {
String name = te.getName();
String ext = getExtension(name)[1];
if (exts.contains(ext)) {
internalImportFile(project, options, name, sis);
}
}
}
} else if (is instanceof ZipInputStream) {
ZipInputStream zis = (ZipInputStream) is;
ZipEntry ze;
while ((ze = zis.getNextEntry()) != null) {
if (!ze.isDirectory()) {
String name = ze.getName();
String ext = getExtension(name)[1];
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))) {
output.write(buffer, 0, n);
count += n;
try {
while (-1 != (n = input.read(buffer))) {
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;
}

2
src/main/java/com/metaweb/gridworks/commands/edit/EditOneCellCommand.java
View File

@ -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;

4
src/main/java/com/metaweb/gridworks/commands/info/ExportRowsCommand.java
View File

@ -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());

7
src/main/java/com/metaweb/gridworks/commands/info/GetAllProjectMetadataCommand.java
View File

@ -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()) {
writer.key(id.toString());
m.get(id).write(writer, options);
for (Entry<Long,ProjectMetadata> e : m.entrySet()) {
writer.key(e.getKey().toString());
e.getValue().write(writer, options);
}
writer.endObject();

4
src/main/java/com/metaweb/gridworks/commands/recon/ReconJudgeOneCellCommand.java
View File

@ -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,

7
src/main/java/com/metaweb/gridworks/expr/functions/Get.java
View File

@ -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 ?
((Number) to).intValue() : length;
int end = (to != null && to instanceof Number) ? ((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) {

7
src/main/java/com/metaweb/gridworks/expr/functions/Slice.java
View File

@ -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 ?
((Number) to).intValue() : length;
int end = (to != null && to instanceof Number) ? ((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) {

1
src/main/java/com/metaweb/gridworks/history/ChangeSequence.java
View File

@ -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));

10
src/main/java/com/metaweb/gridworks/model/Project.java
View File

@ -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());
project.rows.add(row);
maxCellCount = Math.max(maxCellCount, row.cells.size());
line = reader.readLine();
if (line != null) {
Row row = Row.load(line);
project.rows.add(row);
maxCellCount = Math.max(maxCellCount, row.cells.size());
}
}
}
}

15
src/main/java/com/metaweb/gridworks/model/Recon.java
View File

@ -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 public int Feature_typeMatch = 0;
static public int Feature_nameMatch = 1;
static public int Feature_nameLevenshtein = 2;
static public int Feature_nameWordDistance = 3;
static public int Feature_max = 4;
static final public int Feature_typeMatch = 0;
static final public int Feature_nameMatch = 1;
static final public int Feature_nameLevenshtein = 2;
static final public int Feature_nameWordDistance = 3;
static final 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);

16
src/main/java/com/metaweb/gridworks/model/Row.java
View File

@ -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()) {
writer.key((String) key);
writer.value(extra.get(key));
for (Entry<Object,Object> e : extra.entrySet()) {
writer.key((String) e.getKey());
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 {
private static final long serialVersionUID = -651032866647686293L;
protected static class CellTuple extends ArrayList<Cell> implements HasFields {
private static final long serialVersionUID = -651032866647686293L;
public Object getField(String name, Properties bindings) {
Object[] r = new Object[this.size()];

5
src/main/java/com/metaweb/gridworks/model/changes/ColumnAdditionChange.java
View File

@ -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));
}
}
}
}

5
src/main/java/com/metaweb/gridworks/model/changes/ColumnRemovalChange.java
View File

@ -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);
}
}
}
}

18
src/main/java/com/metaweb/gridworks/model/changes/DataExtensionChange.java
View File

@ -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));
}
}
}

9
src/main/java/com/metaweb/gridworks/model/changes/MassRowChange.java
View File

@ -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);

7
src/main/java/com/metaweb/gridworks/model/recon/HeuristicReconConfig.java
View File

@ -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");

2
src/main/java/com/metaweb/gridworks/operations/MultiValuedCellJoinOperation.java
View File

@ -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();

2
src/main/java/com/metaweb/gridworks/operations/MultiValuedCellSplitOperation.java
View File

@ -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();

8
src/main/java/com/metaweb/gridworks/operations/OperationRegistry.java
View File

@ -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);

9
src/main/java/com/metaweb/gridworks/protograph/transpose/TripleLoaderTransposedNodeFactory.java
View File

@ -90,13 +90,8 @@ public class TripleLoaderTransposedNodeFactory implements TransposedNodeFactory
}
protected class AnonymousTransposedNode extends TransposedNodeWithChildren {
AnonymousNode node;
protected AnonymousTransposedNode(
AnonymousNode node
) {
this.node = node;
}
protected AnonymousTransposedNode(AnonymousNode 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(" }");

3
src/main/java/com/metaweb/gridworks/util/ParsingUtilities.java
View File

@ -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();

2
src/server/java/com/metaweb/util/signal/SignalHandler.java
View File

@ -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.");
}
}

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thirdparty/apache-ant-1.8.0.tar.gz vendored
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