id int64 1 49k | buggy stringlengths 34 37.5k | fixed stringlengths 2 37k |
|---|---|---|
2,601 | private String token;
private static final Gson gson = new GsonBuilder()
.disableHtmlEscaping()
.registerTypeAdapter(Date.class, new DateAsTimeSinceEpochTypeAdapter(TimeUnit.SECONDS))
.create();
<BUG>public AuthenticationTokenSupplier(final String issuer, final String keyId, final PrivateKey privateKey) throws NoSuchAlgorithmException, InvalidKeyException {
</BUG>
Objects.requireNonNull(issuer);
Objects.requireNonNull(keyId);
Objects.requireNonNull(privateKey);
| public AuthenticationTokenSupplier(final String issuer, final String keyId, final ECPrivateKey privateKey) throws NoSuchAlgorithmException, InvalidKeyException {
|
2,602 | import java.net.InetSocketAddress;
import java.nio.charset.StandardCharsets;
import java.security.InvalidKeyException;
import java.security.KeyFactory;
import java.security.NoSuchAlgorithmException;
<BUG>import java.security.PrivateKey;
</BUG>
import java.security.spec.InvalidKeySpecException;
import java.security.spec.PKCS8EncodedKeySpec;
import java.util.Collection;
| import java.security.interfaces.ECPrivateKey;
|
2,603 | try {
final byte[] keyBytes = new byte[decodedPrivateKey.readableBytes()];
decodedPrivateKey.readBytes(keyBytes);
final PKCS8EncodedKeySpec keySpec = new PKCS8EncodedKeySpec(keyBytes);
final KeyFactory keyFactory = KeyFactory.getInstance("EC");
<BUG>signingKey = keyFactory.generatePrivate(keySpec);
</BUG>
} catch (final InvalidKeySpecException e) {
throw new InvalidKeyException(e);
} finally {
| final ByteBuf decodedPrivateKey = Base64.decode(wrappedEncodedPrivateKey);
signingKey = (ECPrivateKey) keyFactory.generatePrivate(keySpec);
|
2,604 | chart.addYAxisLabels(AxisLabelsFactory.newAxisLabels(labels));
chart.addXAxisLabels(AxisLabelsFactory.newNumericRangeAxisLabels(0, max));
chart.setBarWidth(BarChart.AUTO_RESIZE);
chart.setSize(600, 500);
chart.setHorizontal(true);
<BUG>chart.setTitle("Total Evaluations by User");
showChartImg(resp, chart.toURLString());
}</BUG>
private List<Entry<String, Integer>> sortEntries(Collection<Entry<String, Integer>> entries) {
List<Entry<String, Integer>> result = new ArrayList<Entry<String, Integer>>(entries);
| chart.setDataEncoding(DataEncoding.TEXT);
return chart;
}
|
2,605 | checkEvaluationsEqual(eval4, foundissueProto.getEvaluations(0));
checkEvaluationsEqual(eval5, foundissueProto.getEvaluations(1));
}
public void testGetRecentEvaluationsNoneFound() throws Exception {
DbIssue issue = createDbIssue("fad", persistenceHelper);
<BUG>DbEvaluation eval1 = createEvaluation(issue, "someone", 100);
DbEvaluation eval2 = createEvaluation(issue, "someone", 200);
DbEvaluation eval3 = createEvaluation(issue, "someone", 300);
issue.addEvaluations(eval1, eval2, eval3);</BUG>
getPersistenceManager().makePersistent(issue);
| [DELETED] |
2,606 | public int read() throws IOException {
return inputStream.read();
}
});
}
<BUG>}
protected DbEvaluation createEvaluation(DbIssue issue, String who, long when) {</BUG>
DbUser user;
Query query = getPersistenceManager().newQuery("select from " + persistenceHelper.getDbUserClass().getName()
+ " where openid == :myopenid");
| @SuppressWarnings({"unchecked"})
protected DbEvaluation createEvaluation(DbIssue issue, String who, long when) {
|
2,607 | eval.setComment("my comment");
eval.setDesignation("MUST_FIX");
eval.setIssue(issue);
eval.setWhen(when);
eval.setWho(user.createKeyObject());
<BUG>eval.setEmail(who);
return eval;</BUG>
}
protected PersistenceManager getPersistenceManager() {
return testHelper.getPersistenceManager();
| issue.addEvaluation(eval);
return eval;
|
2,608 | import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.permission.FsPermission;
import org.apache.hadoop.util.Progressable;
<BUG>import static org.apache.hadoop.fs.s3a.S3AConstants.*;
public class S3AFileSystem extends FileSystem {</BUG>
private URI uri;
private Path workingDir;
private AmazonS3Client s3;
| import static org.apache.hadoop.fs.s3a.Constants.*;
public class S3AFileSystem extends FileSystem {
|
2,609 | public void initialize(URI name, Configuration conf) throws IOException {
super.initialize(name, conf);
uri = URI.create(name.getScheme() + "://" + name.getAuthority());
workingDir = new Path("/user", System.getProperty("user.name")).makeQualified(this.uri,
this.getWorkingDirectory());
<BUG>String accessKey = conf.get(ACCESS_KEY, null);
String secretKey = conf.get(SECRET_KEY, null);
</BUG>
String userInfo = name.getUserInfo();
| String accessKey = conf.get(NEW_ACCESS_KEY, conf.get(OLD_ACCESS_KEY, null));
String secretKey = conf.get(NEW_SECRET_KEY, conf.get(OLD_SECRET_KEY, null));
|
2,610 | } else {
accessKey = userInfo;
}
}
AWSCredentialsProviderChain credentials = new AWSCredentialsProviderChain(
<BUG>new S3ABasicAWSCredentialsProvider(accessKey, secretKey),
new InstanceProfileCredentialsProvider(),
new S3AAnonymousAWSCredentialsProvider()
);</BUG>
bucket = name.getHost();
| new BasicAWSCredentialsProvider(accessKey, secretKey),
new AnonymousAWSCredentialsProvider()
|
2,611 |
awsConf.setSocketTimeout(conf.getInt(SOCKET_TIMEOUT, DEFAULT_SOCKET_TIMEOUT));
</BUG>
s3 = new AmazonS3Client(credentials, awsConf);
<BUG>maxKeys = conf.getInt(MAX_PAGING_KEYS, DEFAULT_MAX_PAGING_KEYS);
partSize = conf.getLong(MULTIPART_SIZE, DEFAULT_MULTIPART_SIZE);
partSizeThreshold = conf.getInt(MIN_MULTIPART_THRESHOLD, DEFAULT_MIN_MULTIPART_THRESHOLD);
</BUG>
if (partSize < 5 * 1024 * 1024) {
| new InstanceProfileCredentialsProvider(),
new AnonymousAWSCredentialsProvider()
bucket = name.getHost();
ClientConfiguration awsConf = new ClientConfiguration();
awsConf.setMaxConnections(conf.getInt(NEW_MAXIMUM_CONNECTIONS, conf.getInt(OLD_MAXIMUM_CONNECTIONS, DEFAULT_MAXIMUM_CONNECTIONS)));
awsConf.setProtocol(conf.getBoolean(NEW_SECURE_CONNECTIONS, conf.getBoolean(OLD_SECURE_CONNECTIONS, DEFAULT_SECURE_CONNECTIONS)) ? Protocol.HTTPS : Protocol.HTTP);
awsConf.setMaxErrorRetry(conf.getInt(NEW_MAX_ERROR_RETRIES, conf.getInt(OLD_MAX_ERROR_RETRIES, DEFAULT_MAX_ERROR_RETRIES)));
awsConf.setSocketTimeout(conf.getInt(NEW_SOCKET_TIMEOUT, conf.getInt(OLD_SOCKET_TIMEOUT, DEFAULT_SOCKET_TIMEOUT)));
maxKeys = conf.getInt(NEW_MAX_PAGING_KEYS, conf.getInt(OLD_MAX_PAGING_KEYS, DEFAULT_MAX_PAGING_KEYS));
partSize = conf.getLong(NEW_MULTIPART_SIZE, conf.getLong(OLD_MULTIPART_SIZE, DEFAULT_MULTIPART_SIZE));
partSizeThreshold = conf.getInt(NEW_MIN_MULTIPART_THRESHOLD, conf.getInt(OLD_MIN_MULTIPART_THRESHOLD, DEFAULT_MIN_MULTIPART_THRESHOLD));
|
2,612 | cannedACL = null;
}
if (!s3.doesBucketExist(bucket)) {
throw new IOException("Bucket " + bucket + " does not exist");
}
<BUG>boolean purgeExistingMultipart = conf.getBoolean(PURGE_EXISTING_MULTIPART, DEFAULT_PURGE_EXISTING_MULTIPART);
long purgeExistingMultipartAge = conf.getLong(PURGE_EXISTING_MULTIPART_AGE, DEFAULT_PURGE_EXISTING_MULTIPART_AGE);
</BUG>
if (purgeExistingMultipart) {
| boolean purgeExistingMultipart = conf.getBoolean(NEW_PURGE_EXISTING_MULTIPART, conf.getBoolean(OLD_PURGE_EXISTING_MULTIPART, DEFAULT_PURGE_EXISTING_MULTIPART));
long purgeExistingMultipartAge = conf.getLong(NEW_PURGE_EXISTING_MULTIPART_AGE, conf.getLong(OLD_PURGE_EXISTING_MULTIPART_AGE, DEFAULT_PURGE_EXISTING_MULTIPART_AGE));
|
2,613 | import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
<BUG>import static org.apache.hadoop.fs.s3a.S3AConstants.*;
public class S3AOutputStream extends OutputStream {</BUG>
private OutputStream backupStream;
private File backupFile;
private boolean closed;
| import static org.apache.hadoop.fs.s3a.Constants.*;
public class S3AOutputStream extends OutputStream {
|
2,614 | this.client = client;
this.progress = progress;
this.fs = fs;
this.cannedACL = cannedACL;
this.statistics = statistics;
<BUG>partSize = conf.getLong(MULTIPART_SIZE, DEFAULT_MULTIPART_SIZE);
partSizeThreshold = conf.getInt(MIN_MULTIPART_THRESHOLD, DEFAULT_MIN_MULTIPART_THRESHOLD);
</BUG>
if (conf.get(BUFFER_DIR, null) != null) {
| partSize = conf.getLong(OLD_MULTIPART_SIZE, DEFAULT_MULTIPART_SIZE);
partSizeThreshold = conf.getInt(OLD_MIN_MULTIPART_THRESHOLD, DEFAULT_MIN_MULTIPART_THRESHOLD);
|
2,615 | if (orders.containsKey(orderId))
return;
OrderBook book = books.get(instrument);
if (book == null)
return;
<BUG>Order order = book.add(side, price, size);
orders.put(orderId, order);</BUG>
if (order.isOnBestLevel())
book.bbo(listener);
| Order order = new Order(book, side, price, size);
orders.put(orderId, order);
|
2,616 | book.bbo(listener);
}
public void modify(long orderId, long size) {
Order order = orders.get(orderId);
if (order == null)
<BUG>return;
boolean onBestLevel = order.isOnBestLevel();
if (size > 0) {
order.setRemainingQuantity(size);
} else {</BUG>
orders.remove(orderId);
| OrderBook book = order.getOrderBook();
long newSize = Math.max(0, size);
book.update(order.getSide(), order.getPrice(), newSize - order.getRemainingQuantity());
if (newSize == 0)
|
2,617 | } else {</BUG>
orders.remove(orderId);
<BUG>order.delete();
}
if (onBestLevel)
order.getOrderBook().bbo(listener);
}</BUG>
public void execute(long orderId, long quantity) {
Order order = orders.get(orderId);
if (order == null)
| book.bbo(listener);
public void modify(long orderId, long size) {
|
2,618 | package com.paritytrading.parity.top;
public class Order {
<BUG>private Level parent;
private long remainingQuantity;
Order(Level parent, long size) {
this.parent = parent;
</BUG>
this.remainingQuantity = size;
| private OrderBook book;
private Side side;
private long price;
Order(OrderBook book, Side side, long price, long size) {
this.book = book;
this.side = side;
this.price = price;
|
2,619 | @Override
public boolean isValidSdkHome(String path) {
if (!checkForJdk(new File(path))) {
return false;
}
<BUG>if (JrtFileSystem.isModularJdk(path) && !JrtFileSystem.isSupported()) {
return false;
}
return true;</BUG>
}
| public void fileDeleted(@NotNull VirtualFileEvent event) {
updateCache(event);
|
2,620 | if (!srcDir.exists() || !srcDir.isDirectory()) return null;
String path = srcDir.getAbsolutePath().replace(File.separatorChar, '/');
return LocalFileSystem.getInstance().findFileByPath(path);
}
}
<BUG>@SuppressWarnings({"HardCodedStringLiteral"})
private static void addDocs(File file, SdkModificator rootContainer) {</BUG>
VirtualFile vFile = findDocs(file, "docs/api");
if (vFile != null) {
rootContainer.addRoot(vFile, JavadocOrderRootType.getInstance());
| @SuppressWarnings("HardCodedStringLiteral")
private static void addDocs(File file, SdkModificator rootContainer) {
|
2,621 | String url = JarFileSystem.PROTOCOL_PREFIX +
jarFile.getAbsolutePath().replace(File.separatorChar, '/') + JarFileSystem.JAR_SEPARATOR + relativePath;
return VirtualFileManager.getInstance().findFileByUrl(url);
}
@Nullable
<BUG>public static VirtualFile findDocs(File file, final String relativePath) {
</BUG>
file = new File(file.getAbsolutePath() + File.separator + relativePath.replace('/', File.separatorChar));
if (!file.exists() || !file.isDirectory()) return null;
String path = file.getAbsolutePath().replace(File.separatorChar, '/');
| private static VirtualFile findDocs(File file, final String relativePath) {
|
2,622 | timeWarp = new OwnLabel(getFormattedTimeWrap(), skin, "warp");
timeWarp.setName("time warp");
Container wrapWrapper = new Container(timeWarp);
wrapWrapper.width(60f * GlobalConf.SCALE_FACTOR);
wrapWrapper.align(Align.center);
<BUG>VerticalGroup timeGroup = new VerticalGroup().align(Align.left).space(3 * GlobalConf.SCALE_FACTOR).padTop(3 * GlobalConf.SCALE_FACTOR);
</BUG>
HorizontalGroup dateGroup = new HorizontalGroup();
dateGroup.space(4 * GlobalConf.SCALE_FACTOR);
dateGroup.addActor(date);
| VerticalGroup timeGroup = new VerticalGroup().align(Align.left).columnAlign(Align.left).space(3 * GlobalConf.SCALE_FACTOR).padTop(3 * GlobalConf.SCALE_FACTOR);
|
2,623 | focusListScrollPane.setFadeScrollBars(false);
focusListScrollPane.setScrollingDisabled(true, false);
focusListScrollPane.setHeight(tree ? 200 * GlobalConf.SCALE_FACTOR : 100 * GlobalConf.SCALE_FACTOR);
focusListScrollPane.setWidth(160);
}
<BUG>VerticalGroup objectsGroup = new VerticalGroup().align(Align.left).space(3 * GlobalConf.SCALE_FACTOR);
</BUG>
objectsGroup.addActor(searchBox);
if (focusListScrollPane != null) {
objectsGroup.addActor(focusListScrollPane);
| VerticalGroup objectsGroup = new VerticalGroup().align(Align.left).columnAlign(Align.left).space(3 * GlobalConf.SCALE_FACTOR);
|
2,624 | headerGroup.addActor(expandIcon);
headerGroup.addActor(detachIcon);
addActor(headerGroup);
expandIcon.setChecked(expanded);
}
<BUG>public void expand() {
</BUG>
if (!expandIcon.isChecked()) {
expandIcon.setChecked(true);
}
| public void expandPane() {
|
2,625 | </BUG>
if (!expandIcon.isChecked()) {
expandIcon.setChecked(true);
}
}
<BUG>public void collapse() {
</BUG>
if (expandIcon.isChecked()) {
expandIcon.setChecked(false);
}
| headerGroup.addActor(expandIcon);
headerGroup.addActor(detachIcon);
addActor(headerGroup);
expandIcon.setChecked(expanded);
public void expandPane() {
public void collapsePane() {
|
2,626 | });
playstop.addListener(new TextTooltip(txt("gui.tooltip.playstop"), skin));
TimeComponent timeComponent = new TimeComponent(skin, ui);
timeComponent.initialize();
CollapsiblePane time = new CollapsiblePane(ui, txt("gui.time"), timeComponent.getActor(), skin, true, playstop);
<BUG>time.align(Align.left);
mainActors.add(time);</BUG>
panes.put(timeComponent.getClass().getSimpleName(), time);
if (Constants.desktop) {
recCamera = new OwnImageButton(skin, "rec");
| time.align(Align.left).columnAlign(Align.left);
mainActors.add(time);
|
2,627 | panes.put(visualEffectsComponent.getClass().getSimpleName(), visualEffects);
ObjectsComponent objectsComponent = new ObjectsComponent(skin, ui);
objectsComponent.setSceneGraph(sg);
objectsComponent.initialize();
CollapsiblePane objects = new CollapsiblePane(ui, txt("gui.objects"), objectsComponent.getActor(), skin, false);
<BUG>objects.align(Align.left);
mainActors.add(objects);</BUG>
panes.put(objectsComponent.getClass().getSimpleName(), objects);
GaiaComponent gaiaComponent = new GaiaComponent(skin, ui);
gaiaComponent.initialize();
| objects.align(Align.left).columnAlign(Align.left);
mainActors.add(objects);
|
2,628 | if (Constants.desktop) {
MusicComponent musicComponent = new MusicComponent(skin, ui);
musicComponent.initialize();
Actor[] musicActors = MusicActorsManager.getMusicActors() != null ? MusicActorsManager.getMusicActors().getActors(skin) : null;
CollapsiblePane music = new CollapsiblePane(ui, txt("gui.music"), musicComponent.getActor(), skin, true, musicActors);
<BUG>music.align(Align.left);
mainActors.add(music);</BUG>
panes.put(musicComponent.getClass().getSimpleName(), music);
}
Button switchWebgl = new OwnTextButton(txt("gui.webgl.back"), skin, "link");
| music.align(Align.left).columnAlign(Align.left);
mainActors.add(music);
|
2,629 | Button rtlDirectionButton, ltrDirectionButton, autoDirectionButton, defaultDirectionButton;
static final int IMAGE_SIZE = 12;
static final int FOREGROUND_COLOR = 0;
static final int BACKGROUND_COLOR = 1;
static final int FONT = 2;
<BUG>List colorAndFontTable;
</BUG>
ColorDialog colorDialog;
FontDialog fontDialog;
Color foregroundColor, backgroundColor;
| Table colorAndFontTable;
|
2,630 | void createSetGetGroup() {
}
void createControlWidgets () {
}
void createColorAndFontGroup () {
<BUG>Group result = new Group (controlGroup, SWT.NONE);
result.setLayoutData(new GridData (SWT.FILL, SWT.FILL, false, false));
result.setText(ControlExample.getResourceString ("Colors"));
colorGroup = result;</BUG>
colorGroup.setLayout (new GridLayout (2, true));
| colorGroup = new Group(controlGroup, SWT.NONE);
|
2,631 | visibleButton.setSelection(true);
backgroundImageButton.setSelection(false);
popupMenuButton.setSelection(false);
}
void createBackgroundModeGroup () {
<BUG>Group result = new Group (controlGroup, SWT.NONE);
result.setLayoutData(new GridData (SWT.FILL, SWT.FILL, false, false));
result.setText(ControlExample.getResourceString("Background_Mode"));
backgroundModeGroup = result;
backgroundModeGroup.setLayout (new GridLayout ());
backgroundModeCombo = new Combo(backgroundModeGroup, SWT.READ_ONLY);</BUG>
backgroundModeCombo.setItems("SWT.INHERIT_NONE", "SWT.INHERIT_DEFAULT", "SWT.INHERIT_FORCE");
| backgroundModeGroup = new Group (controlGroup, SWT.NONE);
backgroundModeGroup.setLayoutData (new GridData (SWT.FILL, SWT.FILL, false, false));
backgroundModeGroup.setText (ControlExample.getResourceString("Background_Mode"));
backgroundModeCombo = new Combo(backgroundModeGroup, SWT.READ_ONLY);
|
2,632 | dialog.setDefaultButton(ok);
ok.setLayoutData(new GridData(GridData.HORIZONTAL_ALIGN_FILL));
ok.addSelectionListener (new SelectionAdapter() {
@Override
public void widgetSelected(SelectionEvent e) {
<BUG>for (int i = 0; i < table.getItemCount(); i++) {
eventsFilter[i] = table.isSelected(i);
}</BUG>
dialog.dispose();
| TableItem [] items = table.getItems();
for (int i = 0; i < EVENT_INFO.length; i++) {
eventsFilter[i] = items[i].getChecked();
|
2,633 | dialog.setSize(bounds.width, clientArea.height - trim.height);
}
dialog.setLocation(bounds.x, clientArea.y);
dialog.open ();
}
<BUG>void createListenersGroup () {
Group result = new Group (controlGroup, SWT.NONE);
result.setLayoutData(new GridData (SWT.FILL, SWT.FILL, true, true, 2, 1));
result.setText(ControlExample.getResourceString ("Listeners"));
listenersGroup = result;
listenersGroup.setLayout (new GridLayout (4, false));
Button listenersButton = new Button (listenersGroup, SWT.PUSH);</BUG>
listenersButton.setText (ControlExample.getResourceString ("Select_Listeners"));
| listenersGroup = new Group (tabFolderPage, SWT.NONE);
listenersGroup.setLayoutData (new GridData (SWT.FILL, SWT.FILL, true, true, 2, 1));
listenersGroup.setText (ControlExample.getResourceString ("Listeners"));
Button listenersButton = new Button (listenersGroup, SWT.PUSH);
|
2,634 | rtlDirectionButton.setText ("SWT.RIGHT_TO_LEFT");
autoDirectionButton = new Button (directionGroup, SWT.RADIO);
autoDirectionButton.setText ("AUTO direction");
}
void createSizeGroup () {
<BUG>Group result = new Group (controlGroup, SWT.NONE);
result.setLayoutData(new GridData (SWT.FILL, SWT.FILL, false, false));
result.setText(ControlExample.getResourceString("Size"));
sizeGroup = result;
sizeGroup.setLayout (new GridLayout());
preferredButton = new Button (sizeGroup, SWT.RADIO);</BUG>
preferredButton.setText (ControlExample.getResourceString("Preferred"));
| sizeGroup = new Group (controlGroup, SWT.NONE);
sizeGroup.setLayoutData (new GridData (SWT.FILL, SWT.FILL, false, false));
sizeGroup.setText (ControlExample.getResourceString("Size"));
preferredButton = new Button (sizeGroup, SWT.RADIO);
|
2,635 | fillHButton.addSelectionListener(selectionListener);
fillVButton.addSelectionListener(selectionListener);
preferredButton.setSelection (true);
}
void createStyleGroup () {
<BUG>Group result = new Group (controlGroup, SWT.NONE);
result.setLayoutData(new GridData (SWT.FILL, SWT.FILL, false, false));
result.setText(ControlExample.getResourceString("Styles"));
styleGroup = result;
styleGroup.setLayout (new GridLayout ());
}</BUG>
Composite createTabFolderPage (TabFolder tabFolder) {
| styleGroup = new Group (controlGroup, SWT.NONE);
styleGroup.setLayoutData (new GridData (SWT.FILL, SWT.FILL, false, false));
styleGroup.setText (ControlExample.getResourceString("Styles"));
|
2,636 | package org.elasticsearch.common.http.client;
import org.apache.lucene.util.IOUtils;
import org.elasticsearch.ElasticsearchTimeoutException;
import org.elasticsearch.Version;
import org.elasticsearch.common.Nullable;
<BUG>import org.elasticsearch.common.SuppressForbidden;
import org.elasticsearch.common.unit.TimeValue;</BUG>
import java.io.*;
import java.net.HttpURLConnection;
import java.net.URL;
| import org.elasticsearch.common.cli.Terminal;
import org.elasticsearch.common.unit.TimeValue;
|
2,637 | package org.elasticsearch.plugins;
import com.google.common.base.Strings;
import com.google.common.collect.ImmutableSet;
import com.google.common.collect.Iterators;
<BUG>import org.apache.lucene.util.IOUtils;
import org.elasticsearch.*;
</BUG>
import org.elasticsearch.bootstrap.JarHell;
import org.elasticsearch.common.SuppressForbidden;
| import org.elasticsearch.ElasticsearchTimeoutException;
import org.elasticsearch.ExceptionsHelper;
import org.elasticsearch.Version;
|
2,638 | boolean downloaded = false;
HttpDownloadHelper.DownloadProgress progress;
if (outputMode == OutputMode.SILENT) {
progress = new HttpDownloadHelper.NullProgress();
} else {
<BUG>progress = new HttpDownloadHelper.VerboseProgress(SysOut.getOut());
</BUG>
}
if (!Files.isWritable(environment.pluginsFile())) {
throw new IOException("plugin directory " + environment.pluginsFile() + " is read only");
| progress = new HttpDownloadHelper.VerboseProgress(terminal.writer());
|
2,639 | downloadHelper.download(pluginUrl, pluginFile, progress, this.timeout);
downloaded = true;
} catch (ElasticsearchTimeoutException e) {
throw e;
} catch (Exception e) {
<BUG>log("Failed: " + ExceptionsHelper.detailedMessage(e));
</BUG>
}
} else {
if (PluginHandle.isOfficialPlugin(pluginHandle.repo, pluginHandle.user, pluginHandle.version)) {
| terminal.println("Failed: %s", ExceptionsHelper.detailedMessage(e));
|
2,640 | checkForOfficialPlugins(pluginHandle.name);
}
}
if (!downloaded) {
for (URL url : pluginHandle.urls()) {
<BUG>log("Trying " + url.toExternalForm() + "...");
try {</BUG>
downloadHelper.download(url, pluginFile, progress, this.timeout);
downloaded = true;
break;
| terminal.println("Trying %s ...", url.toExternalForm());
try {
|
2,641 | downloaded = true;
break;
} catch (ElasticsearchTimeoutException e) {
throw e;
} catch (Exception e) {
<BUG>debug("Failed: " + ExceptionsHelper.detailedMessage(e));
</BUG>
}
}
}
| terminal.println(VERBOSE, "Failed: %s", ExceptionsHelper.detailedMessage(e));
|
2,642 | throw new IOException("failed to download out of all possible locations..., use --verbose to get detailed information");
}
Path tmp = unzipToTemporary(pluginFile);
final List<URL> jars = new ArrayList<>();
ClassLoader loader = PluginManager.class.getClassLoader();
<BUG>if (loader instanceof URLClassLoader) {
for (URL url : ((URLClassLoader) loader).getURLs()) {
jars.add(url);
}</BUG>
}
| Collections.addAll(jars, ((URLClassLoader) loader).getURLs());
|
2,643 | Files.copy(file, target, StandardCopyOption.REPLACE_EXISTING);
return FileVisitResult.CONTINUE;
}
});
}
<BUG>log("Installed " + name + " into " + extractLocation.toAbsolutePath());
} catch (Exception e) {
log("failed to extract plugin [" + pluginFile + "]: " + ExceptionsHelper.detailedMessage(e));
</BUG>
return;
| terminal.println("Installed %s into %s", name, extractLocation.toAbsolutePath());
terminal.printError("failed to extract plugin [%s]: %s", pluginFile, ExceptionsHelper.detailedMessage(e));
|
2,644 | Path site = extractLocation.resolve("_site");
Path tmpLocation = environment.pluginsFile().resolve(extractLocation.getFileName() + ".tmp");
Files.move(extractLocation, tmpLocation);
Files.createDirectories(extractLocation);
Files.move(tmpLocation, site);
<BUG>debug("Installed " + name + " into " + site.toAbsolutePath());
</BUG>
}
}
}
| terminal.println(VERBOSE, "Installed " + name + " into " + site.toAbsolutePath());
|
2,645 | PluginHandle pluginHandle = PluginHandle.parse(name);
boolean removed = false;
checkForForbiddenName(pluginHandle.name);
Path pluginToDelete = pluginHandle.extractedDir(environment);
if (Files.exists(pluginToDelete)) {
<BUG>debug("Removing: " + pluginToDelete);
try {</BUG>
IOUtils.rm(pluginToDelete);
} catch (IOException ex){
throw new IOException("Unable to remove " + pluginHandle.name + ". Check file permissions on " +
| terminal.println(VERBOSE, "Removing: %s", pluginToDelete);
try {
|
2,646 | }
@After
public void clearPathHome() {
System.clearProperty("es.default.path.home");
}
<BUG>protected static String[] args(String command) {
</BUG>
if (!Strings.hasLength(command)) {
return Strings.EMPTY_ARRAY;
}
| public static String[] args(String command) {
|
2,647 | System.out.println(change);
}
}
};
@Override
<BUG>protected Callback<VChild, Void> copyChildCallback()
</BUG>
{
return (child) ->
{
| protected Callback<VChild, Void> copyIntoCallback()
|
2,648 | package jfxtras.labs.icalendarfx.components;
import jfxtras.labs.icalendarfx.properties.component.descriptive.Comment;
<BUG>import jfxtras.labs.icalendarfx.properties.component.misc.IANAProperty;
import jfxtras.labs.icalendarfx.properties.component.misc.UnknownProperty;</BUG>
import jfxtras.labs.icalendarfx.properties.component.recurrence.RecurrenceDates;
import jfxtras.labs.icalendarfx.properties.component.recurrence.RecurrenceRule;
| import jfxtras.labs.icalendarfx.properties.component.misc.NonStandardProperty;
|
2,649 | VEVENT ("VEVENT",
Arrays.asList(PropertyType.ATTACHMENT, PropertyType.ATTENDEE, PropertyType.CATEGORIES,
PropertyType.CLASSIFICATION, PropertyType.COMMENT, PropertyType.CONTACT, PropertyType.DATE_TIME_CREATED,
PropertyType.DATE_TIME_END, PropertyType.DATE_TIME_STAMP, PropertyType.DATE_TIME_START,
PropertyType.DESCRIPTION, PropertyType.DURATION, PropertyType.EXCEPTION_DATE_TIMES,
<BUG>PropertyType.GEOGRAPHIC_POSITION, PropertyType.IANA_PROPERTY, PropertyType.LAST_MODIFIED,
PropertyType.LOCATION, PropertyType.NON_STANDARD, PropertyType.ORGANIZER, PropertyType.PRIORITY,</BUG>
PropertyType.RECURRENCE_DATE_TIMES, PropertyType.RECURRENCE_IDENTIFIER, PropertyType.RELATED_TO,
PropertyType.RECURRENCE_RULE, PropertyType.REQUEST_STATUS, PropertyType.RESOURCES, PropertyType.SEQUENCE,
PropertyType.STATUS, PropertyType.SUMMARY, PropertyType.TIME_TRANSPARENCY, PropertyType.UNIQUE_IDENTIFIER,
| PropertyType.GEOGRAPHIC_POSITION, PropertyType.LAST_MODIFIED,
PropertyType.LOCATION, PropertyType.NON_STANDARD, PropertyType.ORGANIZER, PropertyType.PRIORITY,
|
2,650 | VTODO ("VTODO",
Arrays.asList(PropertyType.ATTACHMENT, PropertyType.ATTENDEE, PropertyType.CATEGORIES,
PropertyType.CLASSIFICATION, PropertyType.COMMENT, PropertyType.CONTACT, PropertyType.DATE_TIME_COMPLETED,
PropertyType.DATE_TIME_CREATED, PropertyType.DATE_TIME_DUE, PropertyType.DATE_TIME_STAMP,
PropertyType.DATE_TIME_START, PropertyType.DESCRIPTION, PropertyType.DURATION,
<BUG>PropertyType.EXCEPTION_DATE_TIMES, PropertyType.GEOGRAPHIC_POSITION, PropertyType.IANA_PROPERTY,
PropertyType.LAST_MODIFIED, PropertyType.LOCATION, PropertyType.NON_STANDARD, PropertyType.ORGANIZER,</BUG>
PropertyType.PERCENT_COMPLETE, PropertyType.PRIORITY, PropertyType.RECURRENCE_DATE_TIMES,
PropertyType.RECURRENCE_IDENTIFIER, PropertyType.RELATED_TO, PropertyType.RECURRENCE_RULE,
PropertyType.REQUEST_STATUS, PropertyType.RESOURCES, PropertyType.SEQUENCE, PropertyType.STATUS,
| PropertyType.EXCEPTION_DATE_TIMES, PropertyType.GEOGRAPHIC_POSITION,
PropertyType.LAST_MODIFIED, PropertyType.LOCATION, PropertyType.NON_STANDARD, PropertyType.ORGANIZER,
|
2,651 | throw new RuntimeException("not implemented");
}
},
DAYLIGHT_SAVING_TIME ("DAYLIGHT",
Arrays.asList(PropertyType.COMMENT, PropertyType.DATE_TIME_START,
<BUG>PropertyType.IANA_PROPERTY, PropertyType.NON_STANDARD, PropertyType.RECURRENCE_DATE_TIMES,
PropertyType.RECURRENCE_RULE, PropertyType.TIME_ZONE_NAME, PropertyType.TIME_ZONE_OFFSET_FROM,</BUG>
PropertyType.TIME_ZONE_OFFSET_TO),
DaylightSavingTime.class)
{
| PropertyType.RECURRENCE_RULE, PropertyType.TIME_ZONE_NAME, PropertyType.TIME_ZONE_OFFSET_FROM,
|
2,652 | throw new RuntimeException("not implemented");
}
},
VALARM ("VALARM",
Arrays.asList(PropertyType.ACTION, PropertyType.ATTACHMENT, PropertyType.ATTENDEE, PropertyType.DESCRIPTION,
<BUG>PropertyType.DURATION, PropertyType.IANA_PROPERTY, PropertyType.NON_STANDARD, PropertyType.REPEAT_COUNT,
PropertyType.SUMMARY, PropertyType.TRIGGER),</BUG>
VAlarm.class)
{
@Override
| DAYLIGHT_SAVING_TIME ("DAYLIGHT",
Arrays.asList(PropertyType.COMMENT, PropertyType.DATE_TIME_START,
PropertyType.NON_STANDARD, PropertyType.RECURRENCE_DATE_TIMES,
PropertyType.RECURRENCE_RULE, PropertyType.TIME_ZONE_NAME, PropertyType.TIME_ZONE_OFFSET_FROM,
PropertyType.TIME_ZONE_OFFSET_TO),
DaylightSavingTime.class)
|
2,653 | private ContentLineStrategy contentLineGenerator;
protected void setContentLineGenerator(ContentLineStrategy contentLineGenerator)
{
this.contentLineGenerator = contentLineGenerator;
}
<BUG>protected Callback<VChild, Void> copyChildCallback()
</BUG>
{
throw new RuntimeException("Can't copy children. copyChildCallback isn't overridden in subclass." + this.getClass());
};
| protected Callback<VChild, Void> copyIntoCallback()
|
2,654 | import jfxtras.labs.icalendarfx.properties.calendar.Version;
import jfxtras.labs.icalendarfx.properties.component.misc.NonStandardProperty;
public enum CalendarProperty
{
CALENDAR_SCALE ("CALSCALE",
<BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER),
CalendarScale.class)</BUG>
{
@Override
public VChild parse(VCalendar vCalendar, String contentLine)
| Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD),
CalendarScale.class)
|
2,655 | CalendarScale calendarScale = (CalendarScale) child;
destination.setCalendarScale(calendarScale);
}
},
METHOD ("METHOD",
<BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER),
Method.class)</BUG>
{
@Override
public VChild parse(VCalendar vCalendar, String contentLine)
| Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD),
Method.class)
|
2,656 | }
list.add(new NonStandardProperty((NonStandardProperty) child));
}
},
PRODUCT_IDENTIFIER ("PRODID",
<BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER),
ProductIdentifier.class)</BUG>
{
@Override
public VChild parse(VCalendar vCalendar, String contentLine)
| public void copyChild(VChild child, VCalendar destination)
CalendarScale calendarScale = (CalendarScale) child;
destination.setCalendarScale(calendarScale);
METHOD ("METHOD",
Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD),
Method.class)
|
2,657 | ProductIdentifier productIdentifier = (ProductIdentifier) child;
destination.setProductIdentifier(productIdentifier);
}
},
VERSION ("VERSION",
<BUG>Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD, ParameterType.IANA_PARAMETER),
Version.class)</BUG>
{
@Override
public VChild parse(VCalendar vCalendar, String contentLine)
| Arrays.asList(ParameterType.VALUE_DATA_TYPES, ParameterType.NON_STANDARD),
Version.class)
|
2,658 | package jfxtras.labs.icalendarfx.components;
import jfxtras.labs.icalendarfx.properties.component.descriptive.Comment;
<BUG>import jfxtras.labs.icalendarfx.properties.component.misc.IANAProperty;
import jfxtras.labs.icalendarfx.properties.component.misc.UnknownProperty;</BUG>
import jfxtras.labs.icalendarfx.properties.component.recurrence.RecurrenceDates;
import jfxtras.labs.icalendarfx.properties.component.recurrence.RecurrenceRule;
| import jfxtras.labs.icalendarfx.properties.component.misc.NonStandardProperty;
|
2,659 | import org.spongepowered.api.world.Locatable;
import org.spongepowered.api.world.Location;
import org.spongepowered.api.world.World;
import javax.annotation.Nullable;
import java.util.List;
<BUG>import java.util.Optional;
import static net.foxdenstudio.sponge.foxcore.plugin.util.Aliases.*;</BUG>
public class CommandDelete extends FCCommandBase {
private static final FlagMapper MAPPER = map -> key -> value -> {
map.put(key, value);
| import java.util.stream.Stream;
import static net.foxdenstudio.sponge.foxcore.plugin.util.Aliases.*;
|
2,660 | .append(Text.of(TextColors.GREEN, "Usage: "))
.append(getUsage(source))
.build());
return CommandResult.empty();
} else if (isIn(REGIONS_ALIASES, parse.args[0])) {
<BUG>if (parse.args.length < 2) throw new CommandException(Text.of("Must specify a name!"));
IRegion region = FGManager.getInstance().getRegion(parse.args[1]);
</BUG>
boolean isWorldRegion = false;
if (region == null) {
| String regionName = parse.args[1];
IRegion region = FGManager.getInstance().getRegion(regionName).orElse(null);
|
2,661 | </BUG>
isWorldRegion = true;
}
if (region == null)
<BUG>throw new CommandException(Text.of("No region exists with the name \"" + parse.args[1] + "\"!"));
if (region instanceof GlobalWorldRegion) {
</BUG>
throw new CommandException(Text.of("You may not delete the global region!"));
}
| if (world == null)
throw new CommandException(Text.of("No world exists with name \"" + worldName + "\"!"));
if (world == null) throw new CommandException(Text.of("Must specify a world!"));
region = FGManager.getInstance().getWorldRegion(world, regionName).orElse(null);
throw new CommandException(Text.of("No region exists with the name \"" + regionName + "\"!"));
if (region instanceof IGlobal) {
|
2,662 | source.getName() + " deleted " + (isWorldRegion ? "world" : "") + "region"
);
return CommandResult.success();
} else if (isIn(HANDLERS_ALIASES, parse.args[0])) {
if (parse.args.length < 2) throw new CommandException(Text.of("Must specify a name!"));
<BUG>IHandler handler = FGManager.getInstance().gethandler(parse.args[1]);
if (handler == null)
throw new ArgumentParseException(Text.of("No handler exists with that name!"), parse.args[1], 1);
if (handler instanceof GlobalHandler)</BUG>
throw new CommandException(Text.of("You may not delete the global handler!"));
| Optional<IHandler> handlerOpt = FGManager.getInstance().gethandler(parse.args[1]);
if (!handlerOpt.isPresent())
IHandler handler = handlerOpt.get();
if (handler instanceof GlobalHandler)
|
2,663 | .excludeCurrent(true)
.autoCloseQuotes(true)
.parse();
if (parse.current.type.equals(AdvCmdParser.CurrentElement.ElementType.ARGUMENT)) {
if (parse.current.index == 0)
<BUG>return ImmutableList.of("region", "handler").stream()
.filter(new StartsWithPredicate(parse.current.token))</BUG>
.map(args -> parse.current.prefix + args)
.collect(GuavaCollectors.toImmutableList());
else if (parse.current.index == 1) {
| return Stream.of("region", "handler")
.filter(new StartsWithPredicate(parse.current.token))
|
2,664 | .excludeCurrent(true)
.autoCloseQuotes(true)
.parse();
if (parse.current.type.equals(AdvCmdParser.CurrentElement.ElementType.ARGUMENT)) {
if (parse.current.index == 0)
<BUG>return ImmutableList.of("region", "handler").stream()
.filter(new StartsWithPredicate(parse.current.token))</BUG>
.map(args -> parse.current.prefix + args)
.collect(GuavaCollectors.toImmutableList());
else if (parse.current.index == 1) {
| return Stream.of("region", "handler")
.filter(new StartsWithPredicate(parse.current.token))
|
2,665 | @Dependency(id = "foxcore")
},
description = "A world protection plugin built for SpongeAPI. Requires FoxCore.",
authors = {"gravityfox"},
url = "https://github.com/FoxDenStudio/FoxGuard")
<BUG>public final class FoxGuardMain {
public final Cause pluginCause = Cause.builder().named("plugin", this).build();
private static FoxGuardMain instanceField;</BUG>
@Inject
private Logger logger;
| private static FoxGuardMain instanceField;
|
2,666 | private UserStorageService userStorage;
private EconomyService economyService = null;
private boolean loaded = false;
private FCCommandDispatcher fgDispatcher;
public static FoxGuardMain instance() {
<BUG>return instanceField;
}</BUG>
@Listener
public void construct(GameConstructionEvent event) {
instanceField = this;
| }
public static Cause getCause() {
return instance().pluginCause;
}
|
2,667 | return configDirectory;
}
public boolean isLoaded() {
return loaded;
}
<BUG>public static Cause getCause() {
return instance().pluginCause;
}</BUG>
public EconomyService getEconomyService() {
return economyService;
| [DELETED] |
2,668 | import org.spongepowered.api.world.Locatable;
import org.spongepowered.api.world.Location;
import org.spongepowered.api.world.World;
import javax.annotation.Nullable;
import java.util.*;
<BUG>import java.util.stream.Collectors;
import static net.foxdenstudio.sponge.foxcore.plugin.util.Aliases.*;</BUG>
public class CommandHere extends FCCommandBase {
private static final String[] PRIORITY_ALIASES = {"priority", "prio", "p"};
private static final FlagMapper MAPPER = map -> key -> value -> {
| import java.util.stream.Stream;
import static net.foxdenstudio.sponge.foxcore.plugin.util.Aliases.*;
|
2,669 | .excludeCurrent(true)
.autoCloseQuotes(true)
.parse();
if (parse.current.type.equals(AdvCmdParser.CurrentElement.ElementType.ARGUMENT)) {
if (parse.current.index == 0)
<BUG>return ImmutableList.of("region", "handler").stream()
.filter(new StartsWithPredicate(parse.current.token))</BUG>
.map(args -> parse.current.prefix + args)
.collect(GuavaCollectors.toImmutableList());
else if (parse.current.index > 0) {
| return Stream.of("region", "handler")
.filter(new StartsWithPredicate(parse.current.token))
|
2,670 | private static FGStorageManager instance;
private final Logger logger = FoxGuardMain.instance().getLogger();</BUG>
private final Set<LoadEntry> loaded = new HashSet<>();
private final Path directory = getDirectory();
private final Map<String, Path> worldDirectories;
<BUG>private FGStorageManager() {
defaultModifiedMap = new CacheMap<>((k, m) -> {</BUG>
if (k instanceof IFGObject) {
m.put((IFGObject) k, true);
return true;
| public final HashMap<IFGObject, Boolean> defaultModifiedMap;
private final UserStorageService userStorageService;
private final Logger logger = FoxGuardMain.instance().getLogger();
userStorageService = FoxGuardMain.instance().getUserStorage();
defaultModifiedMap = new CacheMap<>((k, m) -> {
|
2,671 | String name = fgObject.getName();
Path singleDir = dir.resolve(name.toLowerCase());
</BUG>
boolean shouldSave = fgObject.shouldSave();
if (force || shouldSave) {
<BUG>logger.info((shouldSave ? "S" : "Force s") + "aving handler \"" + name + "\" in directory: " + singleDir);
</BUG>
constructDirectory(singleDir);
try {
fgObject.save(singleDir);
| UUID owner = fgObject.getOwner();
boolean isOwned = !owner.equals(SERVER_UUID);
Optional<User> userOwner = userStorageService.get(owner);
String logName = (userOwner.isPresent() ? userOwner.get().getName() + ":" : "") + (isOwned ? owner + ":" : "") + name;
if (fgObject.autoSave()) {
Path singleDir = serverDir.resolve(name.toLowerCase());
logger.info((shouldSave ? "S" : "Force s") + "aving handler " + logName + " in directory: " + singleDir);
|
2,672 | if (fgObject.autoSave()) {
Path singleDir = dir.resolve(name.toLowerCase());
</BUG>
boolean shouldSave = fgObject.shouldSave();
if (force || shouldSave) {
<BUG>logger.info((shouldSave ? "S" : "Force s") + "aving world region \"" + name + "\" in directory: " + singleDir);
</BUG>
constructDirectory(singleDir);
try {
fgObject.save(singleDir);
| Path singleDir = serverDir.resolve(name.toLowerCase());
logger.info((shouldSave ? "S" : "Force s") + "aving world region " + logName + " in directory: " + singleDir);
|
2,673 | public synchronized void loadRegionLinks() {
logger.info("Loading region links");
try (DB mainDB = DBMaker.fileDB(directory.resolve("regions.foxdb").normalize().toString()).make()) {
Map<String, String> linksMap = mainDB.hashMap("links", Serializer.STRING, Serializer.STRING).createOrOpen();
linksMap.entrySet().forEach(entry -> {
<BUG>IRegion region = FGManager.getInstance().getRegion(entry.getKey());
if (region != null) {
logger.info("Loading links for region \"" + region.getName() + "\"");</BUG>
String handlersString = entry.getValue();
| Optional<IRegion> regionOpt = FGManager.getInstance().getRegion(entry.getKey());
if (regionOpt.isPresent()) {
IRegion region = regionOpt.get();
logger.info("Loading links for region \"" + region.getName() + "\"");
|
2,674 | public synchronized void loadWorldRegionLinks(World world) {
logger.info("Loading world region links for world \"" + world.getName() + "\"");
try (DB mainDB = DBMaker.fileDB(worldDirectories.get(world.getName()).resolve("wregions.foxdb").normalize().toString()).make()) {
Map<String, String> linksMap = mainDB.hashMap("links", Serializer.STRING, Serializer.STRING).createOrOpen();
linksMap.entrySet().forEach(entry -> {
<BUG>IRegion region = FGManager.getInstance().getWorldRegion(world, entry.getKey());
if (region != null) {
logger.info("Loading links for world region \"" + region.getName() + "\"");</BUG>
String handlersString = entry.getValue();
| Optional<IWorldRegion> regionOpt = FGManager.getInstance().getWorldRegion(world, entry.getKey());
if (regionOpt.isPresent()) {
IWorldRegion region = regionOpt.get();
logger.info("Loading links for world region \"" + region.getName() + "\"");
|
2,675 | StringBuilder builder = new StringBuilder();
for (Iterator<IHandler> it = handlers.iterator(); it.hasNext(); ) {
builder.append(it.next().getName());
if (it.hasNext()) builder.append(",");
}
<BUG>return builder.toString();
}</BUG>
private final class LoadEntry {
public final String name;
public final Type type;
| public enum Type {
REGION, WREGION, HANDLER
|
2,676 | .autoCloseQuotes(true)
.leaveFinalAsIs(true)
.parse();
if (parse.current.type.equals(AdvCmdParser.CurrentElement.ElementType.ARGUMENT)) {
if (parse.current.index == 0)
<BUG>return ImmutableList.of("region", "worldregion", "handler", "controller").stream()
</BUG>
.filter(new StartsWithPredicate(parse.current.token))
.collect(GuavaCollectors.toImmutableList());
else if (parse.current.index == 1) {
| return Stream.of("region", "worldregion", "handler", "controller")
|
2,677 | qualHistogram[i] = 0L;
final NestedIntegerArray<RecalDatum> qualTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE); // get the quality score table
for (final RecalDatum value : qualTable.getAllValues()) {
final RecalDatum datum = value;
final int empiricalQual = MathUtils.fastRound(datum.getEmpiricalQuality()); // convert the empirical quality to an integer ( it is already capped by MAX_QUAL )
<BUG>qualHistogram[empiricalQual] += datum.getNumObservations(); // add the number of observations for every key
</BUG>
}
empiricalQualCounts = Arrays.asList(qualHistogram); // histogram with the number of observations of the empirical qualities
quantizeQualityScores(quantizationLevels);
| qualHistogram[empiricalQual] += (long) datum.getNumObservations(); // add the number of observations for every key
|
2,678 | protected Covariate[] covariates;
protected RecalibrationTables recalibrationTables;
public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) {
this.covariates = covariates.clone();
this.recalibrationTables = recalibrationTables;
<BUG>}
public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) {</BUG>
final int offset = pileupElement.getOffset();
final ReadCovariates readCovariates = covariateKeySetFrom(pileupElement.getRead());
final byte qual = pileupElement.getQual();
| @Override
public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) {
|
2,679 | final EventType event = EventType.eventFrom(keys[keyIndex]);
reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), event.toString());
reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEmpiricalQuality());
if (tableIndex == RecalibrationTables.TableType.READ_GROUP_TABLE.index)
reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getEstimatedQReported()); // we only add the estimated Q reported in the RG table
<BUG>reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), datum.getNumObservations());
reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), datum.getNumMismatches());
</BUG>
rowIndex++;
| reportTable.set(rowIndex, columnNames.get(columnIndex++).getFirst(), Math.round(datum.getNumObservations()));
reportTable.set(rowIndex, columnNames.get(columnIndex).getFirst(), Math.round(datum.getNumMismatches()));
|
2,680 | @Ensures("result >= 0.0")
public double getEmpiricalErrorRate() {
if ( numObservations == 0 )
return 0.0;
else {
<BUG>final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT);
final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT);
return doubleMismatches / doubleObservations;</BUG>
}
}
| final double doubleMismatches = numMismatches + SMOOTHING_CONSTANT;
final double doubleObservations = numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT;
return doubleMismatches / doubleObservations;
|
2,681 | public final byte getEmpiricalQualityAsByte() {
return (byte)(Math.round(getEmpiricalQuality()));
}
@Override
public String toString() {
<BUG>return String.format("%d,%d,%d", getNumObservations(), getNumMismatches(), (byte) Math.floor(getEmpiricalQuality()));
</BUG>
}
public String stringForCSV() {
return String.format("%s,%d,%.2f", toString(), (byte) Math.floor(getEstimatedQReported()), getEmpiricalQuality() - getEstimatedQReported());
| return String.format("%d,%d,%d", Math.round(getNumObservations()), Math.round(getNumMismatches()), (byte) Math.floor(getEmpiricalQuality()));
|
2,682 | if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0");
this.numMismatches = numMismatches;
empiricalQuality = UNINITIALIZED;
}
@Requires({"by >= 0"})
<BUG>public synchronized void incrementNumObservations(final long by) {
</BUG>
numObservations += by;
empiricalQuality = UNINITIALIZED;
}
| [DELETED] |
2,683 | </BUG>
numObservations += by;
empiricalQuality = UNINITIALIZED;
}
@Requires({"by >= 0"})
<BUG>public synchronized void incrementNumMismatches(final long by) {
</BUG>
numMismatches += by;
empiricalQuality = UNINITIALIZED;
}
| if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0");
this.numMismatches = numMismatches;
public synchronized void incrementNumObservations(final double by) {
public synchronized void incrementNumMismatches(final double by) {
|
2,684 | numMismatches += by;
empiricalQuality = UNINITIALIZED;
}
@Requires({"incObservations >= 0", "incMismatches >= 0"})
@Ensures({"numObservations == old(numObservations) + incObservations", "numMismatches == old(numMismatches) + incMismatches"})
<BUG>public synchronized void increment(final long incObservations, final long incMismatches) {
</BUG>
incrementNumObservations(incObservations);
incrementNumMismatches(incMismatches);
}
| public synchronized void increment(final double incObservations, final double incMismatches) {
|
2,685 | return 0.0;
else {
final long[][] counts = new long[subnodes.size()][2];
int i = 0;
for ( final RecalDatumNode<T> subnode : subnodes ) {
<BUG>counts[i][0] = subnode.getRecalDatum().getNumMismatches() + 1;
counts[i][1] = subnode.getRecalDatum().getNumObservations() + 2;
</BUG>
i++;
| else if ( subnodes.size() == 1 )
counts[i][0] = Math.round(subnode.getRecalDatum().getNumMismatches()) + 1L;
counts[i][1] = Math.round(subnode.getRecalDatum().getNumObservations()) + 2L;
|
2,686 | package com.projecttango.examples.java.augmentedreality;
import com.google.atap.tangoservice.Tango;
import com.google.atap.tangoservice.Tango.OnTangoUpdateListener;
import com.google.atap.tangoservice.TangoCameraIntrinsics;
import com.google.atap.tangoservice.TangoConfig;
<BUG>import com.google.atap.tangoservice.TangoCoordinateFramePair;
import com.google.atap.tangoservice.TangoEvent;</BUG>
import com.google.atap.tangoservice.TangoOutOfDateException;
import com.google.atap.tangoservice.TangoPoseData;
import com.google.atap.tangoservice.TangoXyzIjData;
| import com.google.atap.tangoservice.TangoErrorException;
import com.google.atap.tangoservice.TangoEvent;
|
2,687 | super.onResume();
if (!mIsConnected) {
mTango = new Tango(AugmentedRealityActivity.this, new Runnable() {
@Override
public void run() {
<BUG>try {
connectTango();</BUG>
setupRenderer();
mIsConnected = true;
} catch (TangoOutOfDateException e) {
| TangoSupport.initialize();
connectTango();
|
2,688 | if (lastFramePose.statusCode == TangoPoseData.POSE_VALID) {
mRenderer.updateRenderCameraPose(lastFramePose, mExtrinsics);
mCameraPoseTimestamp = lastFramePose.timestamp;</BUG>
} else {
<BUG>Log.w(TAG, "Can't get device pose at time: " + mRgbTimestampGlThread);
}</BUG>
}
}
}
@Override
| mRenderer.updateRenderCameraPose(lastFramePose);
mCameraPoseTimestamp = lastFramePose.timestamp;
Log.w(TAG, "Can't get device pose at time: " +
|
2,689 | import org.rajawali3d.materials.Material;
import org.rajawali3d.materials.methods.DiffuseMethod;
import org.rajawali3d.materials.textures.ATexture;
import org.rajawali3d.materials.textures.StreamingTexture;
import org.rajawali3d.materials.textures.Texture;
<BUG>import org.rajawali3d.math.Matrix4;
import org.rajawali3d.math.vector.Vector3;</BUG>
import org.rajawali3d.primitives.ScreenQuad;
import org.rajawali3d.primitives.Sphere;
import org.rajawali3d.renderer.RajawaliRenderer;
| import org.rajawali3d.math.Quaternion;
import org.rajawali3d.math.vector.Vector3;
|
2,690 | translationMoon.setRepeatMode(Animation.RepeatMode.INFINITE);
translationMoon.setTransformable3D(moon);
getCurrentScene().registerAnimation(translationMoon);
translationMoon.play();
}
<BUG>public void updateRenderCameraPose(TangoPoseData devicePose, DeviceExtrinsics extrinsics) {
Pose cameraPose = ScenePoseCalculator.toOpenGlCameraPose(devicePose, extrinsics);
getCurrentCamera().setRotation(cameraPose.getOrientation());
getCurrentCamera().setPosition(cameraPose.getPosition());
}</BUG>
public int getTextureId() {
| public void updateRenderCameraPose(TangoPoseData cameraPose) {
float[] rotation = cameraPose.getRotationAsFloats();
float[] translation = cameraPose.getTranslationAsFloats();
Quaternion quaternion = new Quaternion(rotation[3], rotation[0], rotation[1], rotation[2]);
getCurrentCamera().setRotation(quaternion.conjugate());
getCurrentCamera().setPosition(translation[0], translation[1], translation[2]);
|
2,691 | package com.projecttango.examples.java.helloareadescription;
import com.google.atap.tangoservice.Tango;
<BUG>import com.google.atap.tangoservice.Tango.OnTangoUpdateListener;
import com.google.atap.tangoservice.TangoConfig;</BUG>
import com.google.atap.tangoservice.TangoCoordinateFramePair;
import com.google.atap.tangoservice.TangoErrorException;
import com.google.atap.tangoservice.TangoEvent;
| import com.google.atap.tangoservice.TangoAreaDescriptionMetaData;
import com.google.atap.tangoservice.TangoConfig;
|
2,692 | OnViewChangedNotifier previousNotifier = OnViewChangedNotifier.replaceNotifier(onViewChangedNotifier_);
init_(savedInstanceState);
super.onCreate(savedInstanceState);
OnViewChangedNotifier.replaceNotifier(previousNotifier);
setContentView(layout.new_request);
<BUG>}
@Override</BUG>
public void setContentView(int layoutResID) {
super.setContentView(layoutResID);
onViewChangedNotifier_.notifyViewChanged(this);
| private void init_(Bundle savedInstanceState) {
OnViewChangedNotifier.registerOnViewChangedListener(this);
injectExtras_();
@Override
|
2,693 | if (((SdkVersionHelper.getSdkInt()< 5)&&(keyCode == KeyEvent.KEYCODE_BACK))&&(event.getRepeatCount() == 0)) {
onBackPressed();
}
return super.onKeyDown(keyCode, event);
}
<BUG>public static EditRequestActivity_.IntentBuilder_ intent(Context context) {
return new EditRequestActivity_.IntentBuilder_(context);
}
public static EditRequestActivity_.IntentBuilder_ intent(Fragment supportFragment) {
return new EditRequestActivity_.IntentBuilder_(supportFragment);
}</BUG>
@Override
| [DELETED] |
2,694 | public void onClick(View view) {
EditRequestActivity_.this.addressChange();
}
}
);
<BUG>}
if (hasViews.findViewById(id.requestSend)!= null) {
hasViews.findViewById(id.requestSend).setOnClickListener(new OnClickListener() {
@Override</BUG>
public void onClick(View view) {
| View view = hasViews.findViewById(id.requestSend);
if (view!= null) {
view.setOnClickListener(new OnClickListener() {
@Override
|
2,695 | import org.apache.commons.io.FileUtils;
public class BetterFpsHelper {
public static final String MC_VERSION = "1.9";
public static final String VERSION = "1.2.1";
public static final String URL = "http://guichaguri.github.io/BetterFps/";
<BUG>public static final String UPDATE_URL = "https://raw.githubusercontent.com/Guichaguri/BetterFps/1.8/lastest-version.properties";
public static final LinkedHashMap<String, String> helpers = new LinkedHashMap<String, String>();</BUG>
public static final LinkedHashMap<String, String> displayHelpers = new LinkedHashMap<String, String>();
static {
helpers.put("vanilla", "VanillaMath");
| public static final String UPDATE_URL = "http://widget.mcf.li/mc-mods/minecraft/229876-betterfps.json";
public static final LinkedHashMap<String, String> helpers = new LinkedHashMap<String, String>();
|
2,696 | <BUG>package guichaguri.betterfps;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.Properties;</BUG>
import net.minecraft.client.Minecraft;
| import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import java.io.InputStreamReader;
|
2,697 | import net.minecraft.util.text.event.ClickEvent;
import net.minecraft.util.text.event.HoverEvent;
public class UpdateChecker implements Runnable {
private static boolean updateCheck = false;
private static boolean done = false;
<BUG>private static Properties prop = null;
public static void check() {</BUG>
if(!BetterFpsConfig.getConfig().updateChecker) {
done = true;
return;
| private static String updateVersion = null;
private static String updateDownload = null;
public static void check() {
|
2,698 | thread.setDaemon(true);
thread.start();
}
}
public static void showChat() {
<BUG>if(!done) return;
if(prop == null) return;
if(BetterFpsHelper.VERSION.equals(prop.getProperty("version"))) {
prop = null;
return;
}</BUG>
if(!BetterFps.isClient) return;
| if(updateVersion == null && updateDownload == null) return;
|
2,699 | @CopyMode(Mode.IGNORE) // Ignore the constructor to prevent an infinite loop
public HopperBlock() {
}
@Override
@CopyMode(Mode.APPEND)
<BUG>public void onNeighborBlockChange(World worldIn, BlockPos pos, IBlockState state, Block neighborBlock) {
</BUG>
TileEntity te = worldIn.getTileEntity(pos);
if(te != null) {
TileEntityHopper hopper = (TileEntityHopper)te;
| public void neighborChanged(IBlockState state, World worldIn, BlockPos pos, Block neighborBlock) {
|
2,700 | assertThat(entry.getPortfolioTransaction().getDate(), is(LocalDate.parse("2015-12-23")));
assertThat(entry.getPortfolioTransaction().getShares(), is(Values.Share.factorize(43)));
assertThat(entry.getPortfolioTransaction().getUnitSum(Unit.Type.FEE),
is(Money.of(CurrencyUnit.EUR, 10_09 + 45_88 + 2_52 + 4_12)));
}
<BUG>@Test
public void testDividend() throws IOException</BUG>
{
DABPDFExctractor extractor = new DABPDFExctractor(new Client())
{
| public void testWertpapierVerkauf2() throws IOException
|
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