private static void finalize(
Configuration conf, JobConf jobconf, final Path destPath, String presevedAttributes)
throws IOException {
if (presevedAttributes == null) {
return;
}
EnumSet<FileAttribute> preseved = FileAttribute.parse(presevedAttributes);
if (!preseved.contains(FileAttribute.USER)
&& !preseved.contains(FileAttribute.GROUP)
&& !preseved.contains(FileAttribute.PERMISSION)) {
return;
}
FileSystem dstfs = destPath.getFileSystem(conf);
Path dstdirlist = new Path(jobconf.get(DST_DIR_LIST_LABEL));
SequenceFile.Reader in = null;
try {
in = new SequenceFile.Reader(dstdirlist.getFileSystem(jobconf), dstdirlist, jobconf);
Text dsttext = new Text();
FilePair pair = new FilePair();
for (; in.next(dsttext, pair); ) {
Path absdst = new Path(destPath, pair.output);
updatePermissions(pair.input, dstfs.getFileStatus(absdst), preseved, dstfs);
}
} finally {
checkAndClose(in);
}
}
private void init() {
this.transform_ = this.createJSTransform();
this.mouseWentDown()
.addListener("function(o, e){var o=" + this.getSObjJsRef() + ";if(o){o.mouseDown(o, e);}}");
this.mouseWentUp()
.addListener("function(o, e){var o=" + this.getSObjJsRef() + ";if(o){o.mouseUp(o, e);}}");
this.mouseDragged()
.addListener("function(o, e){var o=" + this.getSObjJsRef() + ";if(o){o.mouseDrag(o, e);}}");
this.mouseMoved()
.addListener(
"function(o, e){var o=" + this.getSObjJsRef() + ";if(o){o.mouseMoved(o, e);}}");
this.touchStarted()
.addListener(
"function(o, e){var o=" + this.getSObjJsRef() + ";if(o){o.touchStarted(o, e);}}");
this.touchEnded()
.addListener(
"function(o, e){var o=" + this.getSObjJsRef() + ";if(o){o.touchEnded(o, e);}}");
this.touchMoved()
.addListener(
"function(o, e){var o=" + this.getSObjJsRef() + ";if(o){o.touchMoved(o, e);}}");
this.setSelectionAreaPadding(0, EnumSet.of(Side.Top));
this.setSelectionAreaPadding(20, EnumSet.of(Side.Left, Side.Right));
this.setSelectionAreaPadding(30, EnumSet.of(Side.Bottom));
if (this.chart_ != null) {
this.chart_.addAxisSliderWidget(this);
}
}
private void internalScrollTo(long newX, long newY, boolean moveViewPort) {
if (this.imageWidth_ != Infinite) {
newX = Math.min(this.imageWidth_ - this.viewPortWidth_, Math.max((long) 0, newX));
}
if (this.imageHeight_ != Infinite) {
newY = Math.min(this.imageHeight_ - this.viewPortHeight_, Math.max((long) 0, newY));
}
if (moveViewPort) {
this.contents_.setOffsets(new WLength((double) -newX), EnumSet.of(Side.Left));
this.contents_.setOffsets(new WLength((double) -newY), EnumSet.of(Side.Top));
}
this.generateGridItems(newX, newY);
this.viewPortChanged_.trigger(this.currentX_, this.currentY_);
}
/**
* Parses a list of tags from the command line, assuming it comes from the GATK Engine tags, and
* returns the corresponding EnumSet.
*
* @param arg the actual engine arg, used for the UserException if there's an error
* @param tags a list of string tags that should be converted to the MissingPedField value
* @return
*/
public static final EnumSet<MissingPedField> parseMissingFieldTags(
final Object arg, final List<String> tags) {
final EnumSet<MissingPedField> missingFields = EnumSet.noneOf(MissingPedField.class);
for (final String tag : tags) {
try {
missingFields.add(MissingPedField.valueOf(tag));
} catch (IllegalArgumentException e) {
throw new UserException.BadArgumentValue(
arg.toString(),
"Unknown tag " + tag + " allowed values are " + MissingPedField.values());
}
}
return missingFields;
}
void expand(int row, int column, int rowSpan, int columnSpan) {
int newNumRows = row + rowSpan;
int curNumColumns = this.getColumnCount();
int newNumColumns = Math.max(curNumColumns, column + columnSpan);
if (newNumRows > this.getRowCount() || newNumColumns > curNumColumns) {
if (newNumColumns == curNumColumns && this.getRowCount() >= this.headerRowCount_) {
this.rowsAdded_ += newNumRows - this.getRowCount();
} else {
this.flags_.set(BIT_GRID_CHANGED);
}
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
for (int r = this.getRowCount(); r < newNumRows; ++r) {
this.rows_.add(new WTableRow(this, newNumColumns));
}
if (newNumColumns > curNumColumns) {
for (int r = 0; r < this.getRowCount(); ++r) {
WTableRow tr = this.rows_.get(r);
tr.expand(newNumColumns);
}
for (int c = curNumColumns; c <= column; ++c) {
this.columns_.add(new WTableColumn(this));
}
}
}
}
/**
* Consctructor for a media widget.
*
* <p>A freshly constructed media widget has no options set, no media sources, and has preload
* mode set to PreloadAuto.
*/
public WAbstractMedia(WContainerWidget parent) {
super(parent);
this.sources_ = new ArrayList<WAbstractMedia.Source>();
this.sourcesRendered_ = 0;
this.mediaId_ = "";
this.flags_ = EnumSet.noneOf(WAbstractMedia.Options.class);
this.preloadMode_ = WAbstractMedia.PreloadMode.PreloadAuto;
this.alternative_ = null;
this.flagsChanged_ = false;
this.preloadChanged_ = false;
this.sourcesChanged_ = false;
this.playing_ = false;
this.volume_ = -1;
this.current_ = -1;
this.duration_ = -1;
this.ended_ = false;
this.readyState_ = WAbstractMedia.ReadyState.HaveNothing;
this.setInline(false);
this.setFormObject(true);
WApplication app = WApplication.getInstance();
app.loadJavaScript("js/WAbstractMedia.js", wtjs1());
this.setJavaScriptMember(
" WAbstractMedia",
"new Wt3_2_3.WAbstractMedia(" + app.getJavaScriptClass() + "," + this.getJsRef() + ");");
}
/**
* Get the active cipher suites.
*
* <p>In TLS 1.1, many weak or vulnerable cipher suites were obsoleted, such as
* TLS_RSA_EXPORT_WITH_RC4_40_MD5. The implementation MUST NOT negotiate these cipher suites in
* TLS 1.1 or later mode.
*
* <p>Therefore, when the active protocols only include TLS 1.1 or later, the client cannot
* request to negotiate those obsoleted cipher suites. That is, the obsoleted suites should not be
* included in the client hello. So we need to create a subset of the enabled cipher suites, the
* active cipher suites, which does not contain obsoleted cipher suites of the minimum active
* protocol.
*
* <p>Return empty list instead of null if no active cipher suites.
*/
CipherSuiteList getActiveCipherSuites() {
if (activeCipherSuites == null) {
if (activeProtocols == null) {
activeProtocols = getActiveProtocols();
}
ArrayList<CipherSuite> suites = new ArrayList<>();
if (!(activeProtocols.collection().isEmpty())
&& activeProtocols.min.v != ProtocolVersion.NONE.v) {
for (CipherSuite suite : enabledCipherSuites.collection()) {
if (suite.obsoleted > activeProtocols.min.v && suite.supported <= activeProtocols.max.v) {
if (algorithmConstraints.permits(
EnumSet.of(CryptoPrimitive.KEY_AGREEMENT), suite.name, null)) {
suites.add(suite);
}
} else if (debug != null && Debug.isOn("verbose")) {
if (suite.obsoleted <= activeProtocols.min.v) {
System.out.println("Ignoring obsoleted cipher suite: " + suite);
} else {
System.out.println("Ignoring unsupported cipher suite: " + suite);
}
}
}
}
activeCipherSuites = new CipherSuiteList(suites);
}
return activeCipherSuites;
}
/*
* Get the active protocol versions.
*
* In TLS 1.1, many weak or vulnerable cipher suites were obsoleted,
* such as TLS_RSA_EXPORT_WITH_RC4_40_MD5. The implementation MUST NOT
* negotiate these cipher suites in TLS 1.1 or later mode.
*
* For example, if "TLS_RSA_EXPORT_WITH_RC4_40_MD5" is the
* only enabled cipher suite, the client cannot request TLS 1.1 or
* later, even though TLS 1.1 or later is enabled. We need to create a
* subset of the enabled protocols, called the active protocols, which
* contains protocols appropriate to the list of enabled Ciphersuites.
*
* Return empty list instead of null if no active protocol versions.
*/
ProtocolList getActiveProtocols() {
if (activeProtocols == null) {
ArrayList<ProtocolVersion> protocols = new ArrayList<>(4);
for (ProtocolVersion protocol : enabledProtocols.collection()) {
boolean found = false;
for (CipherSuite suite : enabledCipherSuites.collection()) {
if (suite.isAvailable()
&& suite.obsoleted > protocol.v
&& suite.supported <= protocol.v) {
if (algorithmConstraints.permits(
EnumSet.of(CryptoPrimitive.KEY_AGREEMENT), suite.name, null)) {
protocols.add(protocol);
found = true;
break;
} else if (debug != null && Debug.isOn("verbose")) {
System.out.println("Ignoring disabled cipher suite: " + suite + " for " + protocol);
}
} else if (debug != null && Debug.isOn("verbose")) {
System.out.println("Ignoring unsupported cipher suite: " + suite + " for " + protocol);
}
}
if (!found && (debug != null) && Debug.isOn("handshake")) {
System.out.println("No available cipher suite for " + protocol);
}
}
activeProtocols = new ProtocolList(protocols);
}
return activeProtocols;
}
/**
* Adds a widget to the grid.
*
* <p>Calls {@link #addWidget(WWidget widget, int row, int column, int rowSpan, int columnSpan,
* EnumSet alignment) addWidget(widget, row, column, rowSpan, columnSpan, EnumSet.of(alignmen,
* alignment))}
*/
public final void addWidget(
WWidget widget,
int row,
int column,
int rowSpan,
int columnSpan,
AlignmentFlag alignmen,
AlignmentFlag... alignment) {
addWidget(widget, row, column, rowSpan, columnSpan, EnumSet.of(alignmen, alignment));
}
/**
* Adds a nested layout item to the grid.
*
* <p>Calls {@link #addLayout(WLayout layout, int row, int column, int rowSpan, int columnSpan,
* EnumSet alignment) addLayout(layout, row, column, rowSpan, columnSpan, EnumSet.of(alignmen,
* alignment))}
*/
public final void addLayout(
WLayout layout,
int row,
int column,
int rowSpan,
int columnSpan,
AlignmentFlag alignmen,
AlignmentFlag... alignment) {
addLayout(layout, row, column, rowSpan, columnSpan, EnumSet.of(alignmen, alignment));
}
/**
* Adds a layout item to the grid.
*
* <p>Calls {@link #addItem(WLayoutItem item, int row, int column, int rowSpan, int columnSpan,
* EnumSet alignment) addItem(item, row, column, rowSpan, columnSpan, EnumSet.of(alignmen,
* alignment))}
*/
public final void addItem(
WLayoutItem item,
int row,
int column,
int rowSpan,
int columnSpan,
AlignmentFlag alignmen,
AlignmentFlag... alignment) {
addItem(item, row, column, rowSpan, columnSpan, EnumSet.of(alignmen, alignment));
}
void repaintRow(WTableRow row) {
if (row.getRowNum() >= (int) (this.getRowCount() - this.rowsAdded_)) {
return;
}
if (!(this.rowsChanged_ != null)) {
this.rowsChanged_ = new HashSet<WTableRow>();
}
this.rowsChanged_.add(row);
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
}
/** Delete a column and all its contents. */
public void deleteColumn(int column) {
for (int i = 0; i < this.getRowCount(); ++i) {
this.rows_.get(i).deleteColumn(column);
}
if ((int) column <= this.columns_.size()) {;
this.columns_.remove(0 + column);
}
this.flags_.set(BIT_GRID_CHANGED);
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
}
private static void updatePermissions(
FileStatus src, FileStatus dst, EnumSet<FileAttribute> preseved, FileSystem destFileSys)
throws IOException {
String owner = null;
String group = null;
if (preseved.contains(FileAttribute.USER) && !src.getOwner().equals(dst.getOwner())) {
owner = src.getOwner();
}
if (preseved.contains(FileAttribute.GROUP) && !src.getGroup().equals(dst.getGroup())) {
group = src.getGroup();
}
if (owner != null || group != null) {
destFileSys.setOwner(dst.getPath(), owner, group);
}
if (preseved.contains(FileAttribute.PERMISSION)
&& !src.getPermission().equals(dst.getPermission())) {
destFileSys.setPermission(dst.getPath(), src.getPermission());
}
}
/** Inserts an empty row. */
public WTableRow insertRow(int row) {
if (row >= this.getRowCount()) {
return this.getRowAt(row);
} else {
WTableRow tableRow = new WTableRow(this, this.getColumnCount());
this.rows_.add(0 + row, tableRow);
this.flags_.set(BIT_GRID_CHANGED);
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
return tableRow;
}
}
private FSDataOutputStream create(Path f, Reporter reporter, FileStatus srcstat)
throws IOException {
if (destFileSys.exists(f)) {
destFileSys.delete(f, false);
}
if (!preserve_status) {
return destFileSys.create(f, true, sizeBuf, reporter);
}
FsPermission permission =
preseved.contains(FileAttribute.PERMISSION) ? srcstat.getPermission() : null;
short replication =
preseved.contains(FileAttribute.REPLICATION)
? srcstat.getReplication()
: destFileSys.getDefaultReplication();
long blockSize =
preseved.contains(FileAttribute.BLOCK_SIZE)
? srcstat.getBlockSize()
: destFileSys.getDefaultBlockSize();
return destFileSys.create(f, permission, true, sizeBuf, replication, blockSize, reporter);
}
private void generateGridItems(long newX, long newY) {
WVirtualImage.Rect newNb =
this.neighbourhood(newX, newY, this.viewPortWidth_, this.viewPortHeight_);
long i1 = newNb.x1 / this.gridImageSize_;
long j1 = newNb.y1 / this.gridImageSize_;
long i2 = newNb.x2 / this.gridImageSize_ + 1;
long j2 = newNb.y2 / this.gridImageSize_ + 1;
for (int invisible = 0; invisible < 2; ++invisible) {
for (long i = i1; i < i2; ++i) {
for (long j = j1; j < j2; ++j) {
long key = this.gridKey(i, j);
WImage it = this.grid_.get(key);
if (it == null) {
boolean v = this.visible(i, j);
if (v && !(invisible != 0) || !v && invisible != 0) {
long brx = i * this.gridImageSize_ + this.gridImageSize_;
long bry = j * this.gridImageSize_ + this.gridImageSize_;
brx = Math.min(brx, this.imageWidth_);
bry = Math.min(bry, this.imageHeight_);
WImage img =
this.createImage(
i * this.gridImageSize_,
j * this.gridImageSize_,
(int) (brx - i * this.gridImageSize_),
(int) (bry - j * this.gridImageSize_));
img.setAttributeValue("onmousedown", "return false;");
this.contents_.addWidget(img);
img.setPositionScheme(PositionScheme.Absolute);
img.setOffsets(new WLength((double) i * this.gridImageSize_), EnumSet.of(Side.Left));
img.setOffsets(new WLength((double) j * this.gridImageSize_), EnumSet.of(Side.Top));
this.grid_.put(key, img);
}
}
}
}
}
this.currentX_ = newX;
this.currentY_ = newY;
this.cleanGrid();
}
/** Inserts an empty column. */
public WTableColumn insertColumn(int column) {
for (int i = 0; i < this.rows_.size(); ++i) {
this.rows_.get(i).insertColumn(column);
}
WTableColumn tableColumn = null;
if ((int) column <= this.columns_.size()) {
tableColumn = new WTableColumn(this);
this.columns_.add(0 + column, tableColumn);
}
this.flags_.set(BIT_GRID_CHANGED);
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
return tableColumn;
}
static EnumSet<FileAttribute> parse(String s) {
if (s == null || s.length() == 0) {
return EnumSet.allOf(FileAttribute.class);
}
EnumSet<FileAttribute> set = EnumSet.noneOf(FileAttribute.class);
FileAttribute[] attributes = values();
for (char c : s.toCharArray()) {
int i = 0;
for (; i < attributes.length && c != attributes[i].symbol; i++) ;
if (i < attributes.length) {
if (!set.contains(attributes[i])) {
set.add(attributes[i]);
} else {
throw new IllegalArgumentException(
"There are more than one '" + attributes[i].symbol + "' in " + s);
}
} else {
throw new IllegalArgumentException("'" + c + "' in " + s + " is undefined.");
}
}
return set;
}
@Deprecated
public static void copy(
Configuration conf,
String srcPath,
String destPath,
Path logPath,
boolean srcAsList,
boolean ignoreReadFailures)
throws IOException {
final Path src = new Path(srcPath);
List<Path> tmp = new ArrayList<Path>();
if (srcAsList) {
tmp.addAll(fetchFileList(conf, src));
} else {
tmp.add(src);
}
EnumSet<Options> flags =
ignoreReadFailures
? EnumSet.of(Options.IGNORE_READ_FAILURES)
: EnumSet.noneOf(Options.class);
final Path dst = new Path(destPath);
copy(conf, new Arguments(tmp, dst, logPath, flags, null, Long.MAX_VALUE, Long.MAX_VALUE, null));
}
/**
* Move a table row from its original position to a new position.
*
* <p>The table expands automatically when the <code>to</code> row is beyond the current table
* dimensions.
*
* <p>
*
* @see WTable#moveColumn(int from, int to)
*/
public void moveRow(int from, int to) {
if (from < 0 || from >= (int) this.rows_.size()) {
logger.error(
new StringWriter()
.append("moveRow: the from index is not a valid row index.")
.toString());
return;
}
WTableRow from_tr = this.getRowAt(from);
this.rows_.remove(from_tr);
if (to > (int) this.rows_.size()) {
this.getRowAt(to);
}
this.rows_.add(0 + to, from_tr);
this.flags_.set(BIT_GRID_CHANGED);
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
}
/**
* Deletes a row and all its contents.
*
* <p>Rows below the given row are shifted up.
*/
public void deleteRow(int row) {
if (this.rowsChanged_ != null) {
this.rowsChanged_.remove(this.rows_.get(row));
if (this.rowsChanged_.isEmpty()) {;
this.rowsChanged_ = null;
}
}
for (int i = 0; i < this.getColumnCount(); ++i) {
WTableCell cell = this.rows_.get(row).cells_.get(i).cell;
if (cell != null) cell.remove();
}
if (row >= (int) (this.getRowCount() - this.rowsAdded_)) {
--this.rowsAdded_;
} else {
this.flags_.set(BIT_GRID_CHANGED);
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
}
;
this.rows_.remove(0 + row);
}
/**
* Adds a layout item to the grid.
*
* <p>Adds the <i>item</i> at (<i>row</i>, <code>column</code>). If an item was already added to
* that location, it is replaced (but not deleted).
*
* <p>An item may span several more rows or columns, which is controlled by <i>rowSpan</i> and
* <code>columnSpan</code>.
*
* <p>The <code>alignment</code> specifies the vertical and horizontal alignment of the item. The
* default value 0 indicates that the item is stretched to fill the entire grid cell. The
* alignment can be specified as a logical combination of a horizontal alignment ( {@link
* AlignmentFlag#AlignLeft}, {@link AlignmentFlag#AlignCenter}, or {@link
* AlignmentFlag#AlignRight}) and a vertical alignment ( {@link AlignmentFlag#AlignTop}, {@link
* AlignmentFlag#AlignMiddle}, or {@link AlignmentFlag#AlignBottom}).
*
* <p>
*
* @see WGridLayout#addLayout(WLayout layout, int row, int column, EnumSet alignment)
* @see WGridLayout#addWidget(WWidget widget, int row, int column, EnumSet alignment)
*/
public void addItem(
WLayoutItem item,
int row,
int column,
int rowSpan,
int columnSpan,
EnumSet<AlignmentFlag> alignment) {
columnSpan = Math.max(1, columnSpan);
rowSpan = Math.max(1, rowSpan);
this.expand(row, column, rowSpan, columnSpan);
final Grid.Item gridItem = this.grid_.items_.get(row).get(column);
if (gridItem.item_ != null) {
WLayoutItem oldItem = gridItem.item_;
gridItem.item_ = null;
this.updateRemoveItem(oldItem);
}
gridItem.item_ = item;
gridItem.rowSpan_ = rowSpan;
gridItem.colSpan_ = columnSpan;
gridItem.alignment_ = EnumSet.copyOf(alignment);
this.updateAddItem(item);
}
/**
* Move a table column from its original position to a new position.
*
* <p>The table expands automatically when the <code>to</code> column is beyond the current table
* dimensions.
*
* <p>
*
* @see WTable#moveRow(int from, int to)
*/
public void moveColumn(int from, int to) {
if (from < 0 || from >= (int) this.columns_.size()) {
logger.error(
new StringWriter()
.append("moveColumn: the from index is not a valid column index.")
.toString());
return;
}
WTableColumn from_tc = this.getColumnAt(from);
this.columns_.remove(from_tc);
if (to > (int) this.columns_.size()) {
this.getColumnAt(to);
}
this.columns_.add(0 + to, from_tc);
for (int i = 0; i < this.rows_.size(); i++) {
List<WTableRow.TableData> cells = this.rows_.get(i).cells_;
WTableRow.TableData cell = cells.get(from);
cells.remove(0 + from);
cells.add(0 + to, cell);
}
this.flags_.set(BIT_GRID_CHANGED);
this.repaint(EnumSet.of(RepaintFlag.RepaintInnerHtml));
}
public void resourceChanged() {
this.parent.sourcesChanged_ = true;
this.parent.repaint(EnumSet.of(RepaintFlag.RepaintPropertyAttribute));
}
/**
* Add a media source.
*
* <p>This method specifies a media source (which may be a URL or dynamic resource). You may add
* as many media sources as you want. The browser will select the appropriate media stream to
* display to the user.
*
* <p>This method specifies a media source using the URL, the mime type, and the media attribute.
* HTML allows for empty type and media attributes.
*/
public void addSource(WLink link, String type, String media) {
this.sources_.add(new WAbstractMedia.Source(this, link, type, media));
this.sourcesChanged_ = true;
this.repaint(EnumSet.of(RepaintFlag.RepaintPropertyAttribute));
}
/**
* Removes all source elements.
*
* <p>This method can be used to remove all media sources. Afterward, you may add new media
* sources with calls to {@link WAbstractMedia#addSource(WLink link, String type, String media)
* addSource()}.
*
* <p>Use this to reuse a {@link WAbstractMedia} instantiation to play something else.
*/
public void clearSources() {
for (int i = 0; i < this.sources_.size(); ++i) {;
}
this.sources_.clear();
this.repaint(EnumSet.of(RepaintFlag.RepaintPropertyAttribute));
}
/** Set the preload mode. */
public void setPreloadMode(WAbstractMedia.PreloadMode mode) {
this.preloadMode_ = mode;
this.preloadChanged_ = true;
this.repaint(EnumSet.of(RepaintFlag.RepaintPropertyAttribute));
}
/**
* Set the media element options.
*
* <p>Calls {@link #setOptions(EnumSet flags) setOptions(EnumSet.of(flag, flags))}
*/
public final void setOptions(WAbstractMedia.Options flag, WAbstractMedia.Options... flags) {
setOptions(EnumSet.of(flag, flags));
}
/**
* Set the media element options.
*
* <p>
*
* @see WAbstractMedia.Options
*/
public void setOptions(EnumSet<WAbstractMedia.Options> flags) {
this.flags_ = EnumSet.copyOf(flags);
this.flagsChanged_ = true;
this.repaint(EnumSet.of(RepaintFlag.RepaintPropertyAttribute));
}