protected String getRallyXML(String apiUrl) throws Exception {
String responseXML = "";
DefaultHttpClient httpClient = new DefaultHttpClient();
Base64 base64 = new Base64();
String encodeString =
new String(base64.encode((rallyApiHttpUsername + ":" + rallyApiHttpPassword).getBytes()));
HttpGet httpGet = new HttpGet(apiUrl);
httpGet.addHeader("Authorization", "Basic " + encodeString);
HttpResponse response = httpClient.execute(httpGet);
HttpEntity entity = response.getEntity();
if (entity != null) {
InputStreamReader reader = new InputStreamReader(entity.getContent());
BufferedReader br = new BufferedReader(reader);
StringBuilder sb = new StringBuilder();
String line = "";
while ((line = br.readLine()) != null) {
sb.append(line);
}
responseXML = sb.toString();
}
log.debug("responseXML=" + responseXML);
return responseXML;
}
@Override
protected Transferable createTransferable(JComponent c) {
JTextPane aTextPane = (JTextPane) c;
HTMLEditorKit kit = ((HTMLEditorKit) aTextPane.getEditorKit());
StyledDocument sdoc = aTextPane.getStyledDocument();
int sel_start = aTextPane.getSelectionStart();
int sel_end = aTextPane.getSelectionEnd();
int i = sel_start;
StringBuilder output = new StringBuilder();
while (i < sel_end) {
Element e = sdoc.getCharacterElement(i);
Object nameAttr = e.getAttributes().getAttribute(StyleConstants.NameAttribute);
int start = e.getStartOffset(), end = e.getEndOffset();
if (nameAttr == HTML.Tag.BR) {
output.append("\n");
} else if (nameAttr == HTML.Tag.CONTENT) {
if (start < sel_start) {
start = sel_start;
}
if (end > sel_end) {
end = sel_end;
}
try {
String str = sdoc.getText(start, end - start);
output.append(str);
} catch (BadLocationException ble) {
Debug.error(me + "Copy-paste problem!\n%s", ble.getMessage());
}
}
i = end;
}
return new StringSelection(output.toString());
}
/**
* Removes comments from the specified string and returns the first characters of a query.
*
* @param qu query string
* @param max maximum length of string to return
* @return result
*/
public static String removeComments(final String qu, final int max) {
final StringBuilder sb = new StringBuilder();
int m = 0;
boolean s = false;
final int cl = qu.length();
for (int c = 0; c < cl && sb.length() < max; ++c) {
final char ch = qu.charAt(c);
if (ch == 0x0d) continue;
if (ch == '(' && c + 1 < cl && qu.charAt(c + 1) == ':') {
if (m == 0 && !s) {
sb.append(' ');
s = true;
}
++m;
++c;
} else if (m != 0 && ch == ':' && c + 1 < cl && qu.charAt(c + 1) == ')') {
--m;
++c;
} else if (m == 0) {
if (ch > ' ') sb.append(ch);
else if (!s) sb.append(' ');
s = ch <= ' ';
}
}
if (sb.length() >= max) sb.append("...");
return sb.toString().trim();
}
/**
* Returns a map with variable bindings.
*
* @param opts main options
* @return bindings
*/
public static HashMap<String, String> bindings(final MainOptions opts) {
final HashMap<String, String> bindings = new HashMap<>();
final String bind = opts.get(MainOptions.BINDINGS).trim();
final StringBuilder key = new StringBuilder();
final StringBuilder val = new StringBuilder();
boolean first = true;
final int sl = bind.length();
for (int s = 0; s < sl; s++) {
final char ch = bind.charAt(s);
if (first) {
if (ch == '=') {
first = false;
} else {
key.append(ch);
}
} else {
if (ch == ',') {
if (s + 1 == sl || bind.charAt(s + 1) != ',') {
bindings.put(key.toString().trim(), val.toString());
key.setLength(0);
val.setLength(0);
first = true;
continue;
}
// literal commas are escaped by a second comma
s++;
}
val.append(ch);
}
}
if (key.length() != 0) bindings.put(key.toString().trim(), val.toString());
return bindings;
}
public String _range(String args[]) {
verifyCommand(args, _rangeHelp, _rangePattern, 2, 3);
Version version = null;
if (args.length >= 3) version = new Version(args[2]);
else {
String v = domain.getProperty("@");
if (v == null) return null;
version = new Version(v);
}
String spec = args[1];
Matcher m = RANGE_MASK.matcher(spec);
m.matches();
String floor = m.group(1);
String floorMask = m.group(2);
String ceilingMask = m.group(3);
String ceiling = m.group(4);
String left = version(version, floorMask);
String right = version(version, ceilingMask);
StringBuilder sb = new StringBuilder();
sb.append(floor);
sb.append(left);
sb.append(",");
sb.append(right);
sb.append(ceiling);
String s = sb.toString();
VersionRange vr = new VersionRange(s);
if (!(vr.includes(vr.getHigh()) || vr.includes(vr.getLow()))) {
domain.error(
"${range} macro created an invalid range %s from %s and mask %s", s, version, spec);
}
return sb.toString();
}
public static void verifyCommand(
String args[],
@SuppressWarnings("unused") String help,
Pattern[] patterns,
int low,
int high) {
String message = "";
if (args.length > high) {
message = "too many arguments";
} else if (args.length < low) {
message = "too few arguments";
} else {
for (int i = 0; patterns != null && i < patterns.length && i < args.length; i++) {
if (patterns[i] != null) {
Matcher m = patterns[i].matcher(args[i]);
if (!m.matches())
message +=
String.format(
"Argument %s (%s) does not match %s%n", i, args[i], patterns[i].pattern());
}
}
}
if (message.length() != 0) {
StringBuilder sb = new StringBuilder();
String del = "${";
for (String arg : args) {
sb.append(del);
sb.append(arg);
del = ";";
}
sb.append("}, is not understood. ");
sb.append(message);
throw new IllegalArgumentException(sb.toString());
}
}
/**
* If the outbound level is BINARY, convert the string field to binary, then pad to the left with
* the appropriate number of zero bits to reach a number of bits specified by the bitLength
* attribute of the TDT definition file.
*/
private void binaryPadding(Map<String, String> extraparams, Field tdtfield) {
String fieldname = tdtfield.getName();
int reqbitlength = tdtfield.getBitLength();
String value;
String binaryValue = fieldToBinary(tdtfield, extraparams);
if (binaryValue.length() < reqbitlength) {
int extraBitLength = reqbitlength - binaryValue.length();
StringBuilder zeroPaddedBinaryValue = new StringBuilder("");
for (int i = 0; i < extraBitLength; i++) {
zeroPaddedBinaryValue.append("0");
}
zeroPaddedBinaryValue.append(binaryValue);
value = zeroPaddedBinaryValue.toString();
} else {
if (binaryValue.length() > reqbitlength)
throw new TDTException(
"Binary value ["
+ binaryValue
+ "] for field "
+ fieldname
+ " exceeds maximum allowed "
+ reqbitlength
+ " bits. Decimal value was "
+ extraparams.get(fieldname));
value = binaryValue;
}
extraparams.put(fieldname, value);
}
public String getCoordinates(RevisionRef r) {
StringBuilder sb = new StringBuilder(r.groupId).append(":").append(r.artifactId).append(":");
if (r.classifier != null) sb.append(r.classifier).append("@");
sb.append(r.version);
return sb.toString();
}
private static String convert(List<List<Particle>> lists) {
StringBuilder sb = new StringBuilder();
for (List<Particle> list : lists) {
if (list.isEmpty()) sb.append('.');
else sb.append('X');
}
return sb.toString();
}
/** Takes a string and hides its extension */
public static String hideExtension(final String str) {
String[] arr = str.split("\\.");
if (arr.length <= 1) return str; // there was no "." in str.
StringBuilder sb = new StringBuilder("");
for (int i = 0; i < arr.length - 1; ++i) {
if (sb.length() > 0) sb.append(".");
sb.append(arr[i]);
}
return sb.toString();
}
private static String expand(String str) {
if (str == null) {
return null;
}
StringBuilder result = new StringBuilder();
Pattern re = Pattern.compile("^(.*?)\\$\\{([^}]*)\\}(.*)");
while (true) {
Matcher matcher = re.matcher(str);
if (matcher.matches()) {
result.append(matcher.group(1));
String property = matcher.group(2);
if (property.equals("/")) {
property = "file.separator";
}
String value = System.getProperty(property);
if (value != null) {
result.append(value);
}
str = matcher.group(3);
} else {
result.append(str);
break;
}
}
return result.toString();
}
public String toString() {
StringBuilder sb = new StringBuilder(this.getClass().getSimpleName()).append('{');
for (TypedValues typed : _values) {
sb.append(typed);
}
return sb.append('}').toString();
}
@SuppressWarnings("deprecation")
public void testAllResolved() {
assertNotNull("Expected a Bundle Context", context);
StringBuilder sb = new StringBuilder();
for (Bundle b : context.getBundles()) {
if (b.getState() == Bundle.INSTALLED
&& b.getHeaders().get(aQute.bnd.osgi.Constants.FRAGMENT_HOST) == null) {
try {
b.start();
} catch (BundleException e) {
sb.append(b.getBundleId())
.append(" ")
.append(b.getSymbolicName())
.append(";")
.append(b.getVersion())
.append("\n");
sb.append(" ").append(e.getMessage()).append("\n\n");
System.err.println(e.getMessage());
}
}
}
Matcher matcher = IP_P.matcher(sb);
String out =
matcher.replaceAll(
"\n\n " + aQute.bnd.osgi.Constants.IMPORT_PACKAGE + ": $1;version=[$2,$3)\n");
assertTrue("Unresolved bundles\n" + out, sb.length() == 0);
}
private String blankSectionHeaders(String markup, StringBuffer context) {
Pattern p = Pattern.compile("(={2,})([^=]+)\\1");
Matcher m = p.matcher(markup);
int lastPos = 0;
StringBuilder sb = new StringBuilder();
while (m.find()) {
sb.append(markup.substring(lastPos, m.start()));
sb.append(getSpaceString(m.group().length()));
String title = m.group(2).trim();
if (!title.equalsIgnoreCase("see also")
&& !title.equalsIgnoreCase("external links")
&& !title.equalsIgnoreCase("references")
&& !title.equalsIgnoreCase("further reading")) context.append("\n").append(title);
lastPos = m.end();
}
sb.append(markup.substring(lastPos));
return sb.toString();
}
protected void executeQuery(Statement stmt, String q) throws SQLException {
q = q.replace("$PREFIX", getPrefix());
LOG.info(" Executing " + q);
ResultSet rs = stmt.executeQuery(q);
StringBuilder header = new StringBuilder();
for (int i = 1; i <= rs.getMetaData().getColumnCount(); i++) {
if (i > 1) {
header.append("|");
}
header.append(rs.getMetaData().getColumnName(i));
}
LOG.info(header);
int seq = 0;
while (true) {
boolean valid = rs.next();
if (!valid) break;
seq++;
StringBuilder line = new StringBuilder();
for (int i = 1; i <= rs.getMetaData().getColumnCount(); i++) {
if (i > 1) {
line.append("|");
}
line.append(rs.getString(i));
}
LOG.info(seq + ":" + line);
}
}
private void appendTestMethod(@Nonnull StackTraceElement current) {
content.append(" <li>");
content.append(current.getClassName()).append('#');
content
.append(LESS_THAN_CHAR.matcher(current.getMethodName()).replaceFirst("<"))
.append(": ");
content.append(current.getLineNumber());
}
protected void selected(CharPos start, CharPos end) {
StringBuilder buf = new StringBuilder();
synchronized (msgs) {
boolean sel = false;
for (Message msg : msgs) {
if (!(msg.text() instanceof RichText)) continue;
RichText rt = (RichText) msg.text();
RichText.Part part = null;
if (sel) {
part = rt.parts;
} else if (msg == start.msg) {
sel = true;
for (part = rt.parts; part != null; part = part.next) {
if (part == start.part) break;
}
}
if (sel) {
for (; part != null; part = part.next) {
if (!(part instanceof RichText.TextPart)) continue;
RichText.TextPart tp = (RichText.TextPart) part;
CharacterIterator iter = tp.ti();
int sch;
if (tp == start.part) sch = tp.start + start.ch.getInsertionIndex();
else sch = tp.start;
int ech;
if (tp == end.part) ech = tp.start + end.ch.getInsertionIndex();
else ech = tp.end;
for (int i = sch; i < ech; i++) buf.append(iter.setIndex(i));
if (part == end.part) {
sel = false;
break;
}
buf.append(' ');
}
if (sel) buf.append('\n');
}
if (msg == end.msg) break;
}
}
Clipboard cl;
if ((cl = java.awt.Toolkit.getDefaultToolkit().getSystemSelection()) == null)
cl = java.awt.Toolkit.getDefaultToolkit().getSystemClipboard();
try {
final CharPos ownsel = selstart;
cl.setContents(
new StringSelection(buf.toString()),
new ClipboardOwner() {
public void lostOwnership(Clipboard cl, Transferable tr) {
if (selstart == ownsel) selstart = selend = null;
}
});
} catch (IllegalStateException e) {
}
}
public String toString() {
StringBuilder sb = new StringBuilder();
for (int i = 0; i < urls.size(); i++) {
if (i > 0) {
sb.append("|");
}
sb.append(
String.format("%d,%d=\"%s\"", locations.get(i)[0], locations.get(i)[1], urls.get(i)));
}
return sb.toString();
}
private void end(StringBuilder ans, Pretty pretty, String indent) {
if (endEncloser == null) return;
if (!pretty.pretty) ans.append(endEncloser);
else {
Utilities.assureEndsWithNewLine(ans);
ans.append(indent + endEncloser);
if (pretty.comments && endComment.length() > 0) ans.append("#" + endComment);
Utilities.assureEndsWithNewLine(ans);
}
}
/**
* Pads a binary value supplied as a string first parameter to the left with leading zeros in
* order to reach a required number of bits, as expressed by the second parameter, reqlen. Returns
* a string value corresponding to the binary value left padded to the required number of bits.
*/
private String padBinary(String binary, int reqlen) {
String rv;
int l = binary.length();
int pad = (reqlen - (l % reqlen)) % reqlen;
StringBuilder buffer = new StringBuilder("");
for (int i = 0; i < pad; i++) {
buffer.append("0");
}
buffer.append(binary);
rv = buffer.toString();
return rv;
}
private void start(StringBuilder ans, Pretty pretty, String indent) {
if (startEncloser == null) return;
if (!pretty.pretty) {
ans.append(startEncloser);
} else {
String comment;
if (pretty.comments && startComment.length() > 0) comment = " #" + startComment;
else comment = "";
ans.append(indent + startEncloser + comment);
Utilities.assureEndsWithNewLine(ans);
}
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
String del = "[";
for (Link r = this; r != null; r = r.previous) {
sb.append(del);
sb.append(r.key);
del = ",";
}
sb.append("]");
return sb.toString();
}
// Derived from http://stackoverflow.com/a/3054692/250076
public static File getRelativeFile(File targetFile, File baseFile) {
try {
targetFile = targetFile.getCanonicalFile();
baseFile = baseFile.getCanonicalFile();
} catch (IOException ignored) {
}
String pathSeparator = File.separator;
String basePath = baseFile.getAbsolutePath();
String normalizedTargetPath = normalize(targetFile.getAbsolutePath(), pathSeparator);
String normalizedBasePath = normalize(basePath, pathSeparator);
String[] base = normalizedBasePath.split(Pattern.quote(pathSeparator));
String[] target = normalizedTargetPath.split(Pattern.quote(pathSeparator));
StringBuilder common = new StringBuilder();
int commonIndex = 0;
while (commonIndex < target.length
&& commonIndex < base.length
&& target[commonIndex].equals(base[commonIndex])) {
common.append(target[commonIndex]).append(pathSeparator);
commonIndex++;
}
if (commonIndex == 0) {
throw new Error(
"No common path element found for '"
+ normalizedTargetPath
+ "' and '"
+ normalizedBasePath
+ '\'');
}
boolean baseIsFile = true;
if (baseFile.exists()) {
baseIsFile = baseFile.isFile();
} else if (basePath.endsWith(pathSeparator)) {
baseIsFile = false;
}
StringBuilder relative = new StringBuilder();
if (base.length != commonIndex) {
int numDirsUp = baseIsFile ? base.length - commonIndex - 1 : base.length - commonIndex;
for (int i = 0; i < numDirsUp; i++) {
relative.append("..").append(pathSeparator);
}
}
relative.append(normalizedTargetPath.substring(common.length()));
return new File(relative.toString());
}
protected String replace(String key, Link link) {
if (link != null && link.contains(key)) return "${infinite:" + link.toString() + "}";
if (key != null) {
key = key.trim();
if (key.length() > 0) {
Processor source = domain;
String value = null;
if (key.indexOf(';') < 0) {
Instruction ins = new Instruction(key);
if (!ins.isLiteral()) {
SortedList<String> sortedList = SortedList.fromIterator(domain.iterator());
StringBuilder sb = new StringBuilder();
String del = "";
for (String k : sortedList) {
if (ins.matches(k)) {
String v = replace(k, new Link(source, link, key));
if (v != null) {
sb.append(del);
del = ",";
sb.append(v);
}
}
}
return sb.toString();
}
}
while (value == null && source != null) {
value = source.getProperties().getProperty(key);
source = source.getParent();
}
if (value != null) return process(value, new Link(source, link, key));
value = doCommands(key, link);
if (value != null) return process(value, new Link(source, link, key));
if (key != null && key.trim().length() > 0) {
value = System.getProperty(key);
if (value != null) return value;
}
if (!flattening && !key.equals("@"))
domain.warning("No translation found for macro: " + key);
} else {
domain.warning("Found empty macro key");
}
} else {
domain.warning("Found null macro key");
}
return "${" + key + "}";
}
/**
* Returns a string built using a particular grammar. Single-quotes strings are counted as literal
* strings, whereas all other strings appearing in the grammar require substitution with the
* corresponding value from the extraparams hashmap.
*/
private String buildGrammar(String grammar, Map<String, String> extraparams) {
StringBuilder outboundstring = new StringBuilder();
String[] fields = Pattern.compile("\\s+").split(grammar);
for (int i = 0; i < fields.length; i++) {
if (fields[i].substring(0, 1).equals("'")) {
outboundstring.append(fields[i].substring(1, fields[i].length() - 1));
} else {
outboundstring.append(extraparams.get(fields[i]));
}
}
return outboundstring.toString();
}
/**
* returns the multiple alignment as a string in a fashion identical to that in a file of
* ALN/CLUSTALW format (except from the fact that info about residues' match is missing. Aka, the
* 3rd line of a file of ALN/CLUSTALW ('*', '.', ':' chars) is missing).
*
* <p>(Note: CLUSTALW doesn't necessarily have the match characters... -Tim)
*/
public String toString() {
StringBuilder sb = new StringBuilder();
int tl = maxTagLength();
int i = 0, last = gappedAlignments.keySet().size() - 1;
for (String tag : gappedAlignments.keySet()) {
sb.append(StringUtils.padString(tag, tl));
sb.append(" ");
sb.append(gappedAlignments.get(tag).gappedString());
if (i < last) {
sb.append("\n");
}
i += 1;
}
return sb.toString();
}
@Override
public synchronized void run() {
while (!quit) {
// filter_input();
try {
Thread.sleep(1); // poll at 1kHz
// grab data from shared buffer and move it the local one
ourBuffer.append(sharedBuffer.take());
// System.out.print(ourBuffer);
// create a matcher to find an open tag in the buffer
int endCloseTag;
int startOpenTag;
Matcher closeTagMatcher = closeTagPattern.matcher(ourBuffer);
// look or a closing tag in our buffer
if (closeTagMatcher.find()) {
endCloseTag = closeTagMatcher.end();
openTag = "<" + ourBuffer.charAt(closeTagMatcher.start() + 2) + ">";
// find corresponding opening tag
startOpenTag = ourBuffer.indexOf(openTag);
// send the input string to the GUI for processing
if (startOpenTag >= 0 && startOpenTag < endCloseTag) {
gui.incoming(ourBuffer.substring(startOpenTag, endCloseTag));
// clear our buffer
ourBuffer.delete(startOpenTag, endCloseTag);
} else {
ourBuffer.delete(0, endCloseTag);
}
}
} catch (Exception e) {
System.out.print(e + "\n");
}
}
}
static String outputOf(Reader r) throws IOException {
final StringBuilder sb = new StringBuilder();
final char[] buf = new char[1024];
int n;
while ((n = r.read(buf)) > 0) sb.append(buf, 0, n);
return sb.toString();
}
private String getAuthorizeUrl() {
StringBuilder url = new StringBuilder();
url.append(this.service_.getAuthorizationEndpoint());
boolean hasQuery = url.toString().indexOf('?') != -1;
url.append(hasQuery ? '&' : '?')
.append("client_id=")
.append(Utils.urlEncode(this.service_.getClientId()))
.append("&redirect_uri=")
.append(Utils.urlEncode(this.service_.getGenerateRedirectEndpoint()))
.append("&scope=")
.append(Utils.urlEncode(this.scope_))
.append("&response_type=code")
.append("&state=")
.append(Utils.urlEncode(this.oAuthState_));
return url.toString();
}
private void appendRepetitionCountIfNeeded(@Nonnull CallPoint callPoint) {
int repetitionCount = callPoint.getRepetitionCount();
if (repetitionCount > 0) {
content.append('x').append(1 + repetitionCount);
}
}