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(
"${range} macro created an invalid range %s from %s and mask %s", s, version, spec);
}
return sb.toString();
}
@Override
public void processingInstruction(String target, String data) throws SAXException {
_logger.fine("Processing Instruction " + target);
_logger.fine("Processing Instruction data: " + data);
if (target.equals("assemble")) {
if (!_stack.isEmpty()) {
ElementInfo element = _stack.get(_stack.size() - 1);
Matcher matcher = PROCESSING_INSTRUCTION.matcher(data);
while (matcher.find()) {
if (matcher.groupCount() == 2) {
String name = matcher.group(1);
if (name.charAt(0) == '@') {
element.inst.put(name, matcher.group(2));
} else {
element.args.add(guessUntypedValue(name, matcher.group(2)));
}
_logger.fine(
"Processing Instruction for "
+ element.data.getClass()
+ "\n\ttarget = "
+ target
+ "\n\t"
+ name
+ "="
+ matcher.group(2));
}
}
}
}
}
public void testBaseUrlPath() throws Exception {
sau1 = setupSimAu(simAuConfig(tempDirPath));
createContent(sau1);
crawlContent(sau1);
CachedUrlSet cus1 = sau1.getAuCachedUrlSet();
tempDirPath2 = getTempDir().getAbsolutePath() + File.separator;
Configuration config2 = simAuConfig(tempDirPath2);
config2.put("base_url", "http://anotherhost.org/some/path/");
SimulatedArchivalUnit sau2 = setupSimAu(config2);
createContent(sau2);
crawlContent(sau2);
CachedUrlSet cus2 = sau1.getAuCachedUrlSet();
List urls1 = auUrls(sau1);
List urls2 = auUrls(sau2);
Pattern pat1 = Pattern.compile("http://www\\.example\\.com(/.*)$");
Pattern pat2 = Pattern.compile("http://anotherhost\\.org/some/path(/.*)$");
List<String> l1 = auUrls(sau1);
List<String> l2 = auUrls(sau2);
assertEquals(l1.size(), l2.size());
for (int ix = 0; ix < l1.size(); ix++) {
Matcher m1 = pat1.matcher(l1.get(ix));
assertTrue(m1.matches());
Matcher m2 = pat2.matcher(l2.get(ix));
assertTrue(m2.matches());
assertEquals(m1.group(1), m2.group(1));
}
}
/**
* Get dependencies of a source file.
*
* @param path The canonical path of source file.
* @return Path of dependencies.
*/
private ArrayList<String> getDependencies(String path) {
if (!dependenceMap.containsKey(path)) {
ArrayList<String> dependencies = new ArrayList<String>();
Matcher m = PATTERN_REQUIRE.matcher(read(path, charset));
while (m.find()) {
// Decide which root path to use.
// Path wrapped in <> is related to root path.
// Path wrapped in "" is related to parent folder of the source file.
String root = null;
if (m.group(1).equals("<")) {
root = this.root;
} else {
root = new File(path).getParent();
}
// Get path of required file.
String required = m.group(2);
File f = new File(root, required);
if (f.exists()) {
dependencies.add(canonize(f));
} else {
App.exit("Cannot find required file " + required + " in " + path);
}
}
dependenceMap.put(path, dependencies);
}
return dependenceMap.get(path);
}
/**
* Leave only the value for RCS keywords.
*
* <p>For example, <code>$Revision: 1.1 $</code> becomes <code>1.0</code>.
*/
public String replaceRcsKeywords(String text) {
if (matcher == null) {
matcher =
Pattern.compile(
"\\$(Author|Date|Header|Id|Locker|Log|Name|RCSFile|Revision|Source|State): (.+?) \\$")
.matcher(text);
} else {
matcher.reset(text);
}
StringBuffer buffer = new StringBuffer();
while (matcher.find()) {
String string = matcher.group(2);
// For the Date: keyword, have a shot at reformatting string
if ("Date".equals(matcher.group(1))) {
try {
DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
Date date = dateFormat.parse(string);
string = date.toString();
} catch (ParseException e) {
} // if we can't parse, return unchanged
}
matcher.appendReplacement(buffer, string);
}
matcher.appendTail(buffer);
return buffer.toString();
}
protected Map<String, String> getAttributes() {
if (attributes != null) {
return attributes;
}
attributes = new HashMap<String, String>();
matcher = ADDITIONAL_ATTRIBUTES_PATTERN.matcher(firstLine);
if (matcher.find()) {
String s;
Matcher attributeMatcher;
s = matcher.group(2);
attributeMatcher = ADDITIONAL_ATTRIBUTE_PATTERN.matcher(s);
while (attributeMatcher.find()) {
String key;
String value;
key = attributeMatcher.group(1);
value = attributeMatcher.group(2);
attributes.put(key.toLowerCase(Locale.ENGLISH), value);
}
}
return attributes;
}
public boolean checkCondition(String format, ScoreBoardEvent event) {
boolean triggerCondition = true;
Matcher m = conditionPattern.matcher(format);
if (!m.find()) throw new IllegalArgumentException("No conditions in format : " + format);
do {
String specifier = m.group(1);
String comparator = m.group(2);
String targetValue = m.group(3);
if (null == comparator || null == targetValue) continue;
String value = scoreBoardValues.get(specifier).getValue();
if (triggerCondition) {
triggerCondition = false;
// If current trigger event value == previous value after processing
// (e.g. conversion to min:sec) then ignore, to prevent multiple consecutive
// identical triggers
if (value.equals(
scoreBoardValues.get(specifier).getPreviousValue(event.getPreviousValue())))
return false;
}
try {
if (!checkConditionValue(value, comparator, targetValue)) return false;
} catch (IllegalArgumentException iaE) {
return false;
}
} while (m.find());
return true;
}
private InstanceList readFile() throws IOException {
String NL = System.getProperty("line.separator");
Scanner scanner = new Scanner(new FileInputStream(fileName), encoding);
ArrayList<Pipe> pipeList = new ArrayList<Pipe>();
pipeList.add(new CharSequence2TokenSequence(Pattern.compile("\\p{L}\\p{L}+")));
pipeList.add(new TokenSequence2FeatureSequence());
InstanceList testing = new InstanceList(new SerialPipes(pipeList));
try {
while (scanner.hasNextLine()) {
String text = scanner.nextLine();
text = text.replaceAll("\\x0d", "");
Pattern patten = Pattern.compile("^(.*?),(.*?),(.*)$");
Matcher matcher = patten.matcher(text);
if (matcher.find()) {
docIds.add(matcher.group(1));
testing.addThruPipe(new Instance(matcher.group(3), null, "test instance", null));
}
}
} finally {
scanner.close();
}
return testing;
}
private static String expand(String str) {
if (str == null) {
return null;
}
StringBuilder result = new StringBuilder();
Pattern re = Pattern.compile("^(.*?)\\$\\{([^}]*)\\}(.*)");
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 Coords(String entry) {
Matcher m = coordsPattern.matcher(entry);
if (!m.matches()) {
throw new IllegalArgumentException(entry);
}
chrom = m.group(1);
start = Integer.parseInt(m.group(2));
end = Integer.parseInt(m.group(3));
strand = m.group(4).charAt(0);
}
public static int[] decodePrimerName(String pname) {
Matcher m = primerNamePattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
int[] a = new int[3];
a[0] = Integer.parseInt(m.group(1));
a[1] = Integer.parseInt(m.group(2));
a[2] = Integer.parseInt(m.group(3));
return a;
}
/**
* Initializes the date format.
*
* @param d input
* @param e example format
* @param ii input info
* @throws QueryException query exception
*/
final void date(final byte[] d, final String e, final InputInfo ii) throws QueryException {
final Matcher mt = DATE.matcher(Token.string(d).trim());
if (!mt.matches()) throw dateError(d, e, ii);
yea = toLong(mt.group(1), false, ii);
// +1 is added to BC values to simplify computations
if (yea < 0) yea++;
mon = (byte) (Strings.toInt(mt.group(3)) - 1);
day = (byte) (Strings.toInt(mt.group(4)) - 1);
if (mon < 0 || mon >= 12 || day < 0 || day >= dpm(yea, mon)) throw dateError(d, e, ii);
if (yea <= MIN_YEAR || yea > MAX_YEAR) throw DATERANGE_X_X.get(ii, type, chop(d, ii));
zone(mt, 5, d, ii);
}
/**
* Initializes the timezone.
*
* @param matcher matcher
* @param pos first matching position
* @param value value
* @param ii input info
* @throws QueryException query exception
*/
final void zone(final Matcher matcher, final int pos, final byte[] value, final InputInfo ii)
throws QueryException {
final String z = matcher.group(pos);
if (z == null) return;
if ("Z".equals(z)) {
tz = 0;
} else {
final int th = Strings.toInt(matcher.group(pos + 2));
final int tm = Strings.toInt(matcher.group(pos + 3));
if (th > 14 || tm > 59 || th == 14 && tm != 0) throw INVALIDZONE_X.get(ii, value);
final int mn = th * 60 + tm;
tz = (short) ("-".equals(matcher.group(pos + 1)) ? -mn : mn);
}
}
public void _sendString(String text) {
if (writeCommand == null) return;
/* intercept sessions -i and deliver it to a listener within armitage */
if (sessionListener != null) {
Matcher m = interact.matcher(text);
if (m.matches()) {
sessionListener.actionPerformed(new ActionEvent(this, 0, m.group(1)));
return;
}
}
Map read = null;
try {
synchronized (this) {
if (window != null && echo) {
window.append(window.getPromptText() + text);
}
}
if ("armitage.push".equals(writeCommand)) {
read = (Map) connection.execute(writeCommand, new Object[] {session, text});
} else {
connection.execute(writeCommand, new Object[] {session, text});
read = readResponse();
}
processRead(read);
fireSessionWroteEvent(text);
} catch (Exception ex) {
ex.printStackTrace();
}
}
public static String getChrom(String chromName) {
Matcher m = chromPattern.matcher(chromName);
if (!m.matches()) {
return chromName;
}
return m.group(1);
}
/**
* Import an XQuery library module from the given document. The namespace and preferred prefix of
* the module are extracted from the module itself. The MIME type of the document is set to
* "application/xquery" as a side-effect.
*
* @param module the non-XML document that holds the library module's source
* @return this service, to chain calls
* @throws DatabaseException if the module is an XML document, or the module declaration cannot be
* found at the top of the document
*/
public QueryService importModule(Document module) {
if (module instanceof XMLDocument)
throw new DatabaseException("module cannot be an XML document: " + module);
Matcher matcher = MODULE_DECLARATION_DQUOTE.matcher(module.contentsAsString());
if (!matcher.find()) {
matcher = MODULE_DECLARATION_SQUOTE.matcher(module.contentsAsString());
if (!matcher.find())
throw new DatabaseException("couldn't find a module declaration at the top of " + module);
}
module.metadata().setMimeType("application/xquery");
String moduleNamespace = matcher.group(1);
// TODO: should do URILiteral processing here to replace entity and character references and
// normalize
// whitespace, but since it seems that eXist doesn't do it either (bug?) there's no reason to
// rush.
Document prevModule = moduleMap.get(moduleNamespace);
if (prevModule != null && !prevModule.equals(module))
throw new DatabaseException(
"module "
+ moduleNamespace
+ " already bound to "
+ prevModule
+ ", can't rebind to "
+ module);
moduleMap.put(moduleNamespace, module);
return this;
}
/**
* Takes a line and looks for an archive request tag. If one is found, the information from the
* tag is returned as an <CODE>ArchiveRequest</CODE>. If a tag is found, the data in the tag is
* stored in the <CODE>HashMap</CODE> provided.
*
* @param currentLine The line in which to look for the archive tag.
* @param group The <CODE>ArchiveGroup</CODE> to which to add the <CODE>ArchiveRequest</CODE>. Can
* be <CODE>null</CODE>.
* @param template The <CODE>Template</CODE> to which the <CODE>ArchiveRequest</CODE> belongs.
* @return The archive request tag data as an instance of <CODE>ArchiveRequest</CODE>, <CODE>null
* </CODE> if the line passed in does not contain an arFile tag.
*/
private ArchiveRequest parseArchiveRequestTag(
String currentLine, ArchiveGroup group, Template template) {
ArchiveRequest archiveTag;
Matcher currentMatcher = archiveRequestPattern.matcher(currentLine);
if (currentMatcher.find()) {
String fileName = currentMatcher.group(1);
archiveTag = template.getArchiveRequest(fileName);
if (archiveTag == null) {
archiveTag = new ArchiveRequest(fileName);
template.addArchiveRequest(archiveTag);
}
if (group != null) {
// Creating a new request object because the requests
// in the groups flagged as not in database will mean the
// group - request association is not in database. Requests
// in the archiveRequests map flagged as not in database
// means the request record is not there.
String requestFileName = archiveTag.getFileName();
String requestFileLocation = archiveTag.getFileLocation();
ArchiveRequest groupRequest = new ArchiveRequest(requestFileLocation, requestFileName);
group.addArchiveRequest(groupRequest);
}
} else archiveTag = null;
return archiveTag;
}
public static String removePrimerLR(String pname) {
Matcher m = primerLRPattern.matcher(pname);
if (!m.matches()) {
throw new IllegalArgumentException(pname);
}
return m.group(1);
}
public String parse(String format) {
StringBuffer buffer = new StringBuffer();
Matcher m = formatPattern.matcher(format);
while (m.find()) m.appendReplacement(buffer, getFormatSpecifierValue(m.group()));
m.appendTail(buffer);
return buffer.toString();
}
/**
* Takes a line and looks for an archive tag. If one is found, the information from the tag is
* returned as a <CODE>Signal</CODE>. If a signal ID is given in the tag, the data in the tag is
* stored in the <CODE>HashMap</CODE> provided.
*
* @param currentLine The line in which to look for the archive tag.
* @return The archive tag data as an instance of <CODE>Signal</CODE>, <CODE>null</CODE> if the
* line passed in does not contain an arReq tag.
*/
private Signal parseArchiveTag(String currentLine) {
Signal archiveTag;
Matcher currentMatcher = archivePattern.matcher(currentLine);
if (currentMatcher.find()) {
archiveTag = new Signal(currentMatcher.group(1));
String frequency = currentMatcher.group(2);
BigDecimal frequencyValue;
if (frequency == null) frequencyValue = null;
else frequencyValue = new BigDecimal(frequency);
archiveTag.setArchiveFrequency(frequencyValue);
String type = currentMatcher.group(3);
if (type == null) type = "Monitor";
archiveTag.setArchiveType(type);
archiveTag.setArchiveIndicator("Y");
} else archiveTag = null;
return archiveTag;
}
/**
* Initializes the time format.
*
* @param d input format
* @param e expected format
* @param ii input info
* @throws QueryException query exception
*/
final void time(final byte[] d, final String e, final InputInfo ii) throws QueryException {
final Matcher mt = TIME.matcher(Token.string(d).trim());
if (!mt.matches()) throw dateError(d, e, ii);
hou = (byte) Strings.toInt(mt.group(1));
min = (byte) Strings.toInt(mt.group(2));
sec = toDecimal(mt.group(3), false, ii);
if (min >= 60
|| sec.compareTo(BD60) >= 0
|| hou > 24
|| hou == 24 && (min > 0 || sec.compareTo(BigDecimal.ZERO) > 0)) throw dateError(d, e, ii);
zone(mt, 5, d, ii);
if (hou == 24) {
hou = 0;
add(DAYSECONDS);
}
}
private void addNonTerminal(String EBNF) {
String p = "<([\\w-]+)>[\\s]*::=(" + "([\\s]*(<[\\w-]+>|(\"[^\"]*\")|[|\\[\\]{}])" + ")+)";
Matcher m = Pattern.compile(p).matcher(EBNF);
m.find();
NonTerminal nt = new NonTerminal(m.group(1));
List<? extends EBNFBranch> branches = EBNFBranch.getBranches(m.group(2));
assert (branches.size() > 0);
if (nonTerminals.size() == 0) {
startSymbol = nt;
}
nonTerminals.put(nt, branches);
}
public String getArtifactIdFromCoord(String coord) {
Matcher m = COORD_P.matcher(coord);
if (m.matches()) {
return m.group(2);
} else {
return null;
}
}
/**
* Replaces instances of Java reserved words that could not appear in a valid Java condition or
* Java variable name that are being used as variable names in string.
*
* @param string the string in which the Java reserved words should be replaced.
* @return string with the Java reserved words replaced with a substitute names.
*/
private static String replaceReservedWords(String string) {
// cheap hack so that pattern never need to look for a key word at
// the beginning or end of string. That way one may simplify the pattern
// to looking for a reserved word that is not prefixed or suffix with a
// letter or number.
string = "(" + string + ")";
for (int i = 0; i < reservedWords.length; i++) {
String reservedWord = reservedWords[i];
Pattern p = Pattern.compile("([\\W])(" + reservedWord + ")([\\W])");
Matcher m = p.matcher(string);
while (m.find()) {
string = m.replaceFirst(m.group(1) + "daikon" + reservedWord + m.group(3));
m = p.matcher(string);
}
}
return string.substring(1, string.length() - 1);
}
public synchronized String format(String message) {
Matcher matcher = variablePattern.matcher(message);
while (matcher.find()) {
String variable = matcher.group();
variable = variable.substring(1);
if (variable.startsWith("{") && variable.endsWith("}"))
variable = variable.substring(1, variable.length() - 1);
String value = variables.get(variable);
if (value == null) value = "";
message =
message.replaceFirst(Pattern.quote(matcher.group()), Matcher.quoteReplacement(value));
}
matcher = colorPattern.matcher(message);
while (matcher.find())
message =
message.substring(0, matcher.start()) + "\247" + message.substring(matcher.end() - 1);
return message;
}
public URLFinder(String text) {
Matcher matcher = dfPattern.matcher(text);
urls = new ArrayList<String>();
locations = new ArrayList<Integer[]>();
while (matcher.find()) {
urls.add(matcher.group(1));
locations.add(new Integer[] {matcher.start(1), matcher.end(1)});
}
}
public BasicSpellChecker(String file) throws IOException {
BufferedReader in = new BufferedReader(new FileReader(file));
Pattern p = Pattern.compile("\\w+");
for (String temp = ""; temp != null; temp = in.readLine()) {
Matcher m = p.matcher(temp.toLowerCase());
while (m.find())
nWords.put((temp = m.group()), nWords.containsKey(temp) ? nWords.get(temp) + 1 : 1);
}
in.close();
}
/**
* Removes anything at the start of the markup that is indented. Normally this indicates notes
* that the author should have used a template for, such as a "For other uses, see ****" note.
*
* @param markup the text to be stripped
* @return the stripped markup
*/
public static String stripIndentedStart(String markup) {
Pattern p = Pattern.compile("(.*?)\n", Pattern.DOTALL);
Matcher m = p.matcher(markup);
StringBuffer sb = new StringBuffer();
int newStart = 0;
while (m.find()) {
// System.out.println(" - \"" + m.group() + "\"\n\n") ;
if (m.group().matches("(?s)([\\s\\W]*)([\\:\\*]+)(.*)") || m.group().matches("\\W*"))
newStart = m.end();
else break;
}
sb.append(markup.substring(newStart));
return sb.toString();
}
private List<String> convertFollowupPatientIds(List<String> patientIds) {
List<String> convertedPatientIds = new ArrayList<String>();
for (String patientId : patientIds) {
Matcher patientIdMatcher = FOLLOW_UP_PATIENT_ID_REGEX.matcher(patientId);
convertedPatientIds.add(patientIdMatcher.find() ? patientIdMatcher.group(1) : patientId);
}
return convertedPatientIds;
}
private void buildXmlPropertiesFile() {
System.out.println(
"\nBuilding and checking your pipeline properties file -> " + truncPipePropFile);
StringBuilder toPrint = new StringBuilder();
// walk through the prop file
String[] prop = IO.loadFileIntoStringArray(truncPipePropFile);
Pattern val = Pattern.compile("(<entry key.+>)([D|A|B].*)</entry>");
boolean missingFile = false;
for (String s : prop) {
// does it match a file needing prepending? Data/, Apps/, Bed/
Matcher mat = val.matcher(s);
if (mat.matches()) {
File test = new File(referenceDir, mat.group(2));
if (test.exists()) {
System.out.println("Found\t" + test);
toPrint.append(mat.group(1));
toPrint.append(test.toString());
toPrint.append("</entry>");
} else {
System.out.println("Misssing\t" + test);
missingFile = true;
}
}
// threads?
else if (s.contains("threads"))
toPrint.append("<entry key=\"threads\">" + threads + "</entry>");
// nope just save it and add a line return
else toPrint.append(s);
toPrint.append("\n");
}
// anything missing? if so exit
if (missingFile)
Misc.printErrAndExit(
"\nFailed to find all of the files in your properties file, see above.\n");
// OK, write it out
completePipelinePropFile = new File(outputDirectory, "pipelineProperties.xml");
if (IO.writeString(toPrint.toString(), completePipelinePropFile) == false)
Misc.printErrAndExit("Problem writing -> " + truncPipePropFile);
}